from:"Björn Grüning"

[galaxy-dev] Galaxy community paper

2022-03-10 Thread Björn Grüning


Hi all,

we have been accepted to publish an updated version of the Galaxy 
community paper 


If you’ve made substantial contributions to the Galaxy community 
ecosystem (core framework, tools, GTN, public server maintenance, user 
support, etc.) over the past two years, please add your details as an 
author into this form:


https://bit.ly/nar-author-2022

Thank you all!
Bjoern
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[galaxy-dev] Re: Question on RNA STAR Revision: 13:850f3679b9b4

2019-11-25 Thread Björn Grüning


Hi Sarah,

which GTF file are you using? Please make sure every exon line has a 
transcript_id.


Cheers,
Bjoern

Am 25.11.19 um 10:53 schrieb Sarah Maman:

?Hello,


Please could you help me to run this wrapper : RNA STAR Gapped-read mapper for 
RNA-seq data (Galaxy Version 2.7.2b)

without this error:

terminate called after throwing an instance of 'std::out_of_range'
   what():  basic_string::at
/galaxydata/galaxy-prod/my_job_working_directory/000/282/282124/tool_script.sh: 
line 9: 48744 Aborted (core dumped) STAR --runThreadN 
${GALAXY_SLOTS:-4}...


Even if I increase the number of genome bins for coordinate-sorting, output 
files are all empty and I read this stderr above.


Thanks in advance,

Sarah Maman


INRA | SIGENAE | GenPhySE | INRA Occitanie-Toulouse

Tél. : +33(0)5.61.28.57.08

Télétravail lundi / vendredi

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[galaxy-dev] Re: Memory limit for a Travis CI build

2019-07-28 Thread Björn Grüning


Hi Jin,

the real error is here:

https://travis-ci.org/galaxyproject/tools-iuc/jobs/564531462#L2147

I added also a review to your PR, this is great work! Thanks for your 
contribution!


Ciao,
Bjoern

Am 28.07.19 um 05:27 schrieb Jin Li:

Hi all,

I submitted a PR to Galaxy Tools IUC
(https://github.com/galaxyproject/tools-iuc/pull/2506). The Travis CI
build exited with an error code 35072. The error may be caused by
running out of memory.
https://travis-ci.org/galaxyproject/tools-iuc/jobs/564531462

In fact, my program does not use too much memory on the test case (<
1GB). May I ask what is the memory limit to pass a Travis CI build?
How could I request more memory if it is too small? Thank you.

Best regards,
Jin
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[galaxy-dev] Re: Installing a database on local instance Galaxy

2019-07-27 Thread Björn Grüning


Hi,

this will help you hopefully for the blast tools:

https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus#configuration

In short you need to download the UniProt blast DB and edit a file 
called: blastdb_p.loc


Keep in mind Galaxy is framework in which you can run thousands of 
community maintained tools ... it can happen that those tools needs some 
manual work to make them work. This really depends on the tools you have 
installed.


Ciao,
Bjoern

Am 27.07.19 um 10:00 schrieb goutham sarovaram:

Hello,
My name is Goutham I'm currently doing RNA-Seq analysis on a local instance
of Galaxy installed on a workstation at our research center.
As I have been tasked with adminstrative duties for this system I would
like to know how I can install databases on to the local instance
(Databases download from Uniprot and Pfam etc.) For running blast+ and
other tools associated with the trinotate pipeline which I'm trying to
operate through Galaxy.
Best regards.
(The instance is hosted on a Kubuntu 18 LTS with a dual Xeon E series and
64 DDR4 memory, any suggestions for better optimizations are welcome)
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[galaxy-dev] Re: conda not installing deps.

2019-07-26 Thread Björn Grüning


Hi Jochen,

what is not working? Do you have any error message.

Ciao,
Bjoern

Am 25.07.19 um 15:45 schrieb Jochen Bick:

Hi

we have a new galaxy 19.01 instance and conda is somehow not running
correctly:

galaxy.yml

   #dependency_resolvers_config_file: config/dependency_resolvers_conf.xml
   conda_prefix: /opt/galaxy/tools/_conda
   #conda_exec: null
   #conda_debug: false
   #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
   #conda_use_local: false
   conda_auto_install: true
   conda_auto_init: true
   conda_copy_dependencies: true

   job_working_directory: /opt/galaxy/daten/jobs_directory

any ideas?

Thanks Jochen





--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
jochen.b...@usys.ethz.ch 
www.ap.ethz.ch

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[galaxy-dev] Re: How to include a large datafile in a bioconda package?

2019-07-24 Thread Björn Grüning


Hi Jin,

you can use a post-link script in conda.

Like here: 
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picrust2/post-link.sh


This way the data can be fetch during tool installation.

See more information here: 
https://docs.conda.io/projects/conda-build/en/latest/resources/link-scripts.html


Ciao,
Bjoern

Am 24.07.19 um 18:43 schrieb Jin Li:

Hi Brad,

Thank you for your quick reply. I can put the data file to Zenodo so
that I will have a permanent location for it.

As for re-computing the data file locally, it may need several days to
run, so it may be quite inefficient to do the computing. I am
expecting an automatic download of the data file when installing the
package. Do we have a convention to do that? Thank you.

Best regards,
Jin

On Wed, Jul 24, 2019 at 11:31 AM Langhorst, Brad  wrote:


Hi:

I’d be concerned about that file changing or disappearing and causing 
irreproducibility.
If the URL were to a permanent location (e.g. NCBI or zenodo) maybe it’s ok.

Could it be re-computed locally if necessary (like a genome index)?

Maybe others know of examples where this is done.


Brad

On Jul 24, 2019, at 12:24 PM, Jin Li  wrote:

Hi all,

I am not sure if this mailing list is a good place to ask a bioconda
question. Sorry to bother if not. I want to ask how to include a large
data file when publishing a bioconda package. Our program depends on a
pre-computed data file, which is too large to be included in the
source code package. The data file can be accessed via a public URL.
Can I put the downloading command in `build.sh` when publishing a
bioconda package? If not, do we have a convention to deal with
dependent large datafiles? Thank you.

Best regards,
Jin
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Bradley W. Langhorst, Ph.D.
Development Group Leader
New England Biolabs




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[galaxy-dev] Re: How to resolve the dependency of self-compiled C++ programs when publishing a tool?

2019-07-11 Thread Björn Grüning


Hi Jin,

if it is a Bio-related package, follow these instructions:

https://bioconda.github.io/contributor/index.html

For anything else these once:

https://conda-forge.org/#contribute

Cheers,
Bjoern

Am 11.07.19 um 09:18 schrieb Jin Li:

Hi Devon,

Thank you for your instant reply. May I ask how could I quickly put a
C++ program in either conda-forge or bioconda? I am new to these
package repositories. Thank you.

Best regards,
Jin

On Thu, Jul 11, 2019 at 2:03 AM Devon Ryan  wrote:


Put your tool in either conda-forge or bioconda, that will take care
of the issue.
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany

On Thu, Jul 11, 2019 at 8:44 AM Jin Li  wrote:


Hi all,

I want to publish our own tool to the Galaxy Tool Shed. Our tool is
our own developed C++ program. Our compiled binaries may not
necessarily run in other machines due to different OS platforms. How
could I resolve the tool dependency of our own compiled binaries?
Thank you.

Best regards,
Jin
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[galaxy-dev] Re: Error

2019-06-26 Thread Björn Grüning


Hi Nancy,

this looks like a timout during a download of conda packages.

I assume anaconda.org had some hiccups, please try again. Those URLs 
should exists.


Ciao,
Bjoern

Am 25.06.19 um 22:59 schrieb Nancy Ide:

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[galaxy-dev] Re: New to supporting Galaxy (local deployment) seeking help related to upload problem and log file locations

2019-06-22 Thread Björn Grüning


Hi Zack,

can you provide us some more information of how you deploy your Galaxy?
Are you using nginx or another proxy? Can you share your job_conf.xml 
file with us?


What means does not work? Jobs are turning grey? But never turn yellow? 
Or do they turn red? Is any other tool working?


Cheers,
Bjoern

Am 20.06.19 um 16:37 schrieb ze...@attain.com:

I've recently been asked to support a local Galaxy deployment.  As I
am new to the software, I'm having a hard time tracking down logs and
honestly understanding how the system works.

The actual problem is the scientist in question is not able to upload
files.  The only upload feature I noticed running on the server was
an sftp-server, so I restarted that, but it doesn't appear to have
fixed anything.  Which lead me down the path of tracking down log
files to help me troubleshoot, but I am unable to track those down.

I have looked through several of the previous discussions regarding
uploading, and have not been able to find the answer to my question.

Any help would be appreciated.

thanks

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Re: [galaxy-dev] A question about Galaxy

2019-02-21 Thread Björn Grüning


Hi Abdullah,

this should work without problems. Just transfer the /export/ directory 
to the other server.


Ciao,
Bjoern

Am 20.02.19 um 12:39 schrieb Abdullah El Kurdi:

Dear all,
I would like to ask if is there any way that I could copy my galaxy 
docker instance from a server to another including the "export" 
directory, without having to re-install all the tools again.


Thanks in advance.

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Re: [galaxy-dev] Bugfix for CollectRNAmetrics (Picardtools)

2019-01-29 Thread Björn Grüning

Hi,

the best way is to fix the upstream tool definition.

https://github.com/galaxyproject/tools-iuc/blob/master/tools/picard/picard_CollectRnaSeqMetrics.xml

A pull request would be great!
Thanks,
Bjoern

Am 29.01.19 um 11:21 schrieb Previti:

Dear all,

I just fixed a bug that prevented CollectRNAmetrics (a Picard-Tool,
galaxy version 2.7.1) from working with GTF annotation files:

The pre-processing step that converts gtf to the genepred format needs
two extra parameters (marked red):

gtfToGenePred-genePredExt -geneNameAsName2 'test.gtf' refFlat.tab.raw

The format of my GTF is:

Seqname Source Feature Start End Score Strand Frame
Attributes
3R FlyBase gene 722370 722621 . - . gene_id "FBgn0085804";
gene_name "CR41571"; gene_source "FlyBase"; gene_biotype "pseudogene";

I'm assuming this is the "standard" GTF format (according to ensembl)

How's the best way to make this type of thing known...?

Cheers,
Christopher

--
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4661

christopher.prev...@dkfz.de
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
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der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.

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Re: [galaxy-dev] Central German Galaxy User Group Meeting 2

2019-01-08 Thread Björn Grüning

Hi Kristian,

Am 08.01.19 um 17:40 schrieb Matthias Bernt:

Hi Kristian,

- Die , oder funktionieren nur
für ein einziges Tool?

Genau.

Wenn man einen ganzen Workflow testen muss, dann kann man das wie
machen? Wir hatten dazu mal wft4galaxy benutzt, evtl. gibts noch was
besseres?

Habe ich selber noch keine Erfahrung mit gemacht.

Kannst zum Beispiel mal bei usegalaxy-eu schauen:

https://github.com/usegalaxy-eu/workflow-testing/blob/master/.travis.yml

https://github.com/usegalaxy-eu/workflow-testing/blob/master/run_galaxy_workflow_tests.sh

die scheinen planemo zu nutzen.

Waere mal eine passende Frage fuer galaxy-dev@lists.galaxyproject.org ...

Yes, planemo is the way to go I think.

There is some documentation in
https://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-tutorial-technical/tutorial.html#testing-the-workflow-recommended

In https://github.com/usegalaxy-eu/workflow-testing/ you can look at
many examples. Despite the broken Jenkins server, which is running out
of disc-space all of these workflows actually passing the tests :)

- Erzeugt PLANEMO sowohl eine Galaxy-XML als auch CONDA-rules?

Nein, nur das Galaxy xml.

- Wenn ich CONDA Regeln erzeuge, wie gelangt das automatisch nach
BIOCONTAINER?

Wenn dein recipe in bioconda gemerged wurde wird automatisch ein
container mit erzeugt .. soweit ich weiss.

Jupp.
https://quay.io/organization/biocontainers

- Hast du schon einmal von der Common Tool Description (CTD) gehört?
Damit kann man mit einer Tool-Beschreibung Tools für verschiedene
Workflow-Systeme erzeugen. Weißt du ob das mittlerweile gut funktioniert?

Davon habe ich noch nichts gehoert. Kannst du mir mal einen link
schicken - taete mich interessieren.

This works for all OpenMS and Seqan tools. It does not produce
super-duper quality tools, but they tend to work. Matthias, all our
OpenMS wrappers are generated with that.

Description here:

https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms#generating-openms-wrappers

Ciao,
Bjoern

Gruesse,
Matthias

Viele Grüße, *Kristian

On 7. Jan 2019, at 17:46 , Matthias Bernt > wrote:

Hi,

wir werden versuchen zumindest den Vormittag per skype zu
uebertragen. Am besten einfach mich (mbatle) ab ca 8:45 mal anschreiben.

Gruesse,
Matthias

On 05.01.19 11:50, Peters, Kristian wrote:

Hallo Matthias,
Januar ist bei mir sehr gefüllt und es sind noch ein paar wichtige
Sachen oben drauf gekommen. Daher hatte ich mich vorsichtshalber
nicht in den Doodle eingetragen. Vielleicht ist es möglich, per
Telefonkonferenz (Hangout, Skype) remote teilzunehmen? Das würde mir
viel Zeit am Dienstag ersparen.

Viele Grüße, *Kristian
On 4. Jan 2019, at 19:40 , Neumann, Steffen > wrote:

Hi Matthias,

ich habe die Koordination von einem grösseren Antrag geerbt,
und werde daher am Dienstag nicht nach Leipzig kommen können :-(

Kristian hat in den letzten Wochen ebenfalls
an einem Workflow für MetFrag gearbeitet,
zu dem wir bis jetzt PhenoMeNal packaging haben.

Gruss,
Steffen

On Fri, 2019-01-04 at 18:46 +0100, Matthias Bernt wrote:

Dear all,

our meeting (workshop on building Galaxy tools and conda packages)
will
take place next Tuesday (Feb 8th). Below we compiled the most
important
informations for you. Just write an email if you have any further
questions.

We are currently expecting the eight participants who registered
here:
https://dudle.inf.tu-dresden.de/7yxdfay2/. Let me know if you
changed
you plans.

The meeting will take place in the KUBUS (Tagungsbüro 131) at the
UFZ.
How to reach the UFZ is described here:
https://www.ufz.de/index.php?de=34272 The KUBUS is in front of the
UFZ.
So you don't need to enter through the main gate.

Plan:

- We will start at 9:00.
- For the morning we plan to introduce you to the basics of
- building tools for Galaxy with planemo and
- building conda packages
- For lunch there is a "Kantine" at the UFZ.
- In order to practice the learned topics we planned to use the
afternoon as a kind of hackaton where you can (start to) build
your own Galaxy tool or conda package. We will be there for
questions
and introduce advanced topics as needed.

Therefore it would be great if you 'bring' a tool of your choice,
eg
your own tool for wrapping, this could be e.g. a shell, R, or
python
script or some software package that can be compiled.

In case that you don't have an idea we have prepared one or two
examples.

Important:

Since some of the required software is quite large we would like to
ask you to prepare a few things if possible (at least the first
point).

1. You will need a linux command line

If your laptop runs Windows you could install VirtualBox and install
a
linux in this box. Linux images for VirtualBox that are ready to use
are
available, eg.
https://www.osboxes.org/ubuntu/#ubuntu-1804-vbox

2. Download and prepare

Re: [galaxy-dev] learning pulsar for galaxy

2018-10-03 Thread Björn Grüning


Hi,


Hello,

We are working on a project in providing a Cloud based research platform 
for Health Informatics and Bioinformatics. Long story short, one of the 
components to be provided by the project is a Galaxy Server for our 
genomics researchers; and on the other hand, GWU also has a HPC system 
for high performance and high throughput computing.


Our Galaxy Server for this project is hosing in the Cloud (Azure) and 
the HPC cluster is onsite at GW. To allow a galaxy server to utilize 
external compute power of a HPC, galaxy has provided job runner plugins 
of DRMAA for job schedulers as well as Pulsar. For our situation, the 
HPC is a remote system w.r.t. the Galaxy server in the cloud and thus 
there isn't a shared file system between them. It seems to me that 
Pulsar would be the appropriate solution for us. Am I on the right track?



You are on the right track, indeed! Pulsar is what you are searching for :)

Cheers,
Bjoern



Any suggestions are much appreciated!

Best,
Adam
---
Adam K. L. Wong, PhD.
High Performance Computing Specialist for Genomics
Division of Information Technology
The George Washington University
Email: aklw...@gwu.edu 


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Re: [galaxy-dev] Using Singularity images to resolve dependences in Galaxy 18.05

2018-09-19 Thread Björn Grüning


Hi Peter,

yes this is working :)
Usegalaxy.eu is using it for a few tools.

Documentation is here ;) 
https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L484


Also the Docker compose image is can also use Singularity if you want to 
reverse engineer it :)


Ciao,
Bjoern

Am 19.09.2018 um 10:12 schrieb Peter van Heusden:

Hi there

Is it possible to use Singularity images to resolve dependencies in 
Galaxy 18.05? If so is there documentation somewhere?


I have a Galaxy server where for at least some of the dependencies conda 
will not be a good option so I would like to be able to use singularity 
if at all possible.


Thanks!
Peter


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Re: [galaxy-dev] Salmon references and data manager

2018-09-07 Thread Björn Grüning


Hi Christopher!


Dear Björn,

I just installed Salmon on our Galaxy instance and I have a couple of 
basic questions.


Sure, thanks for getting in touch!

Currently the reference transcriptomes are put in the same data table as 
the genomes, would it be of interest to separate this and give the


transcriptomes their own table? I could probably try to do this...


That I don't understand?
Salmon is using this one here, isn't it?

https://github.com/bgruening/galaxytools/blob/master/tools/salmon/salmon.xml#L233

There is a data manager available that unfortunately has a bug. We fixed 
that and it now populates the reference genome data table.


Do you mean this one?

https://github.com/ieguinoa/data_manager_salmon_index_builder

I would probably modify this as well use the new table. Could this be 
useful? I'm not sure how to proceed...would I give you the modified 
Salmon wrapper for inclusion in the package?


If you can, please feel free to create PRs to the repositories, so we 
can all reviewed it. And then, when we merge, it gets automatically 
updated to the Tool Shed :)


Thanks!
Bjoern


Best regards,

Christopher


--
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Re: [galaxy-dev] java options

2018-08-28 Thread Björn Grüning

Hi Matthias,

Hi Marius,

Thanks for your comments. That's what I thought.

> To me this sounds like something that really should be fixed in the
> tool as presumably this affects every deployer.

Hmm. The 'tool' would be java. As far as I have seen java is
never/seldom in the tool dependencies. Hence, the system's java
installation is used for which we do not know if it is Sun/OpenJDK or
which version it is (in addition the installation will likely not change
on production systems for a long time). So I guess fixing this in java
would not help here in reasonable time anyway.

So, it seems that the best option is to:
- switching back to _JAVA_OPTIONS (which seems to be implemented also on
usegalaxy.org)

- handling the output in each java tool

This is also what usegalaxy.eu is using and we have special destinations
for java tools.

Are there any guidelines for wrapping java based applications (or other
programming languages)?

- add java to dependencies? I think this should be done, or?

This should be part of the dependencies of your tool already, isn't it?
So MSGFplus should depend on a java version of their choice.

See here:
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/msgf_plus/meta.yaml#L15

- if yes: is there a favored conda package?

openjdk if needed.

Ciao,
Bjoern

Cheers,
Matthias

P.S. I just added java to my list of despicable programming languages.

On 27.08.2018 12:00, Marius van den Beek wrote:

Hi Matthias,

if a tool prints something to the stderr that is indeed considered to
indicate a failure, and it's the default mostly because
we don't want to break legacy tools that make this assumption. If you
include a profile version in your tool
or change your command section to detect_errors="exit_code"> this will more reasonably determine

if a tool failed based on the exit code.

Best,
Marius

On Mon, 27 Aug 2018 at 11:52, Matthias Bernt > wrote:

Dear list,

I'm struggling to set java options for galaxy tools. Currently I use
` in my job_conf.xml and in the
script

I explored two ways to set java options:

`_JAVA_OPTIONS="-Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp"`

But then java prints "Picked up _JAVA_OPTIONS: ..." to stderr
which is
be interpreted as error by some tools. If I'm correct this is
currently
the default .. I have seen this happening, but can't remember the
name

of the tool.

So I switched to this 'trick':

`alias java='java -Xmx5G -Xms1G -Djava.io.tmpdir=/work/songalax/tmp'`

but the problem is that the tool script is called and not sourced and
therefore aliases are not used (could this be changed?). Furthermore,
for tools which explicitly set the java options my settings would be
ignored anyway (an example is the MSGFPlusAdapter which calles `java
-Xmx3500m` .. so my -Xmx is overwritten .. I passing
GALAXY_MEMORY_MB to
the corresponding parameter might be a solution for this tool).

Any thought or suggestions on how to set the parameters in a
production

environment are very welcome.

Cheers,
Matthias

--
---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
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Re: [galaxy-dev] Permanently Deleted Data

2018-08-19 Thread Björn Grüning


Hi Michelle,

if you purged your data I don't think the Galaxy admin can do much. If 
you instead just deleted your data you can recover it on your own by 
undeleting data.


If you purged it I think the best way is to restart the trimming :(

Hope that helps,
Bjoern

Am 19.08.2018 um 01:18 schrieb Emm L:

Hello,


I am emailing in desperate hope for some help here. I trimmed my files 
and waited for days for them to finish. When they were finished, I meant 
to purge my deleted data to make space in my account...I accidentally 
purged my entire history. The galaxy account I am using is under the 
email emm.e...@outlook.com



I was wondering if someone in IT could get me back my history. The 
history name is WES for ML3.



Thank you very much.


Michelle Lim



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Re: [galaxy-dev] Installing Tool Dependencies

2018-07-18 Thread Björn Grüning


Hi Gudrun,

it seems this PASS tool is not yet available as Conda package.

Do you know which ToolShed repo this is, you might want to contact the 
developer and ask for an upgrade to conda.


>  I don't know where they come from, I didn't install them explicitly.

This is scary. Can you investigate here a little bit. Maybe some `suite` 
you have installed that had a dependency on PASS?


Ciao,
Bjoern

Am 18.07.2018 um 09:07 schrieb Gudrun Mareike Amedick:

Hi,

I have those four tools, too. And they won't install properly.  I don't know 
where they come from, I didn't install them explicitly. They just popped
up in my dependencies list. I've chosen to ignore them, since they don't seem 
to cause any trouble. But if anyone had this problem too and solved
this, I'd be glad for pointers.

If I try to install them I get the following log:

galaxy.tools.deps.conda_util DEBUG 2018-07-17 10:39:17,261 [p:805,w:1,m:0] 
[uWSGIWorker1Core0] Executing command:
/srv/galaxy/database/dependencies/_conda/bin/conda create -y 
--override-channels --channel iuc --channel bioconda --channel conda-forge 
--channel
defaults --name __pass@_uv_ pass
Fetching package metadata ...

PackageNotFoundError: Packages missing in current channels:
 
   - pass


We have searched for the packages in the following channels:
 
   - https://conda.anaconda.org/iuc/linux-64

   - https://conda.anaconda.org/iuc/noarch
   - https://conda.anaconda.org/bioconda/linux-64
   - https://conda.anaconda.org/bioconda/noarch
   - https://conda.anaconda.org/conda-forge/linux-64
   - https://conda.anaconda.org/conda-forge/noarch
   - https://repo.continuum.io/pkgs/free/linux-64
   - https://repo.continuum.io/pkgs/free/noarch
   - https://repo.continuum.io/pkgs/r/linux-64
   - https://repo.continuum.io/pkgs/r/noarch
   - https://repo.continuum.io/pkgs/pro/linux-64
   - https://repo.continuum.io/pkgs/pro/noarch


Kind regards

 GudrunAm Donnerstag, den 12.07.2018, 20:19 + schrieb Tom Misilo:

Hello,
  
I am trying to help a research here at Florida Tech setup Galaxy locally to process their data. However, I am running into a problem installing some

tool dependencies was on this page 
(https://moin.galaxyproject.org/Admin/Tools/ToolDependencies).
  
For example, I am trying to install BEAM, LPS, PASS, and GPASS. However, I cannot find in the documentation for either the tools themselves or on

Galaxy on how to set these tools up for use in Galaxy. Would you be able to 
assist in this matter?
  
Thank you!

Tom
  
Thomas Misilo

Network Engineer
Florida Institute of Technology
Evans Library
150 W. University Blvd
Melbourne, FL 32901
Phone: 321-674-8831
Fax: 321-724-2559
misi...@fit.edu
  
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Re: [galaxy-dev] Conda problems: Failed to activate conda environment

2018-07-10 Thread Björn Grüning




Am 10.07.2018 um 08:54 schrieb Van Wageningen, GERHARD [gerha...@sun.ac.za]:
So those files are "just not there" due to a faulty install? 


Seems so.
You can try for hisat as well.
The questions is why :(

And the 
repair is to delete the __toolname.x.x.x folders from the _conda/envs 
folder and force conda to reinstall them?



Yes.



Where can I look for the channel priorities and is there a standard rule 
for them?


https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L240

Cheers,
Bjoern



Thanks for your input - must appreciated!


gerhard

----
*From:* Björn Grüning 
*Sent:* 10 July 2018 08:49:04
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za]; 
galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda 
environment

Which means that your conda envs are not what they are supposed to be.

You can fix this by removing the folder and let Galaxy re-created them,
but you should figure out why they are "empty". Maybe a wrong channel
priority or network issues during installation?

Hope that helps.
You could also from insite the env, do a `conda install ...`


Hi - tx for (fast) reply.  Ok ... with this result ...


(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 
/home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version

-bash: trim_galore: command not found

Environment is:

(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 
/home/.galaxy/tooldeps/_conda/envs]$ env

XDG_SESSION_ID=45352
HOSTNAME=storage1.hpc
SELINUX_ROLE_REQUESTED=
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=10.55.40.3 55438 22
PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
SELINUX_USE_CURRENT_RANGE=
QTDIR=/usr/lib64/qt-3.3
OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
QTINC=/usr/lib64/qt-3.3/include
PERL_MB_OPT=--install_base /root/perl5
SSH_TTY=/dev/pts/2
QT_GRAPHICSSYSTEM_CHECKED=1
USER=root
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
MAIL=/var/spool/mail/root
PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
CONDA=/home/.galaxy/tooldeps/_conda
PWD=/home/.galaxy/tooldeps/_conda/envs
LANG=en_ZA.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
LOADEDMODULES=
KDEDIRS=/usr
PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) 
\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]

SELINUX_LEVEL_REQUESTED=
HISTCONTROL=ignoredups
SHLVL=1
HOME=/root
CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
PERL_LOCAL_LIB_ROOT=:/root/perl5
LOGNAME=root
QTLIB=/usr/lib64/qt-3.3/lib
SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
MODULESHOME=/usr/share/Modules
CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
LESSOPEN=||/usr/bin/lesspipe.sh %s
XDG_RUNTIME_DIR=/run/user/0
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
PERL_MM_OPT=INST

Re: [galaxy-dev] Conda problems: Failed to activate conda environment

2018-07-10 Thread Björn Grüning


Which means that your conda envs are not what they are supposed to be.

You can fix this by removing the folder and let Galaxy re-created them, 
but you should figure out why they are "empty". Maybe a wrong channel 
priority or network issues during installation?


Hope that helps.
You could also from insite the env, do a `conda install ...`


Hi - tx for (fast) reply.  Ok ... with this result ...


(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 
/home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version

-bash: trim_galore: command not found

Environment is:

(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 
/home/.galaxy/tooldeps/_conda/envs]$ env

XDG_SESSION_ID=45352
HOSTNAME=storage1.hpc
SELINUX_ROLE_REQUESTED=
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=10.55.40.3 55438 22
PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
SELINUX_USE_CURRENT_RANGE=
QTDIR=/usr/lib64/qt-3.3
OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
QTINC=/usr/lib64/qt-3.3/include
PERL_MB_OPT=--install_base /root/perl5
SSH_TTY=/dev/pts/2
QT_GRAPHICSSYSTEM_CHECKED=1
USER=root
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
MAIL=/var/spool/mail/root
PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
CONDA=/home/.galaxy/tooldeps/_conda
PWD=/home/.galaxy/tooldeps/_conda/envs
LANG=en_ZA.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
LOADEDMODULES=
KDEDIRS=/usr
PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) 
\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]

SELINUX_LEVEL_REQUESTED=
HISTCONTROL=ignoredups
SHLVL=1
HOME=/root
CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
PERL_LOCAL_LIB_ROOT=:/root/perl5
LOGNAME=root
QTLIB=/usr/lib64/qt-3.3/lib
SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
MODULESHOME=/usr/share/Modules
CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
LESSOPEN=||/usr/bin/lesspipe.sh %s
XDG_RUNTIME_DIR=/run/user/0
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
PERL_MM_OPT=INSTALL_BASE=/root/perl5
XAUTHORITY=/tmp/.Xauthority.root
BASH_FUNC_module()=() {  eval `/usr/bin/modulecmd bash $*`
}
_=/usr/bin/env
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1 
/home/.galaxy/tooldeps/_conda/envs]$



----
*From:* Björn Grüning 
*Sent:* 10 July 2018 08:38:15
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za]; 
galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda 
environment

Hi,

can you do:

   . /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3

And see if you can execute trim_galore from the commandline and get the
help?

Ciao,
Bjoern

Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerha...@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We a

Re: [galaxy-dev] Conda problems: Failed to activate conda environment

2018-07-10 Thread Björn Grüning

AXY_SLOTS:-1} -l 6 -o 
'/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'


The job fails when it cannot find “hisat2-build”.

Fatal error: Exit code 127 ()

/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41: 
hisat2-build: command not found


The PATH variable should be exported with installation 
(/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):


PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH; 
export PATH


HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; 
export HISAT2_ROOT_DIR


HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43; 
export HISAT_ROOT_DIR


The conda environment with dependencies seems to be there:

/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin




Björn Grüning ;
galaxy-dev@lists.galaxyproject.org


*From:* Björn Grüning 
*Sent:* 05 July 2018 22:00:58
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za]; 
galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda 
environment

Hi Gerhard,

it seems your tool is picking up the old tool_dependency version and not
the conda version of python.

Have a look at
https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample 


<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>

galaxyproject/galaxy 
<https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample>

github.com
galaxy - Data intensive science for everyone.



to configure the order of dependency resolution in Galaxy.

Cheers,
Bjoern


Hi All

I have recently started learning the Galaxy setup starting with an upgrade.
Made some headway but I was wondering if someone could comment on a 
problem that has emerged.
The system is a Galaxy 18.05 installation (upgraded from 17.01) on an 
Altair PBS scheduler with drmaa setup (working)


Conda problem: Failed to activate conda environment.

Conda works during tool installation or reinstallation.

Galaxy tools have been updated/reinstalled so they all look "green" in 
manage tools.


In Manage Dependencies there are a number of "Dependency resolved but 
version not found" warnings, otherwise the deps look clean.


When running tools in Galaxy errors occur, after the jobs have correctly 
deployed on the cluster.



The galaxy application raised errors like the two below.

"Failed to activate conda environment! Error was:
Fatal Python error: Py_Initialize: Unable to get the locale encoding
    File 
"/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py",

line 123
      raise C"

"

Failed to activate conda environment! Error was: CondaEnvironmentError: 
Environment error: Cannot activate environment bash. User does not have 
write access for conda symlinks.



"


Galaxy started and stopped using supervisord with config below:


Thanks, hopefully someone has seen this before ...


regards, Gerhard



[program:web]
command         = uwsgi --plugin python --virtualenv /home/.galaxy/.venv 
--ini-paste /home/.galaxy/config/galaxy.ini

directory       = /home/.galaxy
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
numprocs        = 1
stopsignal      = INT

[program:handler]
command         = python ./scripts/galaxy-main -c 
/home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s

directory       = /home/.galaxy
process_name    = handler%(process_num)s
numprocs        = 1
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
environment     = 
VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/;

stdout_logfile  = /home/.galaxy/handler%(process_num)s.log
redirect_stderr = true

[group:galaxy]
programs        = handler, web

<http://www.sun.ac.za/english/Pages/Water-crisis.aspx>

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Re: [galaxy-dev] Conda problems: Failed to activate conda environment

2018-07-05 Thread Björn Grüning

Hi Gerhard,

it seems your tool is picking up the old tool_dependency version and not
the conda version of python.

Have a look at
https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample
to configure the order of dependency resolution in Galaxy.

Cheers,
Bjoern

Hi All

I have recently started learning the Galaxy setup starting with an upgrade.
Made some headway but I was wondering if someone could comment on a
problem that has emerged.
The system is a Galaxy 18.05 installation (upgraded from 17.01) on an
Altair PBS scheduler with drmaa setup (working)

Conda problem: Failed to activate conda environment.

Conda works during tool installation or reinstallation.

Galaxy tools have been updated/reinstalled so they all look "green" in
manage tools.

In Manage Dependencies there are a number of "Dependency resolved but
version not found" warnings, otherwise the deps look clean.

When running tools in Galaxy errors occur, after the jobs have correctly
deployed on the cluster.

The galaxy application raised errors like the two below.

"Failed to activate conda environment! Error was:
Fatal Python error: Py_Initialize: Unable to get the locale encoding
File
"/home/.galaxy/tooldeps/python/2.7/iuc/package_python_2_7/8b09fe018cac/lib/python2.7/encodings/__init__.py",
line 123

raise C"

Failed to activate conda environment! Error was: CondaEnvironmentError:
Environment error: Cannot activate environment bash. User does not have
write access for conda symlinks.

Galaxy started and stopped using supervisord with config below:

Thanks, hopefully someone has seen this before ...

regards, Gerhard

[program:web]
command = uwsgi --plugin python --virtualenv /home/.galaxy/.venv
--ini-paste /home/.galaxy/config/galaxy.ini

directory = /home/.galaxy
umask = 022
autostart = true
autorestart = true
startsecs = 10
user = galaxy
numprocs = 1
stopsignal = INT

[program:handler]
command = python ./scripts/galaxy-main -c
/home/.galaxy/config/galaxy.ini --server-name=handler%(process_num)s

directory = /home/.galaxy
process_name = handler%(process_num)s
numprocs = 1
umask = 022
autostart = true
autorestart = true
startsecs = 10
user = galaxy
environment =
VIRTUAL_ENV="/home/.galaxy/.venv",PATH="/home/.galaxy/.venv/bin:%(ENV_PATH)s",http_proxy="http://storage2.eth.hpc:3128/",https_proxy="http://storage2.eth.hpc:3128/;

stdout_logfile = /home/.galaxy/handler%(process_num)s.log
redirect_stderr = true

[group:galaxy]
programs = handler, web

The integrity and confidentiality of this email is governed by these
terms. Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die
volgende bepalings gereël. Vrywaringsklousule

To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] instance management inspiration

2018-06-22 Thread Björn Grüning


HI,

Am 22.06.2018 um 11:47 schrieb Matthias Bernt:

Hi Bjoern,


nothing really fancy for usegalaxy.eu but we maintain this repo here:

https://github.com/usegalaxy-eu/usegalaxy-eu-tools

We have agreed on a set of labels and lint the tools against this 
white list. The tools are installed automatically with ephemeris.


Cool. Is there also a mechanism for ordering the toolpanel? Or do you do 
this manually? If so, how? Via the integrated toolpanel xml file?


In our tool_conf.xml file we have all categories included (most of them 
without tools), and this defines the order.


Quotas are managed manually to a large degree, as we do not have that 
many different once.


OK. Thanks a lot for your reply.



Cheers,
Bjoern

Am 20.06.2018 um 15:54 schrieb Matthias Bernt:

Dear list,

I'm looking for some inspiration for managing my galaxy instance 
(with ansible). In particular I'm looking for ansible roles to

- setup quotas
- manage the tool panel (I need to get order in the chaos)

I'm wondering how the usegalaxy instances manage this? Is there some 
github that I could browse?


Cheers,
Matthias





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Re: [galaxy-dev] instance management inspiration

2018-06-22 Thread Björn Grüning


Hi Matthias,

nothing really fancy for usegalaxy.eu but we maintain this repo here:

https://github.com/usegalaxy-eu/usegalaxy-eu-tools

We have agreed on a set of labels and lint the tools against this white 
list. The tools are installed automatically with ephemeris.


Quotas are managed manually to a large degree, as we do not have that 
many different once.


Cheers,
Bjoern

Am 20.06.2018 um 15:54 schrieb Matthias Bernt:

Dear list,

I'm looking for some inspiration for managing my galaxy instance (with 
ansible). In particular I'm looking for ansible roles to

- setup quotas
- manage the tool panel (I need to get order in the chaos)

I'm wondering how the usegalaxy instances manage this? Is there some 
github that I could browse?


Cheers,
Matthias



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Re: [galaxy-dev] argparse -> tool xml advice

2018-05-28 Thread Björn Grüning


Hi Matthias,

check this one out: https://github.com/erasche/argparse2tool

Cheers,
Bjoern

Am 28.05.2018 um 09:43 schrieb Matthias Bernt:

Dear list,

just a question for advice: I plan to wrap a python script (with lots of 
options) which uses the argparse library. I was wondering if somebody 
has an idea to generate the tool xml (semi-)automatically? For instance, 
by subclassing the formatter, parsing the python code, or parsing the 
command line...


Cheers,
Matthias


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Re: [galaxy-dev] Remove entry from Tool Data Table using via Data Manager

2018-04-22 Thread Björn Grüning


Hi Dan,

as far as I know data-tables are admin only and users can not interact 
with them. You can think about it like a frozen set of reference data, 
that should not be touched for reproducibility reasons.


Can I ask for the use-case?

Cheers,
Bjoern

Am 27.03.2018 um 23:09 schrieb Dan Fornika:

Hello,

I'm working on galaxy integration for an MLST tool called MentaLiST:

https://github.com/WGS-TB/MentaLiST/tree/master/galaxy

I've created data managers that create kmer databases and store their 
locations in a Tool Data Table. I'd like to allow users to remove 
entries from the Tool Data Table. Has anyone seen a Data Manager that 
provides that functionality? Should I create separate data managers for 
add and remove functionality, or can it be integrated into one?


Thanks,

Dan


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Re: [galaxy-dev] fonts on headless compute nodes

2018-04-11 Thread Björn Grüning


Hi Matthias,

can you make sure FASTQC gets the openjdk version from conda-forge and 
not from defaults? This will fix our one problem.


MetaProSIP should add additional dependencies to the conda package. 
Ideally no requirements are needed on the system level. This is not 
always possible, for example for opengl dependent stuff, but we should 
try to fix the conda package as much as possible as this will give us 
also robust containers.


Cheers,
Bjoern

Am 11.04.2018 um 14:51 schrieb Matthias Bernt:

Dear list,

I found that some tools (eg FastQC and MetaProSIP) have problems with 
missing fonts (the former is java and the latter caused by R) on our 
compute nodes which do not have xorg and no fonts installed.


On the cluster head nodes several font related packages are installed:

dejavu-fonts-common-2.33-1.el6.noarch
xorg-x11-fonts-Type1-7.2-11.el6.noarch
liberation-fonts-common-1.05.1.20090721-5.el6.noarch
liberation-sans-fonts-1.05.1.20090721-5.el6.noarch
dejavu-sans-fonts-2.33-1.el6.noarch
urw-fonts-2.4-11.el6.noarch
ghostscript-fonts-5.50-23.2.el6.noarch
xorg-x11-fonts-misc-7.2-11.el6.noarch

It seems that conda no fonts are available. Is there somebody with 
similar problems. Any hint which of the packages is/are actually needed. 
Maybe our admins could install them...


I also found for MetaProSIP that several xorg-... packages are needed. 
Should such dependencies be handled by the conda packages or by the 
Galaxy tool.


Best,
Matthias





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Re: [galaxy-dev] Problem with dependencies: Conda/freebayes

2018-01-11 Thread Björn Grüning


Hi Matthias,

sorry for answering so late!

Do you have any error message from the logs during installation?

What means it is not recognised by Galaxy?
Do you see the conda environment in /tool_deps/_conda/ ?

Is freebayes crashing?

Ciao,
Bjoern


Dear Galaxy Dev Mailing List,

We encountered a problem while installing freebayes and its via Tool
Shed.

Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19);
gawk (4.1.3) (all have the Current Installation Status "Installed
through Conda") but then failed on the last dependency "parallel".
(Status: "Not Installed")

The strange thing is: parallel was installed correctly. Its callable
from the command line, (e.g. parallel --help works fine) and
installed with the latest version. But it's not recognized by
Galaxy.

We are using the Galaxy - Docker image in Version 17.09.

Can you please assist us in resolving this?

Mit freundlichen Grüßen

Matthias Enders 
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Today's Topics:

1. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo)


--

 Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo
 To: Hans-Rudolf Hotz  Cc: galaxy-dev
 Subject: Re: [galaxy-dev] Galaxy
v17.09 impersonation doesn't work Message-ID: 
 
Content-Type: text/plain; charset="utf-8"


Hans-Rudolf,

I just started a brand new galaxy with the default internal database.
I did the minimal change to galaxy.ini so that I could use CAS
authentication. Still, impersonation failed.


Ping

On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz 
wrote:


Hi Ping


Does it work with a fresh installation ( v17.09) staring with an
empty PostgrSQL database?


Hans-Rudolf

On 12/19/2017 03:41 PM, Ping Luo wrote:


Hans-Rudolf,

Yes, I have set the flag to be true

# Allow administrators to log in as other users (useful for 
debugging) allow_user_impersonation = True


We use CAS authentication and our database is Postgresql. Our
current Galaxy is v15.07 and impersonation works well. I have
tried v16.10 before and impersonation didn't work either.

Thanks,

Ping

On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz > wrote:


Hi Ping

The 'impersonate a user' function works for me with v17.09.


I assume, you have set: "allow_user_impersonation = True" in the 
galaxy.ini file?



Do you encounter this problem, for the first time, i.e did it
work before using (v17.05 or earlier) and you only have the
issues after upgrading?

What database do you use?

Do you use external authentication?


Regards, Hans-Rudolf






On 12/18/2017 05:22 PM, Ping Luo wrote:

The impersonation feature in Galaxy v17.09 doesn't work as 
expected.


After clicking the person to impersonate, the webpage shows "you 
have now logged in as xxx, return to home page', where 'xxx' is

the name of the person I want to impersonate. So far so good. But
after I click home, and check the login information, the login
name is still myself.

Is there anything I missed in the configuration file?

Thanks,

Ping


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Re: [galaxy-dev] Dependencies issue with tool installation via ephemeris

2017-09-13 Thread Björn Grüning



On 14.09.2017 00:10, RMSe17 wrote:
> Bjoern,
> 
> Looks like some tools install fine without the
> "install_tool_dependencies: True" but others come up with dependencies
> missing.  I wonder if some tools are older and are missing something
> in conda?  That's just a guess on my part.

This can very well be! Which tool is this?

Cheers,
Bjoern

> Using 17.01 latest, so yea defaults could be different.

17.05 is recent and 17.09 will be released soon!

Cheers,
Bjoern

> Thanks!
> 
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Re: [galaxy-dev] Galaxy server requires a restart to activate tools

2017-09-13 Thread Björn Grüning

Hi,

afaik Marius fixed a few bugs in 17.05 and I know that 17.05 should work
as described not sure 17.01 can be exprected to work this way.

Can you try 17.05?
Thanks,
Bjoern

On 14.09.2017 03:51, RMSe17 wrote:
> Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI.
> After installing a new tool, I can't run it without first restarting
> Galaxy.  This is odd, because I know in 17.01 that should no longer be
> happening.
> 
> The error I get is "This tool was disabled before job completed.
> Please contact your Galaxy administrator.
> 
> In the logs I see "Tool (... tool name) removed from tool config,
> unable to run job
> Cleaning up external metadata files
> Error checking job readiness"
> 
> After Galaxy restarts, the tool runs fine.
> 
> Is there anything typical that could cause this?  Any place I should
> start looking?
> 
> Thanks!
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Re: [galaxy-dev] Dependencies issue with tool installation via ephemeris

2017-09-13 Thread Björn Grüning

Hi,

On 13.09.2017 21:15, RMSe17 wrote:
> Thanks for your help Bjorn, I was already setting
> install_resolver_dependencies to True, but I looked at the example you
> referenced, and saw couple other options that I didn't have set (I
> didn't see them mentioned in the ephemeris documentation).
> 
> Once I set the following in the tools yml list, everything started
> working correctly.
> install_tool_dependencies: True

This should not be needed, it will install old tool dependencies, which
are deprecated.

Which Galaxy version are you using, depending on this the defaults might
change.

Cheers,
Bjoern

> install_repositoty_dependencies: True
> 
> Interestingly according to the comments in the example, these should
> be defaulting to true anyway, but I had to set them explicitly.
> 
> Thanks again for your help!
> 
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Re: [galaxy-dev] Dependencies issue with tool installation via ephemeris

2017-09-06 Thread Björn Grüning

Hi,

please make sure you have set "install_resolver_dependencies: True"

https://github.com/bgruening/docker-galaxy-ngs-preprocessing/blob/master/ngs_preprocessing.yml#L41

This will install you all conda dependencies.
Btw. you can also use Galaxy 17.05. 17.09 will be released soon and also
can need some testing :)

Cheers,
Bjoern

On 06.09.2017 03:54, RMSe17 wrote:
> Hello, I got a new Galaxy install using 17.01 latest.  I wanted to get
> the same tools as are in Galaxy main.  I installed ephemeris with pip,
> used get-tool-list to get a yml file with tools, and then shed-install
> to my Galaxy server.  After a few hours, 452 tools got successfully
> installed, 0 skipped and 0 errored.  However, when looking at Galaxy's
> "manage installed tools", all of the tools that have dependencies are
> in gray state - missing dependencies. (and error out if ran).  If I
> select a tool, and go to "repository actions", "manage tool
> dependencies", I see that dependencies are marked as never installed.
> If I select dependencies and click install, they install - really fast
> (too fast?), and then that tool works fine...   but I'm trying to
> avoid manually telling each tool to install dependencies - there are a
> lot of them :)
> 
> Any suggestions?
> ___
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Re: [galaxy-dev] conda problem

2017-08-31 Thread Björn Grüning

Hi Matthias,

conda-build only supported 80 chars limit for a long time. This has
fixed and all new packages don't have this problem.

So hopefully this PR will fix it:

https://github.com/bioconda/bioconda-recipes/pull/5912

Cheers,
bjeorn

On 31.08.2017 17:19, Matthias Bernt wrote:
> Dear list,
> 
> When running rmarkdown_wgcna I get the following error in the logs:
> 
> PaddingError: Placeholder of length '80' too short in package
> bioconda::r-wgcna-1.51-r3.3.1_0.
> The package must be rebuilt with conda-build > 2.0.
> 
> The command that seems to lead to this is:
> 
> Executing command:
> /gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_conda/bin/conda
> create -y --name mulled-v1-3bfe8da4ed798836281cc963619917
> 317ae960c9a828f7ea05d1670c65b19619 pandoc=1.15.0.6-0 r-getopt=1.20.0
> r-rmarkdown=1.2 r-plyr=1.8.4 r-highcharter=0.4.0 r-dt=0.2
> r-htmltools=0.3.5 r-wgcna=1.51
> 
> Any ideas?
> 
> Best,
> Matthias
> 
> 
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Re: [galaxy-dev] toolshed and testtoolshed

2017-08-23 Thread Björn Grüning

Hi Matthias,

update of the MTS is triggerd. It can take a while, so many tools.
In fact galaxyp uses the same mechanism as IUC, but the openms-tools are
so many that the TS upload was cancelled by an Travis timeout.

Sorry for the inconvenience.
Tomorrow everything will be updated,
Bjoern

On 23.08.2017 15:28, Dave Bouvier wrote:
> Matthias,
> 
> - There is a regular sync for repositories owned or maintained by the
> IUC, but I don't think galaxyp has one. Your best bet would be to ask
> Björn (CC'd here) to update it in the main toolshed.
> - No, the hashes are specific to the toolshed, so unfortunately that
> solution is not a solution.
> - You guess correctly, the test toolshed is not recommended to rely on
> for tools.
> 
> -
> Dave Bouvier
> http://galaxyproject.org
> http://usegalaxy.org
> 
> On 08/23/2017 09:20 AM, Matthias Bernt wrote:
>> Dear dev-list,
>>
>> Bjoern Gruening was so nice to provide a fix for one of the galaxy
>> tools (openms_metaprosip). It seems that the fix found its way into
>> the testtoolshed, but not the toolshed.
>>
>> So I was curious how the connection between these two tool sources works.
>>
>> - Is there a regular sync interval? Or does someone need to push a
>> button to get a new version to the toolshed?
>> - Are the versions (and the hashes) of the tools that find their way
>> to the main toolshed identical? Then I could just switch the
>> tool_shed_url in my tool_list.yml file when the desired version or a
>> newer one appears in the main toolshed.
>> - I guess its not a good idea (in general) to provide tools from the
>> testtoolshed in a prodiction instance?
>>
>> Best,
>> Matthias
>>
>>
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Re: [galaxy-dev] Samtools problem in Docker

2017-08-15 Thread Björn Grüning

Hi Deepak,

this is still strange. But as a general remark, don't try to install
package_samtools_1_2 or package_* these are deprecated in favor of Conda
packages.

Glad it is working now for you!
Ciao,
Bjoern

On 15.08.2017 16:31, Deepak Tanwar wrote:
> Hi Björn,
> 
> I tried again from scratch.
> 
> 1. I have installed galaxy-stable image via Kitematic.
> 2. I install samtools: *package_samtools_1_2 (2015-07-17) iuc*
> 3. I have uploaded the bam file. Error:
> 
> Traceback (most recent call last): File
> "/galaxy-central/tools/data_source/upload.py", line 425, in 
> __main__() File "/galaxy-central/tools/data_source/upload.py", line 413,
> in __main__ add_file( dataset, registry, json_file, output_path ) File
> "/galaxy-central/tools/data_source/upload.py", line 340, in add_file if
> link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ): File
> "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in
> dataset_content_needs_grooming version = self._get_samtools_version()
> File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in
> _get_samtools_version raise Exception(message) Exception: Attempting to
> use functionality requiring samtools, but it cannot be located on
> Galaxy's PATH.
> 
> 4. I restarted the galaxy and the uploaded the bam file. Error:
> 
> Traceback (most recent call last): File
> "/galaxy-central/tools/data_source/upload.py", line 425, in 
> __main__() File "/galaxy-central/tools/data_source/upload.py", line 413,
> in __main__ add_file( dataset, registry, json_file, output_path ) File
> "/galaxy-central/tools/data_source/upload.py", line 340, in add_file if
> link_data_only == 'copy_files' and
> datatype.dataset_content_needs_grooming( output_path ): File
> "/galaxy-central/lib/galaxy/datatypes/binary.py", line 295, in
> dataset_content_needs_grooming version = self._get_samtools_version()
> File "/galaxy-central/lib/galaxy/datatypes/binary.py", line 244, in
> _get_samtools_version raise Exception(message) Exception: Attempting to
> use functionality requiring samtools, but it cannot be located on
> Galaxy's PATH.
> 
> 
> 5. Now, I installed  *suite_samtools_1_2 (2015-04-27) devteam* and
> updated the packages. File uploaded successfully!
> 
> 
> 
> 
> 
>> On Aug 14, 2017, at 16:58, Björn Grüning <bjoern.gruen...@gmail.com
>> <mailto:bjoern.gruen...@gmail.com>> wrote:
>>
>> Hi Deepak,
>>
>> as Peter mentioned the Galaxy Docker container can be used as it is.
>> Can you provide the original error message from the TS?
>>
>> Cheers,
>> Bjoern
>>
>> On 14.08.2017 18:17, Deepak Tanwar wrote:
>>> I am using https://hub.docker.com/r/bgruening/galaxy-stable
>>>
>>> I aded path to the samtools because I was getting error after installing
>>> samtools from toolshed.
>>>
>>> Thank you,
>>> Deepak
>>>
>>>> On Aug 14, 2017, at 12:10, Peter Cock <p.j.a.c...@googlemail.com
>>>> <mailto:p.j.a.c...@googlemail.com>
>>>> <mailto:p.j.a.c...@googlemail.com>> wrote:
>>>>
>>>> Galaxy itself uses samtools for many operations, which is different
>>>> from when samtools is called as a dependency of a tool run by the
>>>> Galaxy user.
>>>>
>>>> However, the Docker image ought to take care of that - can you
>>>> give more details of which Docker image you are using (URL,
>>>> version, etc)?
>>>>
>>>> Thanks,
>>>>
>>>> Peter
>>>>
>>>>
>>>> On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar <dktan...@hotmail.com
>>>> <mailto:dktan...@hotmail.com>
>>>> <mailto:dktan...@hotmail.com>> wrote:
>>>>> Hello everyone,
>>>>>
>>>>> I am facing problem in uploading bam files on Galaxy. I am using Docker
>>>>> image of Galaxy.
>>>>>
>>>>> I have installed samtools version 0.1.19 and added it to the path
>>>>> /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools
>>>>>
>>>>> Error: Exception: Attempting to use functionality requiring samtools,
>>>>> but it
>>>>> cannot be located on Galaxy's PATH.
>>>>>
>>>>> Thank you,
>>>>> Deepak
>>>>>
>>>>> ___
>>>>> Please keep all replies on the lis

Re: [galaxy-dev] Samtools problem in Docker

2017-08-14 Thread Björn Grüning

Hi Deepak,

as Peter mentioned the Galaxy Docker container can be used as it is.
Can you provide the original error message from the TS?

Cheers,
Bjoern

On 14.08.2017 18:17, Deepak Tanwar wrote:
> I am using https://hub.docker.com/r/bgruening/galaxy-stable
> 
> I aded path to the samtools because I was getting error after installing
> samtools from toolshed.
> 
> Thank you,
> Deepak
> 
>> On Aug 14, 2017, at 12:10, Peter Cock > > wrote:
>>
>> Galaxy itself uses samtools for many operations, which is different
>> from when samtools is called as a dependency of a tool run by the
>> Galaxy user.
>>
>> However, the Docker image ought to take care of that - can you
>> give more details of which Docker image you are using (URL,
>> version, etc)?
>>
>> Thanks,
>>
>> Peter
>>
>>
>> On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar > > wrote:
>>> Hello everyone,
>>>
>>> I am facing problem in uploading bam files on Galaxy. I am using Docker
>>> image of Galaxy.
>>>
>>> I have installed samtools version 0.1.19 and added it to the path
>>> /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools
>>>
>>> Error: Exception: Attempting to use functionality requiring samtools,
>>> but it
>>> cannot be located on Galaxy's PATH.
>>>
>>> Thank you,
>>> Deepak
>>>
>>> ___
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>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>  https://lists.galaxyproject.org/
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>>>  http://galaxyproject.org/search/
> 
> 
> 
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Re: [galaxy-dev] Bowtie2 index building

2017-08-11 Thread Björn Grüning

Hi,

it seems that your Docker Box only gets 1GB :(

please re-check the configs.
Sorry to be not more helpful!
Bjoern

On 11.08.2017 15:55, Deepak Tanwar wrote:
> Also, I am running this container on a Mac Pro using Kitematic and I
> have docker preference set to use 12 cores and 64 GB RAM.
> 
> Thanks,
> Deepak
> 
> 
>> On Aug 11, 2017, at 9:54 AM, Deepak Tanwar <dktan...@hotmail.com
>> <mailto:dktan...@hotmail.com>> wrote:
>>
>> Hi Björn,
>>
>> If I do docker stats:
>> CONTAINER   CPU %   MEM USAGE / LIMIT MEM %  
>> NET I/O BLOCK I/O   PIDS
>> dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%  
>>158kB / 785kB   11.4GB / 81MB   106
>>
>> And, after ssh into docker machine:
>>
>> FilesystemSize  Used Available Use% Mounted on
>> tmpfs   896.2M186.6M709.6M  21% /
>> tmpfs   497.9M476.0K497.4M   0% /dev/shm
>> /dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
>> cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
>> Users   931.0G683.8G247.2G  73% /Users
>> /dev/sda1       282.7G 14.9G253.2G   6%
>> /mnt/sda1/var/lib/docker/aufs
>>
>> Best regards,
>> Deepak
>>
>>
>>> On Aug 11, 2017, at 9:39 AM, Björn Grüning <bjoern.gruen...@gmail.com
>>> <mailto:bjoern.gruen...@gmail.com>> wrote:
>>>
>>> Hi Deepak,
>>>
>>> how are you running this Container?
>>> Can you check how many memory you have inside the container?
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> On 11.08.2017 15:35, Deepak Tanwar wrote:
>>>> Hello,
>>>>
>>>> I am trying to build Bowtie2 index for hg19.
>>>> I a using Docker image of Galaxy.
>>>>
>>>> Computer I am using have 12 cores and 64 GB of RAM.
>>>>
>>>> Error I am getting is:
>>>>
>>>> Fatal error: Exit code 1 ()
>>>> Building a SMALL index
>>>> Could not allocate space for a joined string of 2897310462 elements.
>>>> Switching to a packed string representation.
>>>> Building a SMALL index
>>>> Could not find approrpiate bmax/dcv settings for building this index.
>>>> Already tried a packed string representation.
>>>> Please try indexing this reference on a computer with more memory.
>>>> Error: Encountered internal Bowtie 2 exception (#1)
>>>> Command: bowtie2-build --wrapper basic-0
>>>> /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
>>>> fa.fa hg19 fa
>>>> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
>>>> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
>>>> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
>>>> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
>>>> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
>>>> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
>>>> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
>>>> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
>>>> Error building index.
>>>>
>>>> Please help!
>>>>
>>>> Thank you,
>>>> Deepak
>>>>
>>>>
>>>>
>>>> ___
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>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>  https://lists.galaxyproject.org/
>>>>
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>>>>  http://galaxyproject.org/search/
>>>>
>>
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> 
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Re: [galaxy-dev] Bowtie2 index building

2017-08-11 Thread Björn Grüning

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
> Hello,
> 
> I am trying to build Bowtie2 index for hg19.
> I a using Docker image of Galaxy.
> 
> Computer I am using have 12 cores and 64 GB of RAM.
> 
> Error I am getting is:
> 
> Fatal error: Exit code 1 ()
> Building a SMALL index
> Could not allocate space for a joined string of 2897310462 elements.
> Switching to a packed string representation.
> Building a SMALL index
> Could not find approrpiate bmax/dcv settings for building this index.
> Already tried a packed string representation.
> Please try indexing this reference on a computer with more memory.
> Error: Encountered internal Bowtie 2 exception (#1)
> Command: bowtie2-build --wrapper basic-0
> /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
> fa.fa hg19 fa 
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Error building index. 
> 
> Please help!
> 
> Thank you,
> Deepak
> 
> 
> 
> ___
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Re: [galaxy-dev] openms python3 & print

2017-08-10 Thread Björn Grüning

Hi Matthias,

please note that this repo is 4 years old. We have changed the wrappers
quite a bit in the last years and now you have it here:

suite_openms

Or every tool has its own repo. Last update yesterday.
Hope that helps,
Bjoern

P.S. I have deprecated the old repo.

On 10.08.2017 15:03, Matthias Bernt wrote:
> Hi,
> 
> I got an error from OpenMS which seems to be related to python3:
> 
> Fatal error: Exit code 1 (Error running OpenMS tool.)
>   File
> "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py",
> line 22
> print "Running shell command %s" % command
>^
> SyntaxError: Missing parentheses in call to 'print'
> 
> Command line was
> 
> python
> /gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py
> --executable 'DecoyDatabase' --config
> /gpfs1/data/galaxy_server/galaxy/jobs_dir/000/240/tmpYOuUf9
> 
> I would volunteer to improve this. But where can I find the sources?
> Would it be better to
> - use the compatibility import (easiest)
> - switch to print()
> - use logging
> 
> Best,
> Matthias
> 
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Re: [galaxy-dev] Adding a visualization plugin to a galaxy local toolshed

2017-07-18 Thread Björn Grüning

Hi Lisa,

the Tool Shed does not yet support visualisations. But you can submit
your visualisation directly to the Galaxy codebase.

For example have a look at this PR:

https://github.com/galaxyproject/galaxy/pull/4310

Hope this helps,
Bjoern

Am 18.07.2017 um 09:21 schrieb Lisa Perus:
> Hi everybody,
> 
> I am currently working on a galaxy visualization plugin which I would
> like to share with my colleagues. As it stands, they devised a local
> toolshed where I can upload my tools and which works very well for
> uploading tools with their wrappers.
> 
> However, I have no idea how to upload a visualization plugin so that
> they can directly install it from the admin menu.
> 
> I tried looking for answers but have not found a solution yet.
> 
> Any advice is welcome!
> 
> Cheers!
> 
> 
> 
> 
> ___
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> 
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Re: [galaxy-dev] ustacks - bad interpreter

2017-07-08 Thread Björn Grüning

Hi,

please also make sure you have a recent conda version. This 80 character
length smalls a lot like an old conda restriction.

Cheers,
Bjoern

Am 07.07.2017 um 18:09 schrieb David Meltzer:
> Good afternoon,
> 
>  
> 
> Thank you for that! I will look in to it!
> 
>  
> 
> Best Regards,
> 
> David Jacob Meltzer
> 
>  
> 
> *From: *Nate Coraor 
> *Date: *Friday, July 7, 2017 at 5:02 PM
> *To: *David Meltzer 
> *Cc: *Yvan Le Bras ,
> "galaxy-dev@lists.galaxyproject.org" 
> *Subject: *Re: [galaxy-dev] ustacks - bad interpreter
> 
>  
> 
> Hi David,
> 
>  
> 
> You may want to have a look at the first line of:
> 
>  
> 
> /home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py
> 
>  
> 
> The shell is claiming it is:
> 
>  
> 
> #!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a1
> 
>  
> 
> When it should be:
> 
>  
> 
> #!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/python
> 
>  
> 
> However, it could be that the line is correct and the output was
> truncated, or the shell has a length limit for the shebang (although the
> truncated string is only 79 characters, I'd be surprised if the limit
> for your shell was that short).
> 
>  
> 
> --nate
> 
>  
> 
> On Fri, Jul 7, 2017 at 8:21 AM, David Meltzer
> > wrote:
> 
> Good afternoon,
> 
>  
> 
> I will do my best!
> 
> 
> Best Regards,
> David
> 
>  
> 
> *From: *Yvan Le Bras  >
> *Date: *Friday, July 7, 2017 at 1:06 PM
> 
> 
> *To: *David Meltzer  >,
> "galaxy-dev@lists.galaxyproject.org
> "
>  >
> *Subject: *RE : [galaxy-dev] ustacks - bad interpreter
> 
>  
> 
> No problem, I was not writing my question clearly...
> 
>  
> 
> I suspect a pb with the stacks_summary related script... Can you
> investigate it, I unfortunately can't work on it for now. .. Maybe
> ""just"" a missing python interpreter invocation somewhere. .. when
> executing stacks_summary. ...
> 
> 
> 
>  Message d'origine 
> De : David Meltzer  >
> Date : 07/07/2017 13:47 (GMT+01:00)
> À : Yvan Le Bras  >, galaxy-dev@lists.galaxyproject.org
> 
> Objet : Re: [galaxy-dev] ustacks - bad interpreter
> 
>  
> 
> Good afternoon,
> 
>  
> 
> I apologize. I misunderstood the question. Yes, stacks_summary has
> been installed correctly as have stacks and velvet.
> 
>  
> 
> Additionally, the tool is outputting three items into the history -
> 
>  
> 
> Summary from Stacks – red (error)
> 
> Ustacks.log – red (error)
> 
> Stacks from Data – green (successful)
> 
>  
> 
> Best Regards,
> 
> David Jacob Meltzer
> 
>  
> 
> *From: *galaxy-dev  > on behalf of
> David Meltzer  >
> *Date: *Friday, July 7, 2017 at 12:31 PM
> *To: *Yvan Le Bras  >, "galaxy-dev@lists.galaxyproject.org
> "
>  >
> *Subject: *Re: [galaxy-dev] ustacks - bad interpreter
> 
>  
> 
> Good afternoon,
> 
>  
> 
> I am sorry. I don’t see a tool called stacks_summary installed on my
> system or available on the toolshed.
> 
>  
> 
> Best Regards,
> 
> David
> 
>  
> 
> *From: *Yvan Le Bras  >
> *Date: *Friday, July 7, 2017 at 12:08 PM
> *To: *David Meltzer  >,
> "galaxy-dev@lists.galaxyproject.org
> "
>  >
> *Subject: *RE : [galaxy-dev] ustacks - bad interpreter
> 
>  
> 
> Hi David,
> 
>  
> 
> A pb with stacks_summary apparently... and ustacks is working well
> apparently... Can you check you have stacks_summary well installed ?
> I think it is but there is a

Re: [galaxy-dev] any introduce for how Mako and JavaScript work in galaxy?

2017-07-07 Thread Björn Grüning

Hi Steven,

we have collected a few tutorials and slides here:

http://galaxyproject.github.io/training-material/topics/dev/

especially this:

https://galaxyproject.github.io/training-material//topics/dev/tutorials/webhooks/tutorial.html

and this:

https://galaxyproject.github.io/training-material//topics/admin/tutorials/advanced-galaxy-customisation/slides.html

Might be interesting for you depending on the modification you need to make.

Hope this helps,
Bjoern

Am 07.07.2017 um 04:11 schrieb Steven Shen:
> Hi everyone,
> 
> I want to make some change for my local galaxy web, actually I can edit
> galaxy_path/static/scripts/bundled/*.js directly.
> 
> It seems mako templates are used for galaxy, as well as many JavaScript
> files, but I don't know how they work. So is there any introduce for how
> mako and JavaScript files working in galaxy?
> 
> Thank you very much.
> 
> Steven
> 
> 
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Re: [galaxy-dev] Java memory requirements for Picard index?

2017-07-07 Thread Björn Grüning

Hi Christopher,

you can increase the JVM memory options via the job_conf.xml file for a
particular tool.

Hope this helps,
Bjoern

Am 06.07.2017 um 13:05 schrieb Previti:
> Dear all,
> I seemly have a java issue (out of memory) when trying to construct a
> picard index for the rat (rn6) genome build using the
> picard_index_builder_data_manager.
> This is strange because other, bigger genomes have not presented any
> problems...
> 
> Does anybody have any suggestions?
> 
> Cheers,
> Christopher Previti
> 
> Fatal error: Exit code 1 ()
> [Thu Jul 06 08:26:48 UTC 2017] picard.sam.CreateSequenceDictionary 
> REFERENCE=/opt/galaxy/galaxy/database/jobs_directory/000/978/dataset_1974_files/rn6.fa
>  OUTPUT=rn6.dictTRUNCATE_NAMES_AT_WHITESPACE=true 
> NUM_SEQUENCES=2147483647 VERBOSITY=INFO QUIET=false 
> VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=50 
> CREATE_INDEX=false CREATE_MD5_FILE=false 
> GA4GH_CLIENT_SECRETS=client_secrets.json
> [Thu Jul 06 08:26:48 UTC 2017] Executing as 
> gal...@xgs-node071.xgs.dkfz-heidelberg.de on Linux 3.10.0-514.el7.x86_64 
> amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.7.1-SNAPSHOT
> [Thu Jul 06 08:26:49 UTC 2017] picard.sam.CreateSequenceDictionary done. 
> Elapsed time: 0.03 minutes.
> Runtime.totalMemory()=1051721728
> To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
>   at 
> htsjdk.samtools.reference.FastaSequenceFile.readSequence(FastaSequenceFile.java:151)
>   at 
> htsjdk.samtools.reference.FastaSequenceFile.nextSequence(FastaSequenceFile.java:81)
>   at 
> picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:156)
>   at 
> picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:137)
>   at 
> picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
>   at 
> picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
>   at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
> Error building index.
> 
> 
> 
> 
> 
> 
> 
> -- 
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
> 
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4434
> 
> christopher.prev...@dkfz.de 
> www.dkfz.de 
> 
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
> 
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
> Absender und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
> untersagt.
> 
> 
> 
> 
> ___
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Re: [galaxy-dev] Singularity Container forks ?

2017-06-16 Thread Björn Grüning

Hi Nikos,

we are discussion various enhancement with the Singularity developers,
one is to suppress warnings.

Can you try this for the time being? This is working fine for me.

$tool_directory:rw,$working_directory:rw,$default_file_path:rw

Looking more closely to your error message it seems to be that
Singularity is interpreting the default_ro, which should not happen.
This should be replace by either ro or rw. Where do you specify this string?

Cheers,
Bjoern


> hi,
> 
> i have question when submitting jobs as real user
> 
> defaults = "$galaxy_root:default_ro,$tool_directory:default_ro"
> 
> singularity gives a WARNING since the home dir is already mounted
> "WARNING: Not mounting requested bind point (already mounted in
> container): default_ro"
> 
> can this be avoided ?
> 
> 
> Thanks,
> 
> 
> 
> 
> On 14/06/2017 07:46 μμ, John Chilton wrote:
>> Sorry for the late response - but earlier this week Björn Grüning and
>> I added various support to Galaxy's development branch for Singularity.
>>
>> The following pull request added Singularity support in job running
>> (https://github.com/galaxyproject/galaxy/pull/4175) - here job
>> destinations may describe the paths to Singularity containers. It may
>> also work with Singularity 2.3 to just specify Docker containers and
>> let it auto-convert - I haven't tested that.
>>
>> For "best practice" tools - these are tools that have only
>> requirements that can resolve via Conda in the best practice Conda
>> channels we can do even more - we can build Singularity containers and
>> use them automatically - either ahead of time or build on the demand
>> during job execution.
>>
>> Here is the PR that added the on-demand building support for such
>> Singularity containers to Galaxy
>> https://github.com/galaxyproject/galaxy/pull/4185 and here is the
>> tooling PR (https://github.com/galaxyproject/galaxy-lib/pull/64) and
>> cached container PR
>> (https://github.com/galaxyproject/galaxy/pull/4179) support. If you or
>> anyone has a chance to try it out and beta test - let the list know
>> how it goes. I plan to talk a little about this work and related
>> Docker and Conda work at the GCC so I hope to see you there!
>>
>> -John
>>
>>
>>
>> On Tue, May 2, 2017 at 8:51 AM, Nikos Nikoloutsakos
>> <nikolou...@admin.grnet.gr <mailto:nikolou...@admin.grnet.gr>> wrote:
>>
>> Hello,
>>
>> Are there any galaxy forks using Singularity images instead of
>> Docker ?
>> Is it trivial enough to replace "docker run" with "singularity exec" ?
>>
>> Thank you,
>> Nikos
>>
>>
>> -- 
>> Nikos Nikoloutsakos
>> Greek Research and Technology Network (GRNET)
>> ☎ +30 210 7471127 <tel:%2B30%20210%207471127>
>> ✉ nikolou...@grnet.gr <mailto:nikolou...@grnet.gr>
>>  hpc.grnet.gr <http://hpc.grnet.gr>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>  https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
>>
>>
> 
> -- 
> Nikos Nikoloutsakos
> Greek Research and Technology Network (GRNET)
> ☎ +30 210 7471127
> ✉ nikolou...@grnet.gr
>  hpc.grnet.gr
> 
> 
> 
> ___
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> 
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Re: [galaxy-dev] bwa_mem and "-t" option

2017-06-01 Thread Björn Grüning

Your are joining GCC? Cool!

Looking forward to see you there!
Bjoern

Am 01.06.2017 um 21:25 schrieb David Kovalic:
> Bjoern,
> 
> Thanks so much, I'll check it out. 
> 
> If I can't figure this out I am sure I can ask around in Montpellier at
> GCC'17! I am looking forward to the meeting and being able to visit
> Montpellier for the first time ever 
> 
> The help is greatly appreciated.
> 
> David
> 
> 
> 
> On Thu, Jun 1, 2017 2:21 PM, Björn Grüning bjoern.gruen...@gmail.com
> <mailto:bjoern.gruen...@gmail.com> wrote:
> 
> __
> 
> HI David,
> 
> 
> have a look at https://galaxyproject.org/admin/config/jobs/
> 
> 
> and this config file:
> 
> 
> 
> https://github.com/galaxyproject/galaxy/blob/dev/config/job_resource_params_conf.xml.sample
> 
> 
> and here:
> 
> 
> 
> https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L791
> 
> 
> I couldn't find more information, hope this gets you started!
> 
> Cheers,
> 
> Bjoern
> 
> 
> Am 01.06.2017 um 20:48 schrieb David Kovalic:
> 
> > Bjoern,
> 
> >
> 
> > Thanks for the response.
> 
> >
> 
> > I agree with the first approach (admin control of the per tool
> 
> > environment). Do you know… are there docs or similar resources you
>     could
> 
> > point me to that describe how to achieve this?
> 
> >
> 
> > Thanks again,
> 
> >
> 
> > David
> 
> >
> 
> >
> 
> >
> 
> > On Sun, May 28, 2017 4:41 AM, Björn Grüning bjoern.gruen...@gmail.com
> 
> > <mailto:bjoern.gruen...@gmail.com> wrote:
> 
> >
> 
> > __
> 
> >
> 
> > Hi David,
> 
> >
> 
> >
> 
> > this is possible via the GALAXY_SLOTS mechanism. An admin can give
> every
> 
> >
> 
> > tool it's own environment and can set GALAXY_SLOTS dynamically.
> 
> >
> 
> > A user can not do this, as this is highly dependent on the node this
> 
> >
> 
> > tool will run and normally a user does not know about this.
> 
> >
> 
> >
> 
> > However, if you really want to offer this to a user, Galaxy also
> offers
> 
> >
> 
> > to enable this option per tool level and will add additional parameter
> 
> >
> 
> > fields to set GALAXY_SLOTS as a user.
> 
> >
> 
> >
> 
> > Cheers,
> 
> >
> 
> > Bjoern
> 
> >
> 
> >
> 
> > Am 26.05.2017 um 20:23 schrieb David Kovalic:
> 
> >
> 
> > > Hi,
> 
> >
> 
> > >
> 
> >
> 
> > > Is it possible, and if so how, to run the galaxy devteam
> 
> >
> 
> > > (version 546ada4a9f43) of bwa_mem with the "-t" option and a
> value >1?
> 
> >
> 
> > >
> 
> >
> 
> > > "-t INT number of threads [1]"
> 
> >
> 
> > >
> 
> >
> 
> > >
> 
> >
> 
> > > This would be quite useful, and used, for accelerating single bwa
> 
> > mem jobs.
> 
> >
> 
> > >
> 
> >
> 
> > > Thanks,
> 
> >
> 
> > >
> 
> >
> 
> > > David
> 
> >
> 
> > >
> 
> >
> 
> > >
> 
> >
> 
> > >
> 
> >
> 
> > > ___
> 
> >
> 
> > > Please keep all replies on the list by using "reply all"
> 
> >
> 
> > > in your mail client. To manage your subscriptions to this
> 
> >
> 
> > > and other Galaxy lists, please use the interface at:
> 
> >
> 
> > > https://lists.galaxyproject.org/
> 
> >
> 
> > >
> 
> >
> 
> > > To search Galaxy mailing lists use the unified search at:
> 
> >
> 
> > > http://galaxyproject.org/search/
> 
> >
> 
> > >
> 
> >
> 
> >
> 
> 
___
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Re: [galaxy-dev] bwa_mem and "-t" option

2017-06-01 Thread Björn Grüning

HI David,

have a look at https://galaxyproject.org/admin/config/jobs/

and this config file:

https://github.com/galaxyproject/galaxy/blob/dev/config/job_resource_params_conf.xml.sample

and here:

https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L791

I couldn't find more information, hope this gets you started!
Cheers,
Bjoern

Am 01.06.2017 um 20:48 schrieb David Kovalic:
> Bjoern,
> 
> Thanks for the response.
> 
> I agree with the first approach (admin control of the per tool
> environment). Do you know… are there docs or similar resources you could
> point me to that describe how to achieve this?
> 
> Thanks again,
> 
> David
> 
> 
> 
> On Sun, May 28, 2017 4:41 AM, Björn Grüning bjoern.gruen...@gmail.com
> <mailto:bjoern.gruen...@gmail.com> wrote:
> 
> __
> 
> Hi David,
> 
> 
> this is possible via the GALAXY_SLOTS mechanism. An admin can give every
> 
> tool it's own environment and can set GALAXY_SLOTS dynamically.
> 
> A user can not do this, as this is highly dependent on the node this
> 
> tool will run and normally a user does not know about this.
> 
> 
> However, if you really want to offer this to a user, Galaxy also offers
> 
> to enable this option per tool level and will add additional parameter
> 
> fields to set GALAXY_SLOTS as a user.
> 
> 
> Cheers,
> 
> Bjoern
> 
> 
> Am 26.05.2017 um 20:23 schrieb David Kovalic:
> 
> > Hi,
> 
> >
> 
> > Is it possible, and if so how, to run the galaxy devteam
> 
> > (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1?
> 
> >
> 
> > "-t INT number of threads [1]"
> 
> >
> 
> >
> 
> > This would be quite useful, and used, for accelerating single bwa
> mem jobs.
> 
> >
> 
> > Thanks,
> 
> >
> 
> > David
> 
> >
> 
> >
> 
> >
> 
> > ___
> 
> > Please keep all replies on the list by using "reply all"
> 
> > in your mail client. To manage your subscriptions to this
> 
> > and other Galaxy lists, please use the interface at:
> 
> > https://lists.galaxyproject.org/
> 
> >
> 
> > To search Galaxy mailing lists use the unified search at:
> 
> > http://galaxyproject.org/search/
> 
> >
> 
> 
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Re: [galaxy-dev] Issue with GATK2 on Galaxy Repository.

2017-05-31 Thread Björn Grüning

Hi,

can you please check the exact version of the GATK jar file?
Currently, only 2.8 is supported. We stopped maintaining it, due to
licensing issues - which might be resolved in a 4.0 version.

If you have GATK2.8, it should work hopefully.
Cheers,
Bjoern

Am 31.05.2017 um 05:36 schrieb OLABODE OLUWASEUN AJAYI:
> Hi Dev,
> 
> I am running a local instance Galaxy for developing a variant calling
> pipeline. I ran into this issue after configuring and installing GATK2
> on my local when running the GATK *Realigner Target Creator on the BAM
> file generated by Mark duplicates.*
> *Can some suggest how to resolve this issue or please point to how to
> debug this issue from the GATK2 wrapper? BTW, I follow the instruction
> by ensuring that my GATK3 environment was set as stated in the
> Galaxy GATk2 readme.txt.*
> *
> *
> Below here was the issue I encountered;
> 
> # ERROR 
> --
> # ERROR A USER ERROR has occurred (version 2.0-7-g7323e98): 
> # ERROR The invalid arguments or inputs must be corrected before the GATK 
> can proceed
> # ERROR Please do not post this error to the GATK forum
> # ERROR
> # ERROR See the documentation (rerun with -h) for this tool to view 
> allowable command-line arguments.
> # ERROR Visit our website and forum for extensive documentation and 
> answers to 
> # ERROR commonly asked questions http://www.broadinstitute.org/gatk
> # ERROR
> # ERROR MESSAGE: Argument with name 'num_cpu_threads_per_data_thread' 
> isn't defined.
> # ERROR 
> --
> 
> 
> 
> On Mon, May 29, 2017 at 6:44 PM, Peter Cock  > wrote:
> 
> Thanks, pull request submitted:
> 
> https://github.com/galaxyproject/galaxy/pull/4121
> 
> 
> Peter
> 
> 
> On Mon, May 29, 2017 at 5:23 PM, Saravanaraj Ayyampalayam
> > wrote:
> > Peter,
> >
> > Here is the git diff output that shows the changes I made:
> >
> > diff --git a/lib/galaxy/jobs/runners/__init__.py
> b/lib/galaxy/jobs/runners/__init__.py
> > index ebf4859..6ee51c8 100644
> > --- a/lib/galaxy/jobs/runners/__init__.py
> > +++ b/lib/galaxy/jobs/runners/__init__.py
> > @@ -419,7 +419,7 @@ class JobState( object ):
> >  job_name += '_%s' % self.job_wrapper.tool.old_id
> >  if self.job_wrapper.user:
> >  job_name += '_%s' % self.job_wrapper.user
> > -self.job_name = ''.join( map( lambda x: x if x in (
> string.letters + string.digits + '_' ) else '_', job_name ) )
> > +self.job_name = ''.join( map( lambda x: x if x in (
> string.ascii_letters + string.digits + '_' ) else '_', job_name ) )
> >
> >  @staticmethod
> >  def default_job_file( files_dir, id_tag ):
> > diff --git a/lib/galaxy/jobs/runners/drmaa.py
> b/lib/galaxy/jobs/runners/drmaa.py
> > index 7c08984..5c5dc62 100644
> > --- a/lib/galaxy/jobs/runners/drmaa.py
> > +++ b/lib/galaxy/jobs/runners/drmaa.py
> > @@ -394,7 +394,7 @@ class DRMAAJobRunner( AsynchronousJobRunner ):
> >  job_name += '_%s' % job_wrapper.tool.old_id
> >  if external_runjob_script is None:
> >  job_name += '_%s' % job_wrapper.user
> > -job_name = ''.join( x if x in ( string.letters +
> string.digits + '_' ) else '_' for x in job_name )
> > +job_name = ''.join( x if x in ( string.ascii_letters +
> string.digits + '_' ) else '_' for x in job_name )
> >  if self.restrict_job_name_length:
> >  job_name = job_name[:self.restrict_job_name_length]
> >  return job_name
> >
> > -Raj
> >
> >> On May 29, 2017, at 11:33 AM, Peter Cock
> > wrote:
> >>
> >> Thanks Saravanaraj,
> >>
> >> You should not need to change the locale, after all many Galaxy
> servers and
> >> their users will be labelling their files in non-English with
> >> "special" characters -
> >> but perhaps en_US.UTF-8 would be safer in your case as it seems
> that few
> >> people use Galaxy with en_US.iso885915 otherwise this would have been
> >> reported before?
> >>
> >> Can you tell us both places you changed string.letters to
> string.ascii_letters
> >> please? I could then submit this as a pull request to get Galaxy
> itself updated
> >> for future release.
> >>
> >> Peter
> >>
> >> On Mon, May 29, 2017 at 4:28 PM, Saravanaraj Ayyampalayam
> > wrote:
> >>> Peter,
> >>>
> >>> You are correct.

Re: [galaxy-dev] bwa_mem and "-t" option

2017-05-28 Thread Björn Grüning

Hi David,

this is possible via the GALAXY_SLOTS mechanism. An admin can give every
tool it's own environment and can set GALAXY_SLOTS dynamically.
A user can not do this, as this is highly dependent on the node this
tool will run and normally a user does not know about this.

However, if you really want to offer this to a user, Galaxy also offers
to enable this option per tool level and will add additional parameter
fields to set GALAXY_SLOTS as a user.

Cheers,
Bjoern

Am 26.05.2017 um 20:23 schrieb David Kovalic:
> Hi,
> 
> Is it possible, and if so how, to run the galaxy devteam
> (version 546ada4a9f43) of bwa_mem with the "-t" option and a value >1?
> 
> "-t INT number of threads [1]"
> 
> 
> This would be quite useful, and used, for accelerating single bwa mem jobs.
> 
> Thanks,
> 
> David
> 
> 
> 
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Re: [galaxy-dev] OpenBabel Requirements

2017-05-20 Thread Björn Grüning

Hi Matthias,

so I spend a few hours to upgrade most (not all) tools to conda. This
was overdue ...

I also put togehter a Docker container:

https://github.com/bgruening/docker-galaxy-chemicaltoolbox

You can start it with:

docker run -i -t -p 8080:80 quay.io/bgruening/galaxy-chemicaltoolbox

Tools included in this container should work everywhere. I found 1 small
bug already and will fix this in the next week, but it should work most
of the times :)

Which tools had the blat dependency? As long as you deal with package_*
repositories you are not using conda packages and then you need to have
these cmake, gcc dependencies isntalled.

Cheers,
Bjoern


Am 19.05.2017 um 13:45 schrieb Matthias Bernt:
> Hi Bjoern,
> 
> I thought I'm using conda .. :). I'm using the ansible
> galaxy-tools-playbook to install tools. I tried before if ansible
> installation and installation via the web interface give the same
> results -- and I recalled that the results were identical. But I was
> wrong -- sorry for the inconvenience.
> 
> Now, when installing via ansible I'm getting identical (compared to
> installation via the web interface) results for blat I choose the
> following options in the tool_list.yaml file.
>   install_tool_dependencies: False
>   install_repository_dependencies: True
>   install_resolver_dependencies: True
> 
> But I still have not understood the dependencies (and dependency
> problems) shown in the web interface... Maybe you could explain this to me?
> 
> In the logs there is first a complaint about missing
>   - blat 35x1*
> then the following packages are installed:
> blat:   35-1 bioconda
> libpng: 1.6.27-0
> zlib:   1.2.8-3
> 
> The admin interface puzzles me: For the blat package:
> - "Dependency Resolver Details" lists blat 35x1 as resolved but not the
> exact version. This seems to be fine.
> - Installed repository dependencies lists package_blat_35x1 as installed
> but missing dependencies. This is odd? Why is this installed at all?
> 
> For the package_blat_35x1
> - Installed repository dependencies lists package_libpng_1_6_7
> - Missing tool dependencies lists blat and libpng. The circular
> dependency to blat is strange, isn't it?
> 
> Thanks again for the support.
> 
> Cheers,
> Matthias
> 
> On 18.05.2017 17:09, Björn Grüning wrote:
>> Hi Matthias,
>>
>> is there any chance you can upgrade your Galaxy and enable conda
>> packages?
>> This would make your life so much easier :)
>>
>> Cheers,
>> Bjoern
>>
>> Am 18.05.2017 um 16:28 schrieb Matthias Bernt:
>>> Hi Bjoern,
>>>
>>> thanks for the explanation. This helped for the openbabel package. Still
>>> there are some packages where I have problems. I guess this is because
>>> on our system the libraries are mostly at non-default locations.
>>>
>>> Currently I have problems to install BLAT. It complains about a missing
>>> zlib. Zlib is installed and the path to the includes is in CPPFLAGS. Is
>>> there any variable that would make it known to the installation process?
>>>
>>> gcc -O -g  -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized
>>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOU
>>> RCE -D_GNU_SOURCE -DMACHTYPE_x86_64 -DCOLOR32   -Wall -Wformat
>>> -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc
>>> -I../../../inc -I../../../../inc -I../../../../../inc
>>> -I/gpfs1/data/galaxy_server/gala
>>> xy-dev/database/dependencies/libpng/1.6.7/devteam/package_libpng_1_6_7/3de32cd300a9/include
>>>
>>>   -o zlibFace.o -c zlibFace.c
>>> make: Leaving directory
>>> `/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtd4Jyr2N/blat/src
>>>
>>>
>>> /lib'
>>> zlibFace.c:4:18: error: zlib.h: No such file or directory
>>>
>>> An additional question for understanding: There are packages for zlib
>>> and cmake (as example). Why are these not used? Is this because there is
>>> still transition to conda -- which will just need time? But from an
>>> earlier post I thought I understood that package_* is the old non-conda
>>> way.
>>> Or is the intended future state that central packages mentioned in
>>> https://galaxyproject.org/toolshed/package-recipes/
>>> are managed on the system .. and not conda?
>>>
>>> Thanks a lot.
>>>
>>> Cheers,
>>> Matthias
>>>
>>>
>>>
>>> On 17.05.2017 20:08, Björn Grüning wrote:
>>>> Hi Matthias,
>>>>
>>>> if you are installing repositories that still rely on the old
>>

Re: [galaxy-dev] conda installation fails

2017-04-19 Thread Björn Grüning

Hi,

I second Marius here, I would not try to fix the miniconda installation,
but rather fix the `tar` installation. This is not the original COS6.8
behaviour right?

Ciao,
Bjoern

Am 19.04.2017 um 17:57 schrieb Matthias Bernt:
> Dear list,
> 
> Just found out that conda is not installing on our CentOS6.8
> installation (might be related to earlier messages).
> 
> The problem is that the shell script installing conda unsets the
> LD_LIBRARY_PATH which makes tar dysfunctional (tar is called by the
> installer).
> 
> The command line that is executed during galaxy's installation is
> 
> wget -q --recursive -O '/tmp/conda_install7tWo7r.sh'
> 'https://repo.continuum.io/miniconda/Miniconda3-4.2.12-Linux-x86_64.sh'
> && bash '/tmp/conda_install7tWo7r.sh' -b -p
> '/gpfs1/data/galaxy_server/galaxy-dev/_conda' &&
> /gpfs1/data/galaxy_server/galaxy-dev/_conda/bin/conda install -y -q
> conda=4.2.13
> 
> Removing the unset LD_LIBRARY_PATH line (and fiddling around with some
> file size checks) is (seemingly) successful.
> 
> There is an open issue on the conda github:
> https://github.com/conda/conda/issues/3632
> 
> Any suggestions? The line removal procedure seems to be quite
> complicated in an automated ansible installation which I try to achieve.
> 
> Cheers,
> Matthias
> 
> 
> 
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Re: [galaxy-dev] Contributing to Galaxy project

2017-03-26 Thread Björn Grüning

Hi Maximilian,

welcome to Galaxy and Biopython! :)
Are you more interested in backend or frontend work?

We have a few issue tagged as beginner-friendly:

https://github.com/galaxyproject/galaxy/issues?q=is%3Aopen+is%3Aissue+label%3Afriendliness%2Ffriendly

Let us know if you have any issue and join us at:

https://gitter.im/galaxyproject/Lobby

Liebe Grüße,
Bjoern

> Dear Ladies and Gentlemen,
>  
> my name is Maximilian Greil. I would like to contribute to the Galaxy
> project. I recently started contributing to the Biopython project and
> would also like to help improving the Galaxy project.
> What would be a good start for a Galaxy beginner to contribute, maybe
> someone here knows some issues for testing or bug fixing to start with?
>  
> Kind regards,
> Maximilian Greil
> 
> 
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Re: [galaxy-dev] Tool dependency installation on older Galaxy installations

2017-03-14 Thread Björn Grüning

Hi Brian,

tools that don't support the traditional dependency management system do
usually not have any tool_dependencies.xml file attached.

This is a pretty good indicator I think.

Sorry for the confusion,
Bjoern


Am 14.03.2017 um 22:58 schrieb Brian Claywell:
> We're running an older version of Galaxy (15.07) locally. Is there
> currently any way to tell what tools in the toolshed (or, worse, what
> versions of a tool with multiple revisions) won't install their
> dependencies properly because they rely on Conda dependency management
> and don't support the old dependency management system any more?
> 
> Thanks!
> 
> 
> Cheers,
> 
> Brian
> 
> -- 
> Brian Claywell | programmer/analyst
> Matsen Group   | matsen.fredhutch.org 
> Fred Hutchinson Cancer Research Center
> 
> 
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Re: [galaxy-dev] SAML Authentication

2017-02-27 Thread Björn Grüning

This all seems correct and I own you so many beers if you get this
implemented! :)

Am 27.02.2017 um 18:34 schrieb Keith Suderman:
> Is anyone using SAML for authentication?  There is a feature request for
> SAML support on GitHub (
> https://github.com/galaxyproject/galaxy/issues/3146), but it doesn't
> look like any work has been done.
> 
> We need to add the ability for our users to authenticate with a SAML
> identity provider (IdP), in particular with InCommon/EduRoam/EduCause et
> al.  Looking at the documentation there appears to be "the old way"
> (configuring Apache/Nginx to do the authentication) and "the new way"
> where Galaxy handles the authentication.  Is it correct to assume that
> to use the new way I should implement an external authenticator,
> something like galaxy/auth/providers/saml.py and then some sort of magic
> to get a config/auth_conf.xml working?  
> 
> I just want to make sure I am heading down the correct path before
> investing too much time.
> 
> - Keith
> 
> Keith Suderman
> Research Associate
> Department of Computer Science
> Vassar College, Poughkeepsie NY
> suder...@cs.vassar.edu 
> 
> 
> 
> 
> 
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Re: [galaxy-dev] ImportError and Project life cycle

2017-02-10 Thread Björn Grüning

Hi Matthias,

to your life cycle question, do you have more information about your
filesystem(s) and what you have specifically in mind? Everything is
possible I guess, from a hack to a advanced solution like iRODS.

My feeling is that this should be implemented on the FS level and not on
the Galaxy level.

Ciao,
Bjoern


> Dear galaxy-dev list,
> 
> I'm currently trying to introduce myself to the galaxy server, i.e.,
> learning how to use and administer a galaxy server.
> 
> I have installed galaxy following this excellent tutorial:
> 
> https://github.com/martenson/dagobah-training
> 
> Then I tried the tool "FASTQ Quality Trimmer by sliding window" which is
> mentioned in NGS101-6 tutorial. I installed the tool from tool shed, but
> I get a python error (the Admin panel shows that all dependencies are
> installed):
> 
> Traceback (most recent call last):
>   File
> "/home/berntm/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.py",
> line 3, in 
> from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
>   File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py", line 7,
> in 
> from six import Iterator, string_types
> ImportError: No module named six
> 
> Do you have an idea what could be wrong? I guess that this is to little
> information, but I did not know which kind of additional information
> would be helpful.
> 
> Another question: At my institution quite a lot of NGS projects are
> carried out. After a project is finished all methods and data are stored
> to a long term read only tape archive. For the future the idea is to use
> galaxy. Which options are there to implement such a project life cycle
> with galaxy?
> 
> A last general question: would it be better to send a separate mail to
> the list when I have multiple questions?
> 
> Best regards,
> Matthias Bernt
> 
> 
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Re: [galaxy-dev] Create a new datatype svg

2017-02-07 Thread Björn Grüning

Hi,

just change it to svg. If the output is empty this could be a tool problem.

Ciao,
Bjoern

Am 07.02.2017 um 14:19 schrieb Jochen Bick:
> Hi Björn,
> 
> thanks, so I just change the format to svg? or is there more to do?
> The output appears to be empty?
> 
> Cheers Jochen
> 
> 
> On 07.02.2017 13:34, Björn Grüning wrote:
>> Hi Jochen,
>>
>> svg is supported, see here:
>>
>> https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample#L282
>>
>> Cheers,
>> Bjoern
>>
>> Am 07.02.2017 um 12:45 schrieb Jochen Bick:
>>> Hi all,
>>>
>>> I'm working on a tool that will have svg as an output file. Is this data
>>> type already established? If not how do I start?
>>>
>>> Cheers Jochen
>>> ___
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Re: [galaxy-dev] Create a new datatype svg

2017-02-07 Thread Björn Grüning

Hi Jochen,

svg is supported, see here:

https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample#L282

Cheers,
Bjoern

Am 07.02.2017 um 12:45 schrieb Jochen Bick:
> Hi all,
> 
> I'm working on a tool that will have svg as an output file. Is this data
> type already established? If not how do I start?
> 
> Cheers Jochen
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Re: [galaxy-dev] How to include local tools with Docker image of Galaxy ?

2017-02-01 Thread Björn Grüning

Hi,

sure this is possible! :)
We have some small documentation about this here:

https://github.com/bgruening/docker-galaxy-stable/#integrating-non-tool-shed-tools-into-the-container--toc

Cheers,
Bjoern

Am 01.02.2017 um 16:31 schrieb Md. Rezaul Karim:
> Dear All,
> 
> I'm a new user of Galaxy. I have been exploring the things and trying to
> use the Docker image of Galaxy. Eventually, I am planning to run the
> docker container on our local Cluster.
> 
> I was wondering if there's any way to include local tools with the
> Dockerfile. For example using the Docker image of Galaxy at
> https://github.com/bgruening/docker-galaxy-stable it shows how to
> include the tools to the Docker image of Galaxy from the Galaxy tool
> shed as follows:
> 
> RUN install-repository \
> "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_numpy_1_7" \
> "--url https://toolshed.g2.bx.psu.edu/ -o iuc --name
> package_perl_pdf_api2_2_023" \
> 
> This command will pull the tools from the Galaxy tool shed and install
> inside the docker container. But, is there's any similar way to include
> my own local tools?
> 
> 
> 
> 
> Regards,
> _
> *Md. Rezaul Karim*, BSc, MSc
> PhD Researcher, INSIGHT Centre for Data Analytics
> National University of Ireland, Galway
> IDA Business Park, Dangan, Galway, Ireland
> Web: http://www.reza-analytics.eu/index.html
> 
> 
> 
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Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

2017-01-24 Thread Björn Grüning

Hi Cris,

yes there is a better channel - it is conda-forge. But it will take you
even more time to submit there and a more strict review.

I would encourage you to submit to conda-forge, but for a starter and to
not discourage you for the first time experience I recommended bioconda
-- here I can assist you more.

It up to you, I will try my best to guide you,
Bjoern

Am 24.01.2017 um 21:27 schrieb Lawrence, Cris W:
> Bjoern
> 
> Sorry to be a pest.  One other question before I attempt any PR.  The
> python-irodsclient is not itself a bioinformatics tool - it’s a wrapper
> for communicating with iRODS - a data management system and its
> dependency, pretty tables, I would surmise, is just a utility.  After
> reading the bioconda policy, I am wondering whether these items belong
> in the bioconda channel.  If not, is there a more appropriate channel?
> 
> - Cris
> 
>> On Jan 24, 2017, at 3:09 PM, bjoern.gruen...@googlemail.com
>> <mailto:bjoern.gruen...@googlemail.com> <bjoern.gruen...@gmail.com
>> <mailto:bjoern.gruen...@gmail.com>> wrote:
>>
>> This depends on how many others are submitting a package. Sorry it
>> takes a while.
>>
>>
>> On Jan 24, 2017 8:40 PM, "Lawrence, Cris W" <cr...@upenn.edu
>> <mailto:cr...@upenn.edu>> wrote:
>>
>> Bjoern:
>>
>> OK….I am following the recipe submission process, but building in
>> travis-ci is taking longer than I would have expected.  I am over
>> 10 minutes now.  Can you give me some idea of how long a travis-ci
>> build should take?
>>
>> - Cris
>>
>>> On Jan 24, 2017, at 1:05 PM, Björn Grüning
>>> <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> wrote:
>>>
>>> Hi Cris,
>>>
>>> submit what ever you have to bioconda and we will review and
>>> merge it.
>>> It will end up in anaconda.org <http://anaconda.org/> magically.
>>>
>>> If you don't want to use bioconda. You need an anaconda account
>>> and then
>>> use `anaconda login`. But be aware that you need to configure
>>> Galaxy to
>>> use your package ... bioconda if pre-configured.
>>>
>>> Hope that helps,
>>> Bjoern
>>>
>>> Am 24.01.2017 um 18:52 schrieb Lawrence, Cris W:
>>>> Bjorn:
>>>>
>>>> Thanks for the tip.  I tried to do a conda build python-irodsclient
>>>>
>>>> BUILD START: python-irodsclient-0.5.0rc1-py27_0
>>>>
>>>> updating index in: //anaconda/conda-bld/osx-64
>>>>
>>>> updating index in: //anaconda/conda-bld/noarch
>>>>
>>>> Can't build /Users/crisl-adm/Tools/python-irodsclient due to
>>>>     unsatisfiable dependencies:
>>>>
>>>> Package missing in current osx-64 channels: 
>>>>
>>>>  - prettytable >=0.7.2
>>>>
>>>>
>>>> So I tried creating a conda package for prettytable.
>>>>
>>>> It looked to build OK….but I guess I need to upload it to anaconda
>>>> before I can build python-irodsclient.  I am an anaconda noob as
>>>> well.
>>>> Looks like I need a login.  Where do I acquire a login?
>>>>
>>>> - Cris
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> On Jan 24, 2017, at 11:17 AM, Björn Grüning
>>>>> <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>
>>>>> <mailto:bjoern.gruen...@gmail.com
>>>>> <mailto:bjoern.gruen...@gmail.com>>> wrote:
>>>>>
>>>>> Hi Chris,
>>>>>
>>>>> I guess the easiest and recommended way is to use conda.
>>>>> We can help you to create a conda package for irodclient if you
>>>>> like.
>>>>>
>>>>> To get you started see here:
>>>>> https://bioconda.github.io/guidelines.html#python
>>>>> <https://bioconda.github.io/guidelines.html#python>
>>>>>
>>>>> Cheers,
>>>>> Bjoern
>>>>>
>>>>> Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
>>>>>> I am a Galaxy noob trying to write a Galaxy tool that needs to
>>>>>> employ
>>>>>> the python-irodsclient module.

Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

2017-01-24 Thread Björn Grüning

Hi Cris,

submit what ever you have to bioconda and we will review and merge it.
It will end up in anaconda.org magically.

If you don't want to use bioconda. You need an anaconda account and then
use `anaconda login`. But be aware that you need to configure Galaxy to
use your package ... bioconda if pre-configured.

Hope that helps,
Bjoern

Am 24.01.2017 um 18:52 schrieb Lawrence, Cris W:
> Bjorn:
> 
> Thanks for the tip.  I tried to do a conda build python-irodsclient
> 
> BUILD START: python-irodsclient-0.5.0rc1-py27_0
> 
> updating index in: //anaconda/conda-bld/osx-64
> 
> updating index in: //anaconda/conda-bld/noarch
> 
> Can't build /Users/crisl-adm/Tools/python-irodsclient due to
> unsatisfiable dependencies:
> 
> Package missing in current osx-64 channels: 
> 
>   - prettytable >=0.7.2
> 
> 
> So I tried creating a conda package for prettytable.
> 
> It looked to build OK….but I guess I need to upload it to anaconda
> before I can build python-irodsclient.  I am an anaconda noob as well.
>  Looks like I need a login.  Where do I acquire a login?
> 
> - Cris
> 
> 
> 
> 
> 
>> On Jan 24, 2017, at 11:17 AM, Björn Grüning <bjoern.gruen...@gmail.com
>> <mailto:bjoern.gruen...@gmail.com>> wrote:
>>
>> Hi Chris,
>>
>> I guess the easiest and recommended way is to use conda.
>> We can help you to create a conda package for irodclient if you like.
>>
>> To get you started see here:
>> https://bioconda.github.io/guidelines.html#python
>>
>> Cheers,
>> Bjoern
>>
>> Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
>>> I am a Galaxy noob trying to write a Galaxy tool that needs to employ
>>> the python-irodsclient module.  I can install it on my laptop via
>>> pip.  But I am trying to make it available to Galaxy via planemo.
>>> Apparently, this module is not available in the conda channels.  How
>>> else can I satisfy my dependency?  Thanks for any and all help.
>>>
>>> - Cris ___
>>> Please keep all replies on the list by using "reply all" in your mail
>>> client.  To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at: https://lists.galaxyproject.org/
>>>
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>>> http://galaxyproject.org/search/mailinglists/
>>>
> 
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Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

2017-01-24 Thread Björn Grüning

Hi Chris,

I guess the easiest and recommended way is to use conda.
We can help you to create a conda package for irodclient if you like.

To get you started see here:
https://bioconda.github.io/guidelines.html#python

Cheers,
Bjoern

Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W:
> I am a Galaxy noob trying to write a Galaxy tool that needs to employ
> the python-irodsclient module.  I can install it on my laptop via
> pip.  But I am trying to make it available to Galaxy via planemo.
> Apparently, this module is not available in the conda channels.  How
> else can I satisfy my dependency?  Thanks for any and all help.
> 
> - Cris ___ 
> Please keep all replies on the list by using "reply all" in your mail
> client.  To manage your subscriptions to this and other Galaxy lists,
> please use the interface at: https://lists.galaxyproject.org/
> 
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> 
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Re: [galaxy-dev] Problem with 'galaxy_packages' dependency resolver in versionless mode

2017-01-20 Thread Björn Grüning

Hi Peter,

can you try to make  /path/to/local_tool_dependencies/my_package/default
a symlink?

Ciao,
Bjoern

Am 20.01.2017 um 16:41 schrieb Peter Briggs:
> Dear developers
> 
> I'm having problems trying to use the 'galaxy_packages' dependency resolver 
> in versionless mode, as described in the docs at:
> 
> https://docs.galaxyproject.org/en/latest/admin/dependency_resolvers.html#galaxy-packages-dependency-resolver
> 
> As I understand this: if I manually create a directory structure of the form 
> e.g. /path/to/local_tool_dependencies/my_package/default/ which contains an 
> env.sh file, and if my dependency_resolvers_conf.xml file includes the line:
> 
>  versionless="true" />
> 
> then at run time Galaxy should be able to resolve the following requirement 
> in a tool XML file:
> 
> my_package
> 
> Unfortunately although the "versioned" galaxy_packages resolver works as 
> expected (when placed ahead of the "versionless" resolver), I don't seem able 
> to get this working with Galaxy v16.10.
> 
> Can anyone point out what I'm doing wrong?
> 
> Thanks!
> 
> Best wishes
> 
> Peter
> 
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> 
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Re: [galaxy-dev] Wrapper for ballgown

2017-01-06 Thread Björn Grüning

Hi Anne,

afaik Dave Bouvier (CCed) was working on this some time back.

With the pure package you can not do much, but it is a first step.

Ciao,
Bjoern

Am 06.01.2017 um 10:19 schrieb Dueck, Anne:
> Hi everyone,
> 
> I was wondering if a wrapper for the ballgown tool is under progress, since 
> the package is out there for quite some time?
> I would appreciate it a lot. Or can you already do some stuff with the 
> package (sorry for this naive question)?
> 
> Best,
> Anne
> 
> 
> 
> 
> 
> 
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Re: [galaxy-dev] Dataset Cleanup

2017-01-05 Thread Björn Grüning

Hi,

this script only deletes files that are marked as deleted. So it might
be that users have old histories and this data will not be removed.

For you account and the used-space. Please go to your admin section, to
users, your user-name and there should be an option to recalculate the
disc-usage for your user.

Hope this helps,
Bjoern

Am 03.01.2017 um 16:41 schrieb McCully, Dwayne (NIH/NIAMS) [C]:
> Hello Everyone,
> 
>  
> 
> I have datasets that go back over a year in the files/000 directory but
> running the following script does not delete the datasets.
> 
> Also, my account says I have 59 GB used and can’t figure out where it’s
> getting that number.  I have almost everything deleted
> 
> in my Galaxy account.
> 
>  
> 
> galaxy_clean.sh
> 
> #!/bin/sh -x
> 
>  
> 
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_userless_histories.sh
> 
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_histories.sh
> 
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_libraries.sh
> 
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_folders.sh
> 
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/delete_datasets.sh
> 
> /home/niamsgalaxy/galaxy/scripts/cleanup_datasets/purge_datasets.sh
> 
> Exit
> 
>  
> 
>  
> 
> Any information on this issue would be appreciated.
> 
>  
> 
> Dwayne
> 
> 
> 
> ___
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Re: [galaxy-dev] devteam dropped support for installing tool dependencies from toolshed?

2016-12-15 Thread Björn Grüning

Hi Peter,

Am 15.12.2016 um 11:28 schrieb Peter Briggs:
> Dear developers
> 
> It looks like some updates to 'devteam'-maintained toolshed tools have
> dropped support for tool_dependencies.xml (e.g. fastqc, freebayes), so
> their dependencies cannot be automatically installed from the toolshed.
> Is this correct? I assume that it's part of the move to enforcing conda
> dependency resolution.

Yes. We really hope we are ready to go for conda, John and Marius have
improved the conda support dramatically in the last months.

Thanks,
Bjoern

> Best wishes
> 
> Peter
> 
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Re: [galaxy-dev] New datatypes with code dependencies

2016-12-14 Thread Björn Grüning

Hi Cristal,

Am 14.12.2016 um 22:07 schrieb Cristel Thomas:
> Hello,
> 
> We'd like to add some datatypes to Galaxy specific to flow cytometry
> (finally). One of the datatype is a binary format which requires rpy2/R
> to be read (no good python module available to do that).
> How do you guys deal with that? 

Is this needed for an converter or for the sniffer?
For the sniffer we do not have a good solution for this I'm afraid.
Does the datatype has a magic bit or something similar?

Cheers,
Bjoern

> Thanks,
> Cris
> 
> 
> ___
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> 
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Re: [galaxy-dev] Is there demand for rate limiting in Galaxy?

2016-11-23 Thread Björn Grüning

Hi Maximilian,

I think there is a demand and partially Galaxy has support for these
kind of limits for a user. Please have a look at:

https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L725

An extension to these would be super cool!
Thanks,
Bjoern

Am 23.11.2016 um 10:51 schrieb Maximilian Friedersdorff:
> 
> 
> 
> Un o’r 4 prifysgol uchaf yn y DU a’r orau yng Nghymru am fodlonrwydd myfyrwyr.
> (Arolwg Cenedlaethol y Myfyrwyr 2016)
> www.aber.ac.uk
> 
> Top 4 UK university and best in Wales for student satisfaction
> (National Student Survey 2016)
> www.aber.ac.uk
> 
> 
> 
> ___
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> 
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Re: [galaxy-dev] Errors when building Galaxy RNA-Seq Docker Image

2016-11-04 Thread Björn Grüning

Hi Stephen,

this was due to a downtime of the TS as far as I can tell.
But I took the opportunity to update the tools and include conda
dependencies. Please pull again and rebuild. It works for me know.

Thanks and let me know if anything is missing!
Cheers,
Bjoern

Am 04.11.2016 um 19:17 schrieb Stephen Kelly:
> I am trying to get this Docker image running:
> 
>  
> 
> https://github.com/bgruening/galaxy-rna-seq
> 
>  
> 
> If I let Docker download and start the container using this command:
> 
>  
> 
> docker run -d -p 8080:80 bgruening/galaxy-rna-seq
> 
>  
> 
> everything appears to work fine. However, if I clone the repo and try to
> build it myself like this:
> 
>  
> 
> docker build -t skelly/galaxy-rna-seq .
> 
>  
> 
> I get a load of errors. Here are a few:
> 
>  
> 
> ...
> 
> ...
> 
> Step 5 : RUN install-tools $GALAXY_ROOT/tools.yaml
> 
> ---> Running in 78e96eb73823
> 
> Enable installation from the Test Tool Shed.
> 
> * Starting PostgreSQL 9.3 database server
> 
>...done.
> 
> starting Galaxy
> 
> ./run.sh: 37: [: --daemon: unexpected operator
> 
> Activating virtualenv at /galaxy_venv
> 
> Requirement already satisfied (use --upgrade to upgrade): pip>=8.1 in
> /galaxy_venv/lib/python2.7/site-packages
> 
> /galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318:
> SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject
> Name Indication) extension to TLS is not available on this platform.
> This may cause the server to present an incorrect TLS certificate, which
> can cause validation failures. You can upgrade to a newer version of
> Python to solve this. For more information, see
> https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.
> 
>   SNIMissingWarning
> 
> /galaxy_venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122:
> InsecurePlatformWarning: A true SSLContext object is not available. This
> prevents urllib3 from configuring SSL appropriately and may cause
> certain SSL connections to fail. You can upgrade to a newer version of
> Python to solve this. For more information, see
> https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
> 
>   InsecurePlatformWarning
> 
> You are using pip version 8.1.2, however version 9.0.0 is available.
> 
> You should consider upgrading via the 'pip install --upgrade pip' command.
> 
> ...
> 
> ...
> 
>  
> 
>  
> 
>  
> 
> But I think the biggest problem is that the tools installation appears
> to fail:
> 
>  
> 
>  
> 
>  
> 
> ...
> 
> ...
> 
> Activating virtualenv at /galaxy_venv
> 
> Galaxy is running.
> 
> (1/10) Installing tool trim_galore from bgruening to section "Quality
> Control" at revision f1e71aeaa923 (TRT: 0:00:00.610888)
> 
>   Tool trim_galore installed successfully (in 0:01:46.048131) at
> revision f1e71aeaa923
> 
> (2/10) Installing tool suite_samtools_1_2 from devteam to section "SAM
> Tools" at revision 5b673ccc8747 (TRT: 0:01:46.874497)
> 
>   * Error installing a tool (after 0:00:05.381866 seconds)! Name:
> suite_samtools_1_2,owner: devteam, revision: 5b673ccc8747, error:
> {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
> 
> (3/10) Installing tool deseq2 from iuc to section "RNA-Seq" at revision
> 89bbd1dbf48d (TRT: 0:01:52.463056)
> 
>   * Error installing a tool (after 0:00:05.147542 seconds)! Name:
> deseq2,owner: iuc, revision: 89bbd1dbf48d, error: {"err_msg": "Uncaught
> exception in exposed API method:", "err_code": 0}
> 
> (4/10) Installing tool deseq2 from iuc to section "RNA-Seq" at revision
> 8702e49e68b6 (TRT: 0:01:57.827642)
> 
>   * Error installing a tool (after 0:00:04.991533 seconds)! Name:
> deseq2,owner: iuc, revision: 8702e49e68b6, error: {"err_msg": "Uncaught
> exception in exposed API method:", "err_code": 0}
> 
> (5/10) Installing tool htseq_count from lparsons to section "RNA-Seq" at
> revision a6dcb86af112 (TRT: 0:02:03.041254)
> 
>   * Error installing a tool (after 0:00:03.671927 seconds)! Name:
> htseq_count,owner: lparsons, revision: a6dcb86af112, error: {"err_msg":
> "Uncaught exception in exposed API method:", "err_code": 0}
> 
> (6/10) Installing tool htseq_count from lparsons to section "RNA-Seq" at
> revision 6f920f33c5eb (TRT: 0:02:06.931447)
> 
>   Tool htseq_count installed successfully (in 0:04:57.743878) at
> revision 6f920f33c5eb
> 
> (7/10) Installing tool all_cufflinks_tool_suite from devteam to section
> "RNA-Seq" at revision d19a1295d99b (TRT: 0:07:04.933382)
> 
>   * Error installing a tool (after 0:00:06.615792 seconds)! Name:
> all_cufflinks_tool_suite,owner: devteam, revision: d19a1295d99b, error:
> {"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
> 
> (8/10) Installing tool tophat2 from devteam to section "RNA-Seq" at
> revision 758594ed0364 (TRT: 0:07:11.768638)
> 
>   Tool tophat2 installed successfully (in 0:01:09.319561) at
> revision

Re: [galaxy-dev] conda management of tools dependent on python3

2016-11-03 Thread Björn Grüning

Hi,

can you check the package? The package should have a dependency on
python3, if not the package seems to be broken :(

Ciao,
Bjoern

Am 03.11.2016 um 21:32 schrieb Wolfgang Maier:
> Hi Björn,
> 
> Hmm, I guess I should have phrased my question more clearly. What I'm
> trying to do is to get Galaxy to satisfy a missing tool dependency at
> *tool runtime* using a bioconda package that is only available for
> Python3. I am able to satisfy the dependency *manually* by running:
> 
> conda create --name __@
> == 
> (following the example at
> https://docs.galaxyproject.org/en/master/admin/conda_faq.html#how-do-conda-dependencies-work-where-do-things-get-installed),
> but when I let *Galaxy autoinstall* the package it will use python2.7
> for the environment, then fail with:
> 
> Error: Unsatisfiable package specifications.
> 
> and a hint that  conflicts with python 2.7. So my question is:
> is there any way to inform Galaxy that the dependency requires a conda
> environment based on python3?
> 
> Best,
> Wolfgang
> 
> 
> On 28.10.2016 19:14, Björn Grüning wrote:
>> Hi Wolfgang,
>>
>> can you describe step by step what you are trying to do?
>>
>> A conda package ships it's own python version, you can see this in the
>> build-string py35_0 for example. So conda can handle all python version
>> independent of the python version of miniconda.
>>
>> Cheers,
>> Bjoern
>>
>>> Dear all,
>>>
>>> I'm still pretty new to conda tool dependencies management and there is
>>> one thing I cannot find documented anywhere:
>>> How can I let conda manage tool dependencies that involve python3?
>>> If I let Galaxy install conda for me, it creates an environment with
>>> python2, then if there is a tool dependency that has a conda package
>>> built for only python3 I'm getting an error because of a conflict
>>> between that package and python2 (not surprisingly), but AFAIU conda
>>> environments are bound to one particular version of python (or is that
>>> incorrect?).
>>>
>>> Thanks for any help with this and best wishes,
>>> Wolfgang
>>> ___
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>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
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>>>
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[galaxy-dev] IEs and fancy visualisations

2016-11-02 Thread Björn Grüning

This is for all Interactive Environment fans that like awesome
visualisations! Our friends from IOBIO have created a blog post about an
fantastic collaboration between IOBIO and Galaxy:

http://iobio.io/2016/11/02/galaxy-integration/

Thanks Chase and Yi - great work!
Bjoern
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Re: [galaxy-dev] odose

2016-10-28 Thread Björn Grüning

Hi Michiel,

the IUC (https://github.com/galaxyproject/tools-iuc) is adopting
wrappers and helping with fixing them. Can you create a PR with
everything what you have against this repo, we will review it and guide
you through the process. Once, this is merged we will help maintaining it.

Thanks,
Bjoern

Am 25.10.2016 um 13:54 schrieb Vos, Michiel:
>  
> 
> Dear Galaxy developers,
> 
>  
> 
> We hereby want to ask if anyone is interested in helping out to repair
> and update our Galaxy tool ‘odose’:
> 
>  
> 
> Webserver 
> 
>  
> 
> Publication
> 
> 
>  
> 
> Public server page
> 
> 
>  
> 
> Github 
> 
>  
> 
> Odose enables users to perform an array of population genetics tests on
> prokaryote genomes. Our tool is currently linked to NCBI to download
> various files, but continuous restructuring at NCBI has resulted in
> broken links which prevent the pipeline from working. Developer Tim te
> Beek has moved on outside academia and does not have the time to fix it,
> but is available to give answer question/give instructions. We believe
> our tool is highly useful for microbiologists and would greatly
> appreciate any help from the Galaxy community to get it working properly
> again! Please get in touch if you would like to know more.
> 
>  
> 
> Best Wishes, Michiel Vos, Mark van Passel and Tim te Beek
> 
>  
> 
>  
> 
>  
> 
> Michiel Vos
> 
> European Centre for Environment and Human Health
> 
> University of Exeter
> 
> ESI Building, Penryn Campus
> 
> TR10 9FE Penryn, UK
> 
> 0044 (0)1326259464
> 
> https://coastalpathogens.wordpress.com/
> 
>  
> 
> 
> 
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Re: [galaxy-dev] conda management of tools dependent on python3

2016-10-28 Thread Björn Grüning

Hi Wolfgang,

can you describe step by step what you are trying to do?

A conda package ships it's own python version, you can see this in the
build-string py35_0 for example. So conda can handle all python version
independent of the python version of miniconda.

Cheers,
Bjoern

> Dear all,
> 
> I'm still pretty new to conda tool dependencies management and there is
> one thing I cannot find documented anywhere:
> How can I let conda manage tool dependencies that involve python3?
> If I let Galaxy install conda for me, it creates an environment with
> python2, then if there is a tool dependency that has a conda package
> built for only python3 I'm getting an error because of a conflict
> between that package and python2 (not surprisingly), but AFAIU conda
> environments are bound to one particular version of python (or is that
> incorrect?).
> 
> Thanks for any help with this and best wishes,
> Wolfgang
> ___
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Re: [galaxy-dev] Help wanted: setting up a production server

2016-10-07 Thread Björn Grüning

Hi Steve,

I wish I could assist you a little bit. But what I can do is to get in
touch with Pieter Lukasse (pie...@thehyve.nl) from Hyve: http://thehyve.nl/

Pieter is the Galaxy expert in this company and he rocks! Maybe you can
figure something out.

Ciao and have a nice weekend!
Bjoern

Am 07.10.2016 um 22:30 schrieb Martin Čech:
> Hi Steve,
> 
> make sure to check out https://wiki.galaxyproject.org/Events
> 
> There are 2 extensive admin trainings going to happen in near future.
> November in Salt Lake City and February in Melbourne.
> 
> Martin
> 
> On Fri, Oct 7, 2016 at 4:23 PM Steve Cassidy  > wrote:
> 
> Hi all,
>   I’m working on setting up a Galaxy server for use with speech and
> language data.  While I can probably get there myself eventually,
> I’m thinking it would be good to get some (paid) help if it were
> available.   
> 
> If you have some experience setting up a public facing Galaxy
> instance, and you have some time available in the next couple of
> weeks, please get in touch.  
> 
> Any location is probably ok as long as we can work out how to
> reimburse you.  We (and the servers) are based in Australia but I’m
> currently in New York.  
> 
> Thanks,
> 
> Steve
> 
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
> 
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Re: [galaxy-dev] Docker ToolShed Imports Issue

2016-09-26 Thread Björn Grüning

Hi Miuki,

can you please show use your tool.yaml file?

Thanks,
Bjoern

Am 18.08.2016 um 16:31 schrieb Yip, Miu ki:
> Hi all,
> 
> I’m trying to import shed tools into Galaxy for Docker. When I build the 
> container, I get this error message:
> 
> TASK [galaxy_tools : Install Tool Shed tools] 
> **
>  [WARNING]: The loop variable 'item' is already in use. You should set the
> `loop_var` value in the `loop_control` option for the task to something else 
> to
> avoid variable collisions and unexpected behavior.
> failed: [localhost] (item={u'owner': u'vlefort', u'tool_shed_url': 
> u'https://toolshed.g2.bx.psu.edu', 
> u'tool_panel_section_label': u'Import Files', u'name': u'phyml'}) => 
> {"changed": false, "cmd": ["/tmp/venv/bin/python", 
> "install_tool_shed_tools.py", "-y", "name: phyml\nowner: 
> vlefort\ntool_panel_section_label: Import Files\ntool_shed_url: 
> https://toolshed.g2.bx.psu.edu\n;, "-a", "admin", "-g", "localhost:8080"], 
> "delta": "0:00:00.781449", "end": "2016-08-17 23:48:07.389199", "failed": 
> true, "failed_when_result": true, "item": {"name": "phyml", "owner": 
> "vlefort", "tool_panel_section_label": "Import Files", "tool_shed_url": 
> "https://toolshed.g2.bx.psu.edu"}, "rc": 0, "start": "2016-08-17 
> 23:48:06.607750", "stderr": "(1/1) Installing tool phyml from vlefort to 
> section \"Import Files\" at revision f6dadc1de75f (TRT: 
> 0:00:00.308611)\r\n\t* Error installing a tool (after phyml)! Name: 
> 0:00:00.247213,owner: vlefort, revision: f6dadc1de75f, error: {\"err_msg\": 
> \"Missing required parameter 'shed_tool_conf'.\", \"err_code\": 
> 47}\r\nInstalled tools (0): []\r\nSkipped tools (0): []\r\nErrored tools 
> (1): [('phyml', u'f6dadc1de75f')]\r\nAll tools listed in 'None' have been 
> processed.\r\nTotal run time: 0:00:00.556216", "stdout": "", "stdout_lines": 
> [], "warnings": []}
> …ignoring
> 
> Is this a conf file issue?
> 
> Best,
> Miuki
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Re: [galaxy-dev] several versions of compiler

2016-09-23 Thread Björn Grüning

Hi,

Am 23.09.2016 um 10:42 schrieb Nikolaos Tur:
> Hi,
> 
> maybe this was discussed or documented already but I'm lost. How to tell
> installed tools by tool_shed that I have newer version of gcc and pls
> use that one instead of default?

Do you want to recompile all tools installed from the TS with a new GCC
version?

> Thank you very much,
> Nikolaos
> 
> 
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[galaxy-dev] Galaxy training contribution fest - 6-7th October

2016-09-20 Thread Björn Grüning

Dear training enthusiast,

the Galaxy Training Network (GTN) is planning a contribution fest to
consolidate our training material and improve the overall training
experience in Galaxy on the 6.-7th October 2016!

More information about the project can be found here:
https://gist.github.com/bgruening/a54a8600c5cddca82424ad13569708c3

and a small presentation here:

http://bgruening.github.io/training-material/shared/slides/project_presentation#/

This will be an online contribution fest and the fun to contribute
should be priority one! There is enough to work on in all areas, from
programming to fix spelling mistakes. So everyone is welcome to improve
the Galaxy training material.

Ciao,
Bérénice and Bjoern


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[galaxy-dev] unified flavor testing

2016-09-17 Thread Björn Grüning

Hi Galaxy dev,

if you are developing and maintain a Galaxy flavor please check out this
little project to make testing easier and more unified.

https://github.com/bgruening/galaxy-flavor-testing

It is just a small Makefile that you can reuse in your own travis
testing to ensure that your flavors are working.

Cheers and a nice weekend!
Bjoern
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Re: [galaxy-dev] job_conf.xml and nativespecification

2016-09-14 Thread Björn Grüning

Hi Laure,

a hacky way it to use dynamic job destinations:

https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping

You can get the username via python and change "nativeSpecification" on
demand.

Hope this helps,
Bjoern

Am 14.09.2016 um 17:07 schrieb Laure QUINTRIC:
> Hi galaxy users,
> 
> while using galaxy with drmaa and real user on drm system, I would like
> to know if there's a way to set the variable PBS_O_LOGNAME to the real
> user name in the job_conf.xml :
> 
> -v PBS_O_LOGNAME=[REAL_USER_NAME??] -q
> test -l mem=100gb 
> 
> Thank you,
> 
> Laure
> 
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Re: [galaxy-dev] Galaxy Proteomics Hackathon

2016-09-10 Thread Björn Grüning

Hi Léo,

this would be awesome! Thanks for the offer!
Bjoern

Am 09.09.2016 um 22:41 schrieb Léo Biscassi:
> I don't know anything about GalaxyP, but I think I can help a little bit
> with conda packages, if that works for you I can join to hackathon.
> 
> Best regards
> 
> On Fri, Sep 9, 2016 at 12:01 PM Björn Grüning <bjoern.gruen...@gmail.com
> <mailto:bjoern.gruen...@gmail.com>> wrote:
> 
> Hi all!
> 
> I would like to spread the news from the GalaxyP team about a new
> hackthon. Please join and help us if you have some time!
> 
> 
> *
> 
> The first Galaxy-P CONDA hackathon will be held on September 27th
> and 28th.
> Galaxy-P and proteomics tool developers will participate in this
> hackathon to "CONDA-package" some of the prioritized proteomics tools
> within Galaxy. The hackathon will be an online event which will start
> with an introduction to Galaxy structure and CONDA packaging by Bjoern
> Gruening.
> 
> https://github.com/galaxyproteomics/tools-galaxyp/issues/57
> 
> Details soon. Please see if you would like to publicize this.
> 
> Thanks and Regards,
> Pratik
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> -- 
> Best regards, *
> *
> *Léo Biscassi*
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[galaxy-dev] Galaxy Proteomics Hackathon

2016-09-09 Thread Björn Grüning

Hi all!

I would like to spread the news from the GalaxyP team about a new
hackthon. Please join and help us if you have some time!


*

The first Galaxy-P CONDA hackathon will be held on September 27th and 28th.
Galaxy-P and proteomics tool developers will participate in this
hackathon to "CONDA-package" some of the prioritized proteomics tools
within Galaxy. The hackathon will be an online event which will start
with an introduction to Galaxy structure and CONDA packaging by Bjoern
Gruening.

https://github.com/galaxyproteomics/tools-galaxyp/issues/57

Details soon. Please see if you would like to publicize this.

Thanks and Regards,
Pratik
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[galaxy-dev] Galaxy Tools XSD - searching for help!

2016-09-05 Thread Björn Grüning

Dear community,

is there someone that is familiar with XSD files and validating XML files?
We need help in updating our Galaxy Tools XSD file:
https://github.com/galaxyproject/Galaxy-XSD/blob/master/galaxy.xsd

The idea is to auto generate documentation out of it and improve planemo
lint. If you have these skills please get in touch with us :)

Thanks!
Bjoern
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[galaxy-dev] Galaxy Docker 16.07

2016-09-04 Thread Björn Grüning

Hi all!

We are proud to present you the next release of our Galaxy Docker Image.

https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.07

https://registry.hub.docker.com/u/bgruening/galaxy-stable/

A few highlights:

* based on Galaxy 16.07, with all it's new features and enhancements
* SFTP Integration (by Alexander Lenail)
* enhanced SLURM documentation (by Marius van den Beek)
* initial Docker compose support

Moreover, our workshop slides with a general Docker introduction and how
to manage the Galaxy Docker container is available here:
https://galaxy.slides.com/bgruening/the-galaxy-docker-project/live#/

Don't forget to checkout our general readme file:
https://github.com/bgruening/docker-galaxy-stable/blob/master/README.md

Thanks to all contributors [1] and enjoy this release!
Bjoern

[1] https://github.com/bgruening/docker-galaxy-stable/graphs/contributors
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Re: [galaxy-dev] how to create users through Galaxy API?

2016-09-02 Thread Björn Grüning

Hi,

and here a script used by the Galaxy Docker project:

https://github.com/bgruening/docker-galaxy-stable/blob/master/galaxy/setup_postgresql.py

Cheers,
Bjoern

Am 30.08.2016 um 11:56 schrieb Peter Cock:
> Thanks Nicola & Peter B.,
> 
> I was hoping we could script new-user creation like this, and
> that someone else had already done this with the Galaxy API
> (and Bioblend). This looks great!
> 
> Thank you both,
> 
> Peter C.
> 
> On Tue, Aug 30, 2016 at 10:43 AM, Peter Briggs
>  wrote:
>> Hello Peter
>>
>> Following on from Nicola's suggestion: a while ago I had a go at writing
>> some command line tools using Bioblend to try and do some of my Galaxy admin
>> tasks via the API, including creating new user accounts so I'd also
>> recommend this route as much much easier than attempting to interact with
>> the API directly.
>>
>> The tools I wrote are here if you'd like to look at some an example of using
>> Bioblend for this, to get you started:
>>
>> https://github.com/pjbriggs/nebulizer/blob/master/nebulizer/users.py
>>
>> As long as the user that the API key belongs to is an admin user (or if
>> you're using a master API key) this works fine.
>>
>> HTH
>>
>> Best wishes
>>
>> Peter
>>
>>
>> On 29/08/16 17:37, Nicola Soranzo wrote:
>>>
>>> Hi Peter,
>>> why not use BioBlend?
>>>
>>>
>>> https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.users
>>>
>>> Cheers,
>>> Nicola
>>>
>>>  Peter Cock ha scritto 
>>>
 Thanks Hans-Rudolf,

 Yes - you are right. The wiki does link there but it wasn't obvious to
 me.
 Reading the UserAPIController link source code suggests as long as
 I am authenticated as a Galaxy Admin, I could use this to create new
 user accounts:


 https://docs.galaxyproject.org/en/master/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create

 Thank looks very promising...

 Peter

 On Mon, Aug 29, 2016 at 4:36 PM, Hans-Rudolf Hotz  wrote:
>
> Hi Peter
>
> I guess it is here:
>
> https://docs.galaxyproject.org/en/master/api_doc.html
>
>
> Regards,  Hans-Rudolf
>
> On 08/29/2016 05:27 PM, Peter Cock wrote:
>>
>>
>> Hi Martin,
>>
>> I'd like to look into creating new users via the API (where we can
>> control the email address and username format for integration with our
>> cluster), and have the web-interface forbid users from
>> self-registration.
>>
>> The read-the-docs site you mentioned in this old email (below) doesn't
>> exist anymore, and the API wiki page doesn't seem to link to something
>> similar:
>>
>> https://wiki.galaxyproject.org/Admin/API
>>
>> Where is the official API documentation now?
>>
>> Thanks,
>>
>> Peter
>>
>> On Mon, Dec 30, 2013 at 4:34 AM, Martin Čech > > wrote:
>>
>> Hi,
>>
>> you specify username, password and email in the body (payload) of
>> the POST as Key:Value pairs.
>>
>> Code from the API method: (
>>
>>
>> https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/users.html#UserAPIController.create
>>
>>
>> 
>> )
>>
>>
>>
>> username=payload['username']email=payload['email']password=payload['password']
>>
>> There are also other conditions that need to be fulfilled (e.g.
>> user
>> creation has to be turned on in the configuration) - you will find
>> these when you look at the source code of the method (because the
>> documentation is not perfect yet, sorry).
>>
>> M.
>>
>>
>>
>>
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>
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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

2016-09-02 Thread Björn Grüning

Hi Katherine,

have a look at this one using repeats:

https://github.com/bgruening/galaxytools/blob/master/tools/deseq2/deseq_helper.py

Ciao,
Bjoern


Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu:
> Hello Galaxy Community,
> I was wondering if anyone had ever come across a situation where they
> have had to pass the contents of a repeat parameter to a code file in a
> Galaxy tool config? Is there any way to do this?
> Katherine
> 
> 
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[galaxy-dev] Introducing Conda as a new standard for Galaxy tool dependencies

2016-08-26 Thread Björn Grüning

Hi all,

Galaxy 16.07 was just released:
https://docs.galaxyproject.org/en/master/releases/16.07_announce.html
and the IUC has some news to share with you.

For a more readable version please see:
https://docs.galaxyproject.org/en/master/admin/conda_faq.html



Galaxy tools (also called wrappers) traditionally use Tool Shed package
recipes to install their dependencies. At the tool’s installation time
the recipe is downloaded and executed in order to provide the underlying
software executables. Introduction of these Galaxy-specific recipes was
a necessary step at the time, however nowadays there are other more
mature and stable options to install software in a similar manner. The
Galaxy community has taken steps to improve the tool dependency system
in order to enable new features and expand its reach. This document aims
to describe these and answer the FAQ.

It is a pleasure to announce the adoption of a new standard for tool
dependencies in Galaxy which has been integrated over the last six
months: Conda packages!
Not only do Conda packages make tool dependencies more reliable and
stable, they are also easier to test and faster to develop than the
traditional Tool Shed package recipes .

Conda is a package manager like apt-get, yum, pip, brew or guix. We
don’t want to argue about the relative merits of various package
managers here, in fact Galaxy supports multiple package managers and we
welcome community contributions (such as implementing a Guix package
manager or enhancing the existing brew support to bring it on par with
Conda).

As a community, we have decided that Conda is the one that best fulfills
our needs. The following are some of the crucial Conda features that led
to this decision:

* Installation of packages does not require root privileges
(Installation at any location  the Galaxy user has write access to)
* Multiple versions of software can be installed in parallel
* HPC-ready
* Faster and more robust package installations through pre-compiled
packages (no build environment complications)
* Independent of programming language (R, Perl, Python, Julia, Java,
pre-compiled binaries, and more)
* Easy to write recipes (1 YAML description file + 1 Bash install script)
* An active, large and growing community (with more and more software
authors managing their own recipes)
* Extensive documentation: Conda documentation
(http://conda.pydata.org/docs/building/build.html) and Conda quick-start
(http://conda.pydata.org/docs/get-started.html)

Below we answer some common questions (collected by Lance Parsons):

1. How do I enable Conda dependency resolution for existing Galaxy
installations?
---

Most Galaxy administrators have not set up a dependency resolvers
configuration file (dependency_resolvers_conf.xml) which means they are
using Galaxy’s default (dependency_resolvers_conf.xml.sample). Galaxy
has enabled Conda dependency resolution by default since release 16.04
(if Conda was installed already), so many existing installations can use
Conda dependencies. Having Conda enabled in
dependency_resolvers_conf.xml means that Galaxy will look for
dependencies using the Conda system when it attempts to run tools. If
conda_auto_install is True, and a dependency is not found, Galaxy will
attempt to install it using the configured Conda channels. A graphical
user interface that allows administrators install Conda packages
directly from Galaxy when tools are installed from the Tool Shed is
available in the 16.07 release of Galaxy.


2. How do Conda dependencies work? Where do things get installed?
-
In contrast to the old dependency system, which was used exclusively by
Galaxy, Conda is a pre-existing, independent project. With Conda it is
possible for an admin to install packages without touching Galaxy at all
– managing your dependencies independently from Galaxy. Galaxy can
handle these dependencies for you, but admins are not required to use
Galaxy for dependency management.

There are a few new config options in the galaxy.ini file, but by
default Galaxy will install Conda (the package manager) and the required
packages in the /_conda/ directory. In this
directory, Galaxy will create an envs folder with all of the
environments managed by Galaxy. Every environment contains a lib, bin,
share, and include subdirectory, depending on the tool, and is
sufficient to get a Galaxy tool up and running. Galaxy simply sources
this folder via Conda and makes everything available before the tool is
executed on your cluster.

To summarize, there are four ways to manage Conda dependencies for use
with Galaxy. For all of these options, Conda dependency management must
be configured in the dependency_resolvers_conf.xml and the galaxy.ini file.

a) Manual Install - Conda dependencies may be installed by
administrators from the command line. Conda (and thus the conda
environments) should be

Re: [galaxy-dev] Putting it all together - toolshed tool + conda dependency

2016-08-25 Thread Björn Grüning

Hi Steve,

you call this baby-steps? I think this is huge! :)

All what you are missing is to enable conda in Galaxy.
Look at Gregs new flavour which is entirely Conda/Galaxy based.

You need to enable these env vars to make Galaxy conda enabled:

https://github.com/gregvonkuster/docker-galaxy-csg/blob/master/Dockerfile#L9

Hope this helps,
Bjoern

Am 25.08.2016 um 12:32 schrieb Steve Cassidy:
> Hi all,
>   I’m making baby steps towards having a repeatable installation for my
> tools.  But I’m now stuck, so help would be appreciated.
> 
> I have a tool that works and is in the test toolshed (alveoimport in
> Data Sources). 
> 
> It depends on my python package which is now part of bioconda (pyalveo,
> version 0.6). 
> 
> I can run my tool via planemo, which works I think because I have
> pyalveo installed in a local venv.  
> 
> If I try to run the docker image (derived from  bgruening/galaxy-stable
> but with the testtoolshed added) I am able to install my tool, but it
> doesn’t pick up the dependency, so it doesn’t work. 
> 
> I tried running with planemo turning on conda dependency resolution
> (following https://pypi.python.org/pypi/planemo/): 
> 
> planemo serve --galaxy_branch release_16.01 --conda_dependency_resolution .
> 
> It seems to have a go, but fails:
> 
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Building dependency
> shell command for dependency 'pyalveo'
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,449 Find dependency pyalveo
> version 0.6
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned
> 
> (isnull? True)
> galaxy.tools.deps DEBUG 2016-08-25 17:32:22,450 Resolver conda returned
> 
> (isnull? True)
> galaxy.tools.deps WARNING 2016-08-25 17:32:22,451 Failed to resolve
> dependency on 'pyalveo', ignoring
> 
> So, what’s the easiest route to a Galaxy deployment with my tool
> installed. The Docker route would be best I think, but what do I have to
> add to bgruening/galaxy-stable to have conda find my dependencies.
> 
> Thanks in advance,
> 
> Steve
> 
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
> 
> 
> 
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Re: [galaxy-dev] Connecting LDAP with Galaxy

2016-08-08 Thread Björn Grüning

Great, thanks Nicola!

Am 08.08.2016 um 23:53 schrieb Nicola Soranzo:
> There is one already: https://github.com/galaxyproject/galaxy/issues/2593
> 
> I may take a stab at it in the next days. 
> 
> Cheers, 
> Nicola 
> 
>  Björn Grüning ha scritto 
> 
>>
>>
>> Am 08.08.2016 um 20:14 schrieb Tiago Antao:
>>> I was reading a bit about this (I manage a LDAP server, but I am far
>>> from a specialist) and the format is actually too flexible: Any UTF-8
>>> encoding with up to 64 characters.
>>>
>>> I suspect basic punctation marks would be enough. Though I could see a
>>> Windows based SSO system (AD) accepting spaces and maybe even that being
>>> a usual convention (just speculating here).
>>>
>>> But _s and .s are probably very common across existing installations.
>>
>> Let's start with that at first :)
>> Do you have time to work on this or can create a tracking issue?
>>
>> Thanks!
>> Bjoern
>>
>>> On 2016-08-08 11:21, James Taylor wrote:
>>>> I don't think there is any good reason. Public username's main purpose
>>>> originally was to generate slugs for URLs so we left out "-".
>>>> Shouldn't break anything to add it.
>>>>
>>>> On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning
>>>> <bjoern.gruen...@gmail.com> wrote:
>>>>> Does anyone know why we have this restriction? Can we change it?
>>>>>
>>>>> Am 08.08.2016 um 17:31 schrieb Tiago Antao:
>>>>>> Sorry, that was what I meant and explained myself poorly.
>>>>>>
>>>>>> This is actually a very serious problem if one wants to integrate
>>>>>> Galaxy
>>>>>> in an existing SSO environment based on LDAP.
>>>>>>
>>>>>> Tiago
>>>>>>
>>>>>> On 2016-08-08 09:28, Nicola Soranzo wrote:
>>>>>>> Actually it's Galaxy (not the LDAP integration) that doesn't allow
>>>>>>> underscores in usernames, in fact if you try to register a new user on
>>>>>>> e.g. usegalaxy.org and the username has an underscore, you'll get this
>>>>>>> error:
>>>>>>>
>>>>>>> Public name must contain only lowercase letters, numbers and "-". It
>>>>>>> also has to be shorter than 255 characters but longer than 2.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Nicola
>>>>>>>
>>>>>>> On 08/08/16 16:08, Tiago Antao wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> A serious problem that I have found with Galaxy integration with LDAP
>>>>>>>> is that it does not allow underscores in the user name, and that is
>>>>>>>> very common with production LDAP servers.
>>>>>>>>
>>>>>>>> On 2016-08-08 09:01, Nicola Soranzo wrote:
>>>>>>>>> Hi Miuki,
>>>>>>>>> the file config/auth_conf.xml.sample contains examples and
>>>>>>>>> documentation of possible values that you have to put in your
>>>>>>>>> config/auth_conf.xml , unfortunately a lot depends on what
>>>>>>>>> LDAP/Active
>>>>>>>>> Directory server you are using and how it is configured. You may
>>>>>>>>> need
>>>>>>>>> to ask advice to the system administrators of your LDAP server.
>>>>>>>>> If you
>>>>>>>>> have specific questions/problems, feel free to ask here on the
>>>>>>>>> mailing
>>>>>>>>> list and/or on the IRC channel.
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>> Nicola
>>>>>>>>>
>>>>>>>>> On 01/08/16 20:45, Yip, Miu ki wrote:
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> I’m trying to configure a new instance of Galaxy and I want to use
>>>>>>>>>> LDAP for user authentication. I have taken a look at this wiki
>>>>>>>>>> page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
>>>>>>>>>>
>>>>>>>>>> I followed the inst

Re: [galaxy-dev] Connecting LDAP with Galaxy

2016-08-08 Thread Björn Grüning



Am 08.08.2016 um 20:14 schrieb Tiago Antao:
> I was reading a bit about this (I manage a LDAP server, but I am far
> from a specialist) and the format is actually too flexible: Any UTF-8
> encoding with up to 64 characters.
> 
> I suspect basic punctation marks would be enough. Though I could see a
> Windows based SSO system (AD) accepting spaces and maybe even that being
> a usual convention (just speculating here).
> 
> But _s and .s are probably very common across existing installations.

Let's start with that at first :)
Do you have time to work on this or can create a tracking issue?

Thanks!
Bjoern

> On 2016-08-08 11:21, James Taylor wrote:
>> I don't think there is any good reason. Public username's main purpose
>> originally was to generate slugs for URLs so we left out "-".
>> Shouldn't break anything to add it.
>>
>> On Mon, Aug 8, 2016 at 12:24 PM, Björn Grüning
>> <bjoern.gruen...@gmail.com> wrote:
>>> Does anyone know why we have this restriction? Can we change it?
>>>
>>> Am 08.08.2016 um 17:31 schrieb Tiago Antao:
>>>> Sorry, that was what I meant and explained myself poorly.
>>>>
>>>> This is actually a very serious problem if one wants to integrate
>>>> Galaxy
>>>> in an existing SSO environment based on LDAP.
>>>>
>>>> Tiago
>>>>
>>>> On 2016-08-08 09:28, Nicola Soranzo wrote:
>>>>> Actually it's Galaxy (not the LDAP integration) that doesn't allow
>>>>> underscores in usernames, in fact if you try to register a new user on
>>>>> e.g. usegalaxy.org and the username has an underscore, you'll get this
>>>>> error:
>>>>>
>>>>> Public name must contain only lowercase letters, numbers and "-". It
>>>>> also has to be shorter than 255 characters but longer than 2.
>>>>>
>>>>> Cheers,
>>>>> Nicola
>>>>>
>>>>> On 08/08/16 16:08, Tiago Antao wrote:
>>>>>> Hi,
>>>>>>
>>>>>> A serious problem that I have found with Galaxy integration with LDAP
>>>>>> is that it does not allow underscores in the user name, and that is
>>>>>> very common with production LDAP servers.
>>>>>>
>>>>>> On 2016-08-08 09:01, Nicola Soranzo wrote:
>>>>>>> Hi Miuki,
>>>>>>> the file config/auth_conf.xml.sample contains examples and
>>>>>>> documentation of possible values that you have to put in your
>>>>>>> config/auth_conf.xml , unfortunately a lot depends on what
>>>>>>> LDAP/Active
>>>>>>> Directory server you are using and how it is configured. You may
>>>>>>> need
>>>>>>> to ask advice to the system administrators of your LDAP server.
>>>>>>> If you
>>>>>>> have specific questions/problems, feel free to ask here on the
>>>>>>> mailing
>>>>>>> list and/or on the IRC channel.
>>>>>>>
>>>>>>> Cheers,
>>>>>>> Nicola
>>>>>>>
>>>>>>> On 01/08/16 20:45, Yip, Miu ki wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I’m trying to configure a new instance of Galaxy and I want to use
>>>>>>>> LDAP for user authentication. I have taken a look at this wiki
>>>>>>>> page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
>>>>>>>>
>>>>>>>> I followed the instructions and when I looked into the
>>>>>>>> auth_conf.xml file, I was unsure of what exactly Galaxy is looking
>>>>>>>> for when trying to connect with LDAP. Are there specific options
>>>>>>>> that I must give it? May I ask how Galaxy uses LDAP to authenticate
>>>>>>>> users?
>>>>>>>>
>>>>>>>> Thank you,
>>>>>>>> Miuki Yip
>>>>>>>> ___
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>>>>>>>> in your mail client.  To manage your subscriptions to this
>>>>>>>> and other Galaxy lists, please use the interface at:
>>>>>>>>https://lists.galaxyproject.org/
>>>>&g

Re: [galaxy-dev] Connecting LDAP with Galaxy

2016-08-08 Thread Björn Grüning

Does anyone know why we have this restriction? Can we change it?

Am 08.08.2016 um 17:31 schrieb Tiago Antao:
> Sorry, that was what I meant and explained myself poorly.
> 
> This is actually a very serious problem if one wants to integrate Galaxy
> in an existing SSO environment based on LDAP.
> 
> Tiago
> 
> On 2016-08-08 09:28, Nicola Soranzo wrote:
>> Actually it's Galaxy (not the LDAP integration) that doesn't allow
>> underscores in usernames, in fact if you try to register a new user on
>> e.g. usegalaxy.org and the username has an underscore, you'll get this
>> error:
>>
>> Public name must contain only lowercase letters, numbers and "-". It
>> also has to be shorter than 255 characters but longer than 2.
>>
>> Cheers,
>> Nicola
>>
>> On 08/08/16 16:08, Tiago Antao wrote:
>>> Hi,
>>>
>>> A serious problem that I have found with Galaxy integration with LDAP
>>> is that it does not allow underscores in the user name, and that is
>>> very common with production LDAP servers.
>>>
>>> On 2016-08-08 09:01, Nicola Soranzo wrote:
 Hi Miuki,
 the file config/auth_conf.xml.sample contains examples and
 documentation of possible values that you have to put in your
 config/auth_conf.xml , unfortunately a lot depends on what LDAP/Active
 Directory server you are using and how it is configured. You may need
 to ask advice to the system administrators of your LDAP server. If you
 have specific questions/problems, feel free to ask here on the mailing
 list and/or on the IRC channel.

 Cheers,
 Nicola

 On 01/08/16 20:45, Yip, Miu ki wrote:
> Hi,
>
> I’m trying to configure a new instance of Galaxy and I want to use
> LDAP for user authentication. I have taken a look at this wiki
> page: https://wiki.galaxyproject.org/Admin/Config/ExternalUserAuth
>
> I followed the instructions and when I looked into the
> auth_conf.xml file, I was unsure of what exactly Galaxy is looking
> for when trying to connect with LDAP. Are there specific options
> that I must give it? May I ask how Galaxy uses LDAP to authenticate
> users?
>
> Thank you,
> Miuki Yip
> ___
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 ___
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>>>
> 
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Re: [galaxy-dev] Adding packages to depot.galaxyproject.org

2016-08-08 Thread Björn Grüning

Hi Peter,

Am 08.08.2016 um 15:54 schrieb Peter Cock:
> On Mon, Aug 8, 2016 at 2:41 PM, Eric Rasche  wrote:
>> Hi Peter,
>>
>> The cargo port is the ideal place for this, however it does not support
>> manual uploads of files.
>>
> 
> Thanks Eric,
> 
> You mean https://github.com/galaxyproject/cargo-port
> 
> Is that something which might be addressed in future? The use case
> is when a previously public file stops working (either temporarily or
> permanently), so you can't use the official URL to make the cached
> copy?
> 
> Would it be OK to use a short lived URL like a personal dropbox URL,
> and then once cached, update urls.tsv with the original official
> (but broken) URL?


Yes this is totally fine. We just need to have a way to verify and check
tarballs before upload and we thought github and PR are a nice fit for this.

Thanks,
Bjoern

> Peter
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Re: [galaxy-dev] provide a field to upload a file as part of tool input

2016-08-06 Thread Björn Grüning

Hi Ryan,

Am 06.08.2016 um 00:54 schrieb Ryan G:
> Hi all - I have a custom tool that can optionally take a file as input.  
> 
> Right now, users have to upload the file into their history, then select
> the file when running the tool.
> 
> Is there a way to let the user select a file local on their computer as
> input to the tool, then when run, the file is uploaded?

This is currently not possible.

> And (second question), how can I make this field optional, such that the
> user does not need to provide a file at all when running the tool?
> 
> Right now, my input field is:
> 
> 

As you already figured out optional="True" :)

Ciao,
Bjoern

> 
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Re: [galaxy-dev] dataset collection datatype

2016-07-29 Thread Björn Grüning

Hi Cristel,

can you share some code. If you use discover_datasets like this,
format="" should indeed work.



Another feature is that the filetype is extracted from the extension if
you use it like this:

https://github.com/bgruening/galaxytools/blob/master/tools/text_processing/split_file_on_column/split_file_on_column.xml

Ciao,
Bjoern

> Hello galaxy developers,
> 
> how do you set the format for datasets in output dataset collections? I
> looked at some xmls from John Chilton, and tried using
> format_source="input", or inherit_format="true". Those unfortunately do
> not work. I also naively tried format="txt" to no avail.
> 
> I can't find anything in the documentation.
> Can someone point me in the right direction?
> 
> Thanks much,
> Cris
> 
> 
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Re: [galaxy-dev] Galaxy in Docker and nginx

2016-07-29 Thread Björn Grüning

Hi Miuki,

are you referring to this project?

https://github.com/bgruening/docker-galaxy-stable

If so you don't need to take care of anything, this one should be
production ready. If not copy what ever you need :)

Ciao,
Bjoern

Am 28.07.2016 um 22:28 schrieb Yip, Miu ki:
> Hi Galaxy Team,
> 
> I'm currently trying to use Galaxy in Docker, and I wanted to know if
> there are special actions that I have to do in Galaxy for nginx. I'm
> trying to set up a reserve proxy and have url forwarding. Do I need
> to inform Galaxy in Docker that nginx is being use?
> 
> Thanks, Miuki 
> ___ Please
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Re: [galaxy-dev] Storing data in the user session

2016-07-28 Thread Björn Grüning

Hi Steve & Mohammed,

I'm working on a user-profile extension to get credentials for a user,
but this will take a few more weeks sorry.

In the meantime can you look at the following idea:

my_programm.py --credentials $USER_CREDENTIALS --arguments

The variable $USER_CREDENTIALS is set during job execution with dynamic
destination mappings
https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping

What do you think, would this work for you?
This assumes you as admin can pass along the user credentials if you
know the username.

If not please get in touch and I will tell you about my plans to extend
the user-preferences maybe you can help me with this to speed things up.

Ciao,
Bjoern


> Hi Bjorn,
>  sure, I don’t want to have the credentials stored in the tool but the tool 
> needs to act on behalf of the user to retrieve data from the repository, so
> it needs access to credentials.  This could for example be a token generated
> via an OAuth2 exchange - basically something that is sent along with every 
> http request to the remote resource to authenticate the user.  
> 
> My thought is that this could be stored in the user profile if this can be 
> made
> available to the tool in the same way that __user_email__ is now. 
> 
> When you say ‘on the framework level’ do you mean by Galaxy? 
> 
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
>> On 28 Jul 2016, at 5:23 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:
>>
>> Hi Steve,
>>
>> can you explain the larger use-case behind it. Imho you should not
>> populate a tool with credentials, this should be handled on the
>> framework level.
>>
>> Hope you are fine,
>> Bjoern
>>
>> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>>> Hi again,
>>>   I’m looking for the right way to store some user credentials in the
>>> galaxy session so that tools can work on behalf of the user with our
>>> repository. 
>>>
>>> Currently users have an API key and they need to upload it as a data
>>> item to that is then passed to each tool that needs it as input.  This
>>> doesn’t seem like the right solution since the API key becomes part of
>>> the history and so would be shared if the history were shared.  
>>>
>>> What would be better would be a way of storing the API key in the user
>>> session and then being able to pass that into a tool.
>>>
>>> I note that there are a few user session variables available in the tool
>>> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>>> There is also a user preferences page where they can fill out a few
>>> details.  However, I can’t see a mechanism to extend this in any way and
>>> have extra properties in the preferences pane that would then be
>>> available to tools via the template file.  
>>>
>>> I can see that the standard practice for the data sources on
>>> usegalaxy.org <http://usegalaxy.org> is to send the user off to a
>>> repository website to find data that is then posted back to the galaxy
>>> server.  This isn’t appropriate for us since the interaction with the
>>> repository is not just for downloading a single dataset - tools will
>>> query the repository, download various kinds of data and possibly upload
>>> new data, so we need to store user credentials in some way. 
>>>
>>> Is there already a good way to achieve this or is this an enhancement to
>>> Galaxy? 
>>>
>>> Thanks,
>>>
>>> Steve
>>>
>>>
>>> —
>>> Department of Computing, Macquarie University
>>> http://web.science.mq.edu.au/~cassidy
>>> <http://web.science.mq.edu.au/%7Ecassidy>
>>>
>>>
>>>
>>> ___
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>>>
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> 
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Re: [galaxy-dev] Storing data in the user session

2016-07-28 Thread Björn Grüning

Hi Steve,

can you explain the larger use-case behind it. Imho you should not
populate a tool with credentials, this should be handled on the
framework level.

Hope you are fine,
Bjoern

Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
> Hi again,
>I’m looking for the right way to store some user credentials in the
> galaxy session so that tools can work on behalf of the user with our
> repository. 
> 
> Currently users have an API key and they need to upload it as a data
> item to that is then passed to each tool that needs it as input.  This
> doesn’t seem like the right solution since the API key becomes part of
> the history and so would be shared if the history were shared.  
> 
> What would be better would be a way of storing the API key in the user
> session and then being able to pass that into a tool.
> 
> I note that there are a few user session variables available in the tool
> xml file: __user__, __user_email__, __user_name__ and __user_id__.
>  There is also a user preferences page where they can fill out a few
> details.  However, I can’t see a mechanism to extend this in any way and
> have extra properties in the preferences pane that would then be
> available to tools via the template file.  
> 
> I can see that the standard practice for the data sources on
> usegalaxy.org  is to send the user off to a
> repository website to find data that is then posted back to the galaxy
> server.  This isn’t appropriate for us since the interaction with the
> repository is not just for downloading a single dataset - tools will
> query the repository, download various kinds of data and possibly upload
> new data, so we need to store user credentials in some way. 
> 
> Is there already a good way to achieve this or is this an enhancement to
> Galaxy? 
> 
> Thanks,
> 
> Steve
> 
> 
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
> 
> 
> 
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Re: [galaxy-dev] Galaxy, Docker Containers, and Installing tools not in Toolshed

2016-07-20 Thread Björn Grüning

Hi,

> Hello Bjoern,
> 
> Thanks for the quick response, I appreciate that.
> 
> Concerning the instructions, I am unclear of a couple of things.
> 
> I have a folder with my tools, there is no preinstalled folder that
> these tools need to go in called my_tools_folder, right?

No, you can create such a folder wherever you want and name it like you
want :)

> Additionally, would I place this tool in the same directory level as
> Galaxy_Central or as the config directory? (My current set up is
> galaxy_storage -> galaxy-central -> config, I have my tools folder in
> the same level as galaxy-central.)

This does not matter, what matters is that the folder path is correct in
the env variable.

> Lastly, the environment variable, is there a specific file that all
> the environment variables are stored for docker Galaxy? I have tried
> looking for an env file, but could not find it.

There is no file. These are real environment variables that are created
by Docker during container start. You can change them during start with
(e.g): docker run -e MY_ENV_VAR=foo bgruening/galaxy-stable

If such a variable, beginning with GALAXY_CONFIG_XXX exists this will be
picked up by Galaxy. Have a look at the container there are a lot
GALAXY_CONFIG_ vars set.

Hope this helps,
Bjoern


> Thanks so much! Miuki ____ From:
> Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, July 20,
> 2016 2:23 AM To: Yip, Miu ki; galaxy-dev@lists.galaxyproject.org 
> Subject: Re: [galaxy-dev] Galaxy, Docker Containers, and Installing
> tools not in Toolshed
> 
> Hi Miuki!
> 
> Am 19.07.2016 um 22:36 schrieb Yip, Miu ki:
>> Hello Galaxy Team,
>> 
>> We're from the Bioinformatics Shared Resources at Cold Spring
>> Harbor Lab and we're trying to create a new flavour of Galaxy for
>> local use in the lab using docker containers.
>> 
>> We want to add tools that are specific for our lab, such as
>> importing files from our system, onto this flavour of Galaxy using
>> Docker containers. Is there a recommended way to do this?
> 
> Can you try the following, assuming that all your tools are in 
> my_tools_tolder.
> 
> ADD ./my_tools_folder /inhouse_tools/
> 
> Now we need a tool_conf.xml file. You can create an additional one,
> no need to modify the existing one. I would propose to include this
> config file also in ./my_tools_folder so it will end up in 
> /inhouse_tools/tool_conf.xml With the following environment variable
> you tell Galaxy about the additional tool_conf file.
> 
> ENV GALAXY_CONFIG_TOOL_CONFIG_FILE = 
> config/tool_conf.xml,config/shed_tool_conf.xml,/inhouse_tools/tool_conf.xml
>
>  Please make sure that your new tools in
> /inhouse_tools/tool_conf.xml have as path "/inhouse_tools/.xml".
> 
> Let me know if this works, we should add this to the readme.
> 
> Thanks, Bjoern
> 
>> I've taken a look at the README from: 
>> https://github.com/bgruening/docker-galaxy-stable
>> 
>> I have been able to successfully create an instance of Galaxy
>> where the homepage is different and tools are imported from the
>> Tool Shed. However, I cannot figure out how to install tools onto
>> Galaxy that are not from the Tool Shed. I have tried creating a
>> container, putting the tools into the tools folder, changing the
>> tool conf and the integrated tool panel xml file. Then committing
>> the container and creating a new image. From the new image, I tried
>> creating another container and running it. This does not create a
>> Galaxy instance with the new tool. (This also does not seem like
>> the best way to go about something like this.)
> 
> 
>> Thank you for your help.
>> 
>> Best, Miuki Yip 
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Re: [galaxy-dev] Suggestion for Structural Variant Analysis onto Galaxy Main

2016-07-15 Thread Björn Grüning

Hi Orlando,

please fill your requests here:

https://github.com/galaxyproject/tools-iuc/issues/

A list of tools and if you have the Test Tool Shed links if there is
already preliminary work.

We can also kickstart you if you want to integrate your own tools into
Galaxy.

Thanks!
Bjoern

Am 14.07.2016 um 21:46 schrieb Wong, Orlando:
> Hello Galaxy dev I would like to suggest the idea of adding
> structural variant analysis tools for large structural variations for
> detecting long insertions, inversions or translocations on to the
> Galaxy Main. Currently, there are tools for detecting small variants,
> less than 50 bp for small indels. There are some of these structural
> variant analysis tools available on the Galaxy toolshed, but none are
> available on Galaxy Main or any of the other public galaxy servers
> listed on the wiki. I think it would be a great addition to Galaxy
> main, if it is possible. Thank you!
> 
> 
> 
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Re: [galaxy-dev] planemo shed_create bug? on planemo/server docker image

2016-07-15 Thread Björn Grüning



Am 14.07.2016 um 09:33 schrieb Steve Cassidy:
> Hi Bjorn, thanks for the response, very happy to go with the future
> way of doing things.  I did see the references to conda but couldn’t
> quite decipher what was needed.
> 
> Are you saying that I should create a new recipe in bioconda for my
> dependency? 

Yes :)

> Does it matter that this is not in the least ‘bio’ -
> these are for our language analysis tools, in the first instance this
> is a tool to pull data from our language repository.

No this does not matter, just put it in :)

> How does Galaxy know about the bioconda channel - is there a
> configuration setting pointing to the channels to find dependencies
> in?

Yes, please look in your galaxy.ini and search for conda.

> Could we create a language-conda channel to house language
> dependencies? Does that question make sense (not totally up on conda
> yet).

Yes this question makes sense, but than you have this additional
overhead of maintaining the build-infrastructure, building a community
around it, merging PR ... and so on.
From my experience this is quite a bit of work!

Cheers,
Bjoern

> Steve
> 
> — Department of Computing, Macquarie University 
> http://web.science.mq.edu.au/~cassidy
> 
>> On 14 Jul 2016, at 5:00 PM, Björn Grüning
>> <bjoern.gruen...@gmail.com> wrote:
>> 
>> Hi Steve,
>> 
>> are you fine restricting your tools to a recent Galaxy version,
>> let's say 6 month old?
>> 
>> If you forget about tool_depenencies.xml files, completely forget
>> these! Conda packaging is the way to go and way more easy for you.
>> 
>> Let me know and I will give a short introduction or follow the 
>> description on https://github.com/bioconda/bioconda-recipes to
>> create a PR and a package for your tool.
>> 
>> This can be used by Galaxy automatically. Thanks, Bjoern
>> 
>> Am 14.07.2016 um 03:49 schrieb Steve Cassidy:
>>> I’m just getting my head around tool dependencies and in doing so
>>> trying to push my tools to a local toolshed which I can handily
>>> run with the planemo/server docker image via Kitematic.
>>> 
>>> That toolshed is set up with an admin user
>>> plan...@test.com<mailto:plan...@test.com> so I have a stanza in
>>> my .planemo.yml:
>>> 
>>> shed_username: "stevecassidy" sheds: http://localhost:32768/: 
>>> key: "" email: "plan...@test.com<mailto:plan...@test.com>" 
>>> password: "planemo"
>>> 
>>> Now I try to create a repository in the toolshed with planemo:
>>> 
>>> $ planemo shed_create --shed_target http://localhost:32768/ 
>>> Repository created cd
>>> '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git
>>> rev-parse HEAD cd
>>> '/Users/steve/projects/hcsvlab-galaxy/tools/alveo' && git diff
>>> --quiet Repository [alveoimport] does not exist in the targeted
>>> Tool Shed.
>>> 
>>> 
>>> Note the conflicting messages here. The repository is created
>>> (and I can confirm that it is there) but then I get the message
>>> that the repo does not exist in the Toolshed.  After a bit of
>>> digging it turns out that this is because the repo is owned by
>>> the user ‘planemo’ rather than my username as declared in
>>> .planemo.yml.  If I add —owner plane to the command then it works
>>> fine.
>>> 
>>> So I’m not sure if this is a bug in the shed_create code or a
>>> weird interaction with the setup on planemo/server.
>>> 
>>> Steve
>>> 
>>> — Department of Computing, Macquarie University 
>>> http://web.science.mq.edu.au/~cassidy
>>> 
>>> 
>>> 
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> 
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Re: [galaxy-dev] Writing test for dataset collection

2016-07-11 Thread Björn Grüning

Hi Christel,

here you can find a lot of tests:

https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_creates_list.xml

This folder is a treasure for small little examples.
Hope this will help!
Cheers,
Bjoern

Am 11.07.2016 um 21:24 schrieb Cristel Thomas:
> Dear galaxy developers,
> 
> Can someone point me to a resource explaining how to write the test section
> of the xml for tools dealing with dataset collections? as input as well as
> output.
> 
> Thanks much,
> Cris
> 
> 
> 
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Re: [galaxy-dev] Using operations on multiple datasets

2016-07-05 Thread Björn Grüning

Hi,

Am 05.07.2016 um 23:18 schrieb D K:
> Sorry for the crosspost to Biostars, but I didn't get a response, so I
> thought I'd post here:
> 
> I just noticed that Galaxy allows creation of lists of datasets by clicking
> on the "Operations on multiple datasets" in the history panel. How does one
> use this with a custom tool (e.g. what does one put between the 
>  tags). Is the list treated as a text file with a list of each
> file? I couldn't find any examples or documentation online. I'd appreciate
> it if someone could point me in the right direction.

You can not use this feature in a tool, it's pure UI. But you can use
multiple="True"

https://github.com/galaxyproject/tools-iuc/blob/180a403421967d36f995941b1a4561349d75cfc5/tools/mothur/merge.files.xml#L32

maybe this helps?
Cheers,
Bjoern

> Thanks!
> 
> 
> 
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Re: [galaxy-dev] Infinite recursion on conda dependency manager

2016-06-15 Thread Björn Grüning

Hi Peter,

please install conda in version 3.19.3. Conda-4 has a bug when using
with --offline and --local.

conda install conda=3.19.3 should work.

https://github.com/galaxyproject/tools-iuc/blob/master/.travis.yml#L15

Thanks,
Bjoern

Am 15.06.2016 um 00:44 schrieb Peter van Heusden:
> Hi there
> 
> I've got a package in our lab conda channel (its still in testing phase)
> called goget. This is specified as a requirement for the build_ctb_gene
> tool like this:
> 
> 
>goget
> 
> 
> When the tool runs, I see infinite recursion on the conda side:
> 
> https://gist.github.com/pvanheus/c16a07a2c954741a311881cc7606df8d
> 
> Any ideas?
> 
> Thanks,
> Peter
> 
> 
> 
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