[galaxy-dev] Questions about run_functional_test.sh

[Kahlke Tim]

Hi Galaxy-developers,

I'm new to galaxy and am trying to set up a full production server.

First comment: Nice work, looks great, well documented!!

I have a question about run_functional_test: am I right that I can run this 
before installing any tools/dependencies? And how long is it supposed to run? I 
started it 14h ago and it's still running ...


Best Regards,
Tim
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Re: [galaxy-dev] Submitting jobs as a real user without using chown, please

[Thon de Boer]

OK...I think I can make this work, since it is not that difficult to make a
directory world writeable...Or at least group writeable since all the users
that will be able to run galaxy are in the same group as svcgalaxy that runs
galaxy...I'll look at those scripts and see what they need to do...

Thanks

Thon

-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu] 
Sent: Thursday, February 21, 2013 5:56 AM
To: Anthonius deBoer
Cc: 'Galaxy-dev Galaxy-dev'
Subject: Re: [galaxy-dev] Submitting jobs as a real user without using
chown, please

On Feb 20, 2013, at 2:37 PM, Anthonius deBoer wrote:

> Ah...Found what root squashing is and yes, that is turned on our isilon
system...
> 
> So out of luck I take it? We need to chown? we cannot fake the 
> submission name in another way ;)

Galaxy must have a way to make the job working directory writable for the
user that the job is running as.  If this means logging in to another system
via ssh that *does* have the ability to change ownership, then you can do
that.  The method is completely customizable because you can set the chown
script to anything that works for you.

However, some means of doing this that is appropriate for your environment
has to exist for Galaxy to perform it.  That said, you might be able to get
away with having the script make the working directory world-writeable
instead of owned by the real user.

--nate

> 
> Thanks
> 
> Thon
> 
> On Feb 20, 2013, at 10:32 AM, Anthonius deBoer  wrote:
> 
>> I cannot run chown even as a sudo command...Same error...
>> What is root squashing? I am reading on the internet that it is very
common not to allow users to change the ownership of files...
>> 
>> 
>> Thon
>> On Feb 20, 2013, at 05:52 AM, Nate Coraor  wrote:
>> 
>>> On Feb 19, 2013, at 11:02 PM, Thon de Boer wrote:
>>> 
>>> > Hi,
>>> > 
>>> > I am trying to setup my galaxy system to allow jobs to be 
>>> > submitted as the real user, since people want to keep an eye on 
>>> > their job on the cluster sometimes and they have no ideas which 
>>> > ones are theirs.
>>> > 
>>> > I tried the approach on the wiki here:
>>> > 
>>> > http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?hig
>>> > hlight=%28submit%29%7C%28jobs%29%7C%28as%29%7C%28user%29#Submittin
>>> > g_Jobs_as_the_Real_User
>>> > 
>>> > but unfortunately, the CHOWN command is not allowed, not even as a 
>>> > sudo user. Probably has to do with the fact that we run our 
>>> > cluster from an isilon system, which I assume is pretty typical.
>>> > 
>>> > The job was actually successfully submitted as the intended user, 
>>> > so that part works, but if we can just get it to work without 
>>> > having to rely on chown that would be awesome.
>>> > 
>>> > Can someone point me in the right direction?
>>> 
>>> Hi Thon,
>>> 
>>> If you run the command from the command line, what results do you get?
>>> 
>>> /usr/bin/sudo -E scripts/external_chown_script.py 
>>> /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directo
>>> ry/000/148 svcgalaxy 1
>>> 
>>> Note that external_chown_script.py can be modified as necessary to allow
you to change ownership in whatever way is appropriate for your site. Since
it should just be an NFS mount, as long as root squashing is not enabled and
your svcgalaxy user has sudo permission to run this script, it should
succeed.
>>> 
>>> --nate
>>> 
>>> > 
>>> > Here's the error.
>>> > 
>>> > galaxy.jobs.runners.local DEBUG 2013-02-19 19:35:31,524 execution 
>>> > of external set_meta for job 148 finished galaxy.jobs DEBUG 
>>> > 2013-02-19 19:35:31,576 (148) Changing ownership of working 
>>> > directory with: /usr/bin/sudo -E scripts/external_chown_script.py
/mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/1
48 svcgalaxy 1 galaxy.jobs ERROR 2013-02-19 19:35:31,653 (148) Failed to
change ownership of
/mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/1
48, failing Traceback (most recent call last):
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.
>>> > py", line 343, in finish
>>> > self.reclaim_ownership()
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.
>>> > py", line 916, in reclaim_ownership self._change_ownership( 
>>> > self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ) 
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.
>>> > py", line 902, in _change_ownership assert p.returncode == 0 
>>> > AssertionError galaxy.jobs DEBUG 2013-02-19 19:35:31,722 fail(): 
>>> > Moved 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_direc
>>> > tory/000/148/galaxy_dataset_332.dat to 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/files/000/dataset
>>> > _332.dat galaxy.datatypes.metadata DEBUG 2013-02-19 19:35:31,924 
>>> > Cleaning up external metadata files
>>> > 
>>> > Thanks
>>> > 
>>> > Thon
>>> > 

Re: [galaxy-dev] History not updating for multiple instances of Galaxy

[Neil.Burdett]

Thanks all that solved the problem. I also deleted my cache and cookies

Thanks for the help
Neil

From: Ross [mailto:ross.laza...@gmail.com]
Sent: Thursday, 21 February 2013 8:27 PM
To: Peter Cock; Burdett, Neil (ICT Centre, Herston - RBWH); 
galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] History not updating for multiple instances of Galaxy


maybe the cookie path for each instance defined in universe_wsgi.ini needs to 
be distinguishable if you're swapping between authenticated instances ?


# If proxy-prefix is enabled and you're running more than one Galaxy instance
# behind one hostname, you will want to set this to the same path as the prefix
# in the filter above.  This value becomes the "path" attribute set in the
# cookie so the cookies from each instance will not clobber each other.
cookie_path = /galaxy

On Thu, Feb 21, 2013 at 7:07 PM, Peter Cock 
mailto:p.j.a.c...@googlemail.com>> wrote:
On Thursday, February 21, 2013, wrote:
Further, when I try "register" I add an email address and password, but the 
system still doesn't log me in

Maybe this is a database configuration issue?

I didn't think I'd need to state any specific entries in universe as I am using 
physically separate directories

i.e. /home/galaxy/galaxy-cte/ 
i.e. /home/galaxy/galaxy-Newcastle/ 

Cheers
Neil


The logging in problem sounds like a cookie path issue to me,
I had something similar when I added second public Galaxy
to our server (in my case, a live on and a dev one).

Peter


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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4J
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[galaxy-dev] wrapper around Upload tool

[Jay Humphrey]

Hi! I have just started my first project with Galaxy. I want to use the 
Upload tool in my workflow to download large files from FTP (Swissprot 
and TREMBL fasta) and use them to make a local BLAST database. Can I 
build another tool as a wrapper around Upload, to enter preset ftp URLs 
(or overrides)?

Thanks
-Jay Humphrey
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Re: [galaxy-dev] Datasets linked into Galaxy do not work

[Sarah Diehl]

Hi Nate,

I found the problem :-). I looked for xsendfile errors in the apache log and 
that told me that the apache user doesn't seem to have access to the linked 
datasets, while the galaxy user has. Thanks for pointing me to the interaction 
between Galaxy and apache.

Best regards,
Sarah

- Ursprüngliche Mail -
Von: "Nate Coraor" 
An: "Sarah Diehl" 
CC: "galaxy-dev@lists.bx.psu.edu List" 
Gesendet: Dienstag, 19. Februar 2013 17:59:24
Betreff: Re: [galaxy-dev] Datasets linked into Galaxy do not work

On Feb 14, 2013, at 4:38 AM, Sarah Diehl wrote:

> Hi Nate,
> 
> copied datasets do work and I run Galaxy from the server root.

Hi Sarah,

I'm having trouble replicating this issue.  Could you send along (privately) 
the relevant portions of your proxy server configuration, and universe_wsgi.ini?

Thanks,
--nate

> 
> Thanks,
> Sarah
> 
> 
> - Original Message -
> From: "Nate Coraor" 
> To: "Sarah Diehl" 
> Cc: "galaxy-dev@lists.bx.psu.edu List" 
> Sent: Wednesday, February 13, 2013 8:22:10 PM
> Subject: Re: [galaxy-dev] Datasets linked into Galaxy do not work
> 
> On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote:
> 
>> Hi all,
>> 
>> I have problems with datasets that were linked into Galaxy data libraries 
>> (as Admin: "Add datasets", select "Upload files from filesystem paths" and 
>> "Link to files without copying to Galaxy"). Those files cannot be looked at, 
>> downloaded or viewed in a genome browser.
>> 
>> Errors in the browser are:
>> The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this 
>> server.
>> The requested URL /library_common/download_dataset_from_folder was not found 
>> on this server.
>> An error occurred while accessing: 
>> http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam
>>  Read error; BinaryCodec in readmode; streamed file (filename not available)
>> 
>> I don't see any errors in the log files.
>> 
>> We do this kind of linking a lot and everything worked fine in the past. I 
>> need to use this feature and need it to work, due to hard disk space and 
>> data duplication.
> 
> Hi Sarah,
> 
> Do display applications work correctly for datasets that were uploaded to a 
> library and copied in to Galaxy rather than linked?  Do you run Galaxy from 
> the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the 
> root?
> 
> Thanks,
> --nate
> 
>> 
>> Any help is appreciated.
>> 
>> Best regards,
>> Sarah
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> 


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[galaxy-dev] help on wig file

[Alfonso Garrido-Lecca]

Hello, 
How can I change the "chromosome" name on a wig file to "chr"? FOr whatever 
reason when I try feeding 
this file with the program i am working with (CEAS package) it gives me an 
error. But when I use a wig file 
with chr it works fine

This is how my wiggle file looks like: 
track type=wiggle_0 name="MACS_in_Galaxy_treat_CHROMOSOME_II" 
description="Shifted Merged MACS 
tag counts for every 1 bp"
variableStep chrom=CHROMOSOME_II span=1
1   3
2   4
3   5

And this is how I need it to be: 
track type=wiggle_0 name="MACS_in_Galaxy_treat_I" description="Shifted Merged 
MACS tag counts for 
every 1 bp"
variableStep chrom=I span=1
570 1
571 1
572 1

thanks
alfonso
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Re: [galaxy-dev] Rendering of < and > in read-me files on Tool Shed

[Peter Cock]

On Thu, Feb 21, 2013 at 7:46 PM, Greg Von Kuster  wrote:
> Hello Peter,
>
> This issue should now be corrected on both Galaxy tool sheds.
>
> Thanks very much,
>
> Greg Von Kuster

Looks good - thanks Greg!

Peter
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[galaxy-dev] Contributing to genome indexes on rsync server

[Brad Chapman]

Hi all;
Is there a way for community members to contribute indexes to the rsync
server? This resource is awesome and I'm working on migrating the
CloudBioLinux retrieval scripts to use this instead of the custom S3
buckets we'd set up previously:

https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/biodata/galaxy.py

It's great to have this as a public shared resource and I'd like to be
able to contribute back. From an initial pass, here are the things I'd
like to do:

- Include bowtie2 indexes for more genomes.

- Include novoalign indexes for a number of commonly used genomes.

- Clean up hg19 to include a full canonically sorted hg19, with indexes.
  Broad has a nice version prepped so GATK will be happy with it, and
  you need to stick with this ordering if you're ever going to use a
  GATK tool on it. Right now there is a partial hg19canon (without the
  random/haplotype chromosomes) and the structure is a bit complex.

What's the best way to contribute these? Right now I have a lot of the
indexes on S3. For instance, the hg19 indexes are here:

https://s3.amazonaws.com/biodata/genomes/hg19-bowtie.tar.xz
https://s3.amazonaws.com/biodata/genomes/hg19-bowtie2.tar.xz
https://s3.amazonaws.com/biodata/genomes/hg19-bwa.tar.xz
https://s3.amazonaws.com/biodata/genomes/hg19-novoalign.tar.xz
https://s3.amazonaws.com/biodata/genomes/hg19-seq.tar.xz
https://s3.amazonaws.com/biodata/genomes/hg19-ucsc.tar.xz

I'm happy to format these differently or upload somewhere that would
make it easy to include. Thanks again for setting this up, I'm looking
forward to working off a shared repository of data,
Brad
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Re: [galaxy-dev] Datatype display_in_upload not respected in upload1

[Daniel Blankenberg]

Hi Nicola,

Thanks again for reporting this error. This has been fixed in stable. 


Thanks for using Galaxy,

Dan


galaxy-central$ hg head
changeset:   8914:31b09605fcc3
branch:  stable
tag: tip
parent:  8908:a0741e6798f2
user:Daniel Blankenberg 
date:Thu Feb 21 15:26:15 2013 -0500
summary: Fix for display_in_upload

changeset:   8913:26d7b89d9f89
user:Daniel Blankenberg 
date:Thu Feb 21 15:26:15 2013 -0500
summary: Fix for display_in_upload


On Feb 21, 2013, at 12:12 PM, Carl Eberhard wrote:

> Good catch - thanks for reporting it:
> 
> https://trello.com/card/display-in-upload-not-respected-in-datatypes-conf-xml/506338ce32ae458f6d15e4b3/662
> 
> Carl
> 
> 
> 
> On Thu, Feb 14, 2013 at 12:50 PM, Nicola Soranzo  wrote:
> Hi all,
> I noticed that when I go in "Get Data" -> "Upload File from your
> computer" (i.e. upload1 tool) the "File Format" list contains also
> datatypes which have display_in_upload="false" in datatypes_conf.xml
> (e.g. "afg", "fli"), while the list does not contain datatypes which
> have no display_in_upload attribute at all (e.g. "bedstrict", "bed6").
> This sounds like a bug to me, but I have not found any reference around.
> 
> Thanks,
> Nicola
> --
> Nicola Soranzo, Ph.D.
> CRS4
> Bioinformatics Program
> Loc. Piscina Manna
> 09010 Pula (CA), Italy
> http://www.bioinformatica.crs4.it/
> 
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Re: [galaxy-dev] Tabular file metadata - columns names

[Carlos Borroto]

On Thu, Feb 21, 2013 at 2:03 PM, Peter Cock  wrote:
> On Thu, Feb 21, 2013 at 6:12 PM, Carlos Borroto
>  wrote:
>> On Wed, Feb 20, 2013 at 9:57 AM, Peter Cock  
>> wrote:
>>> [*] This is one reason why I've just switched the default BLAST+
>>> output from the standard 12 column output to the extended 24
>>> column output in v0.0.17 of the wrappers:
>>> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
>>
>> Hi Peter,
>>
>> Would you consider adding the option to set a custom tabular output? I
>> would like to be able to select exactly which fields to include. For
>> example the alignment data I rarely need it and if I choose 24 column
>> output I'll be wasting a lot of space by including it.
>>
>
> Hi Carlos,
>
> I had deliberately avoid letting users pick the columns - it is
> doable, but has two major downsides. First a more complex
> GUI (if we don't allow the order to change then it is still ~24
> options), and then the worse problem of it being hard to know
> what the output columns are in later work. If the columns are
> consistent, it is much easier to write general instructions (e.g.
> for filtering on percentage identity). If Galaxy let us label the
> columns on the current 'tabular' format, then I'd be more
> positive about this, but until that happens I would prefer not
> to offer arbitrary columns in the BLAST tabular output.
>

I was thinking more like a text box where an advance user could type
in the strings that would be attached to '-outfmt  "6 "'. We could
add as a default value the current strings in tabular 24 to help guide
the user to what is possible. I see your point about this would make
harder to later know what each columns is, but this is an advanced use
and could be labelled as such.

> In the mean time, would you prefer I revert the default to 12
> column tabular output? Just how big are your BLAST files if
> the extra disk space is a serious concern (compared to raw
> sequencing data)?
>

I'm fine with 24 being the default. In fact I'm currently rerunning a
big blast exactly cause I now realized I needed more information than
what is provided by 12. I'm expecting 25 million hits with HSPs of
300bp. I'm expecting to double or triple the previous output. The
current output is around 2.1gb and the raw sequencing data is 1gb. As
you can see it would be nice to get rid of the alignments if I'm not
using them.

> (Separately I was asking about how to offer automatic datatype
> conversion - that would allow easy conversion of BLAST XML
> or even BLAST archive ASN.1 format into tabular on demand,
> making them viable default output formats from a usability point
> of view - but both of those are larger than the default 12 column
> or even 24 column tabular formats.)
>

This would be great and I will probably use it for smaller blast jobs.

Best,
Carlos
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Re: [galaxy-dev] Rendering of < and > in read-me files on Tool Shed

[Greg Von Kuster]

Hello Peter,

This issue should now be corrected on both Galaxy tool sheds.

Thanks very much,

Greg Von Kuster


On Feb 20, 2013, at 12:38 PM, Peter Cock wrote:

> Hi Greg,
> 
> This is probably another minor bug report for your to-do list - would
> you prefer I try to file Trello issues for things like this directly?
> 
> Many of the README files on the Tool Shed have an XML snippet
> in them if they include manual install instructions, but unfortunately
> the less-than and greater-than signs are rendered with HTML escape
> codes. For example, looking at:
> 
> http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list
> 
> The line:
> 
> 
> 
> is shown as:
> 
> 
> 
> Note this does not affect the "Browse repository tip files" view, just
> the main tool overview page.
> 
> Thanks,
> 
> Peter
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Re: [galaxy-dev] Problem running Tophat for Illumina

[Jennifer Jackson]

Hi Greg,

This is a good start, you will want to do "which" on bowtie2 and tophat2 
as well. Each should point to proper binary. You don't seem to have all 
of them installed, specifically "Tophat v1.3.3-1.4.0", which is what 
"Tophat for Illumina" uses.


Correct binary for the path name. See the dependencies link for the 
tools wrappers that use this one (includes "Tophat for Illumina").

>> which bowtie
> /usr/local/galaxy/installs/bin/bowtie-0.12.8/bowtie

Incorrect binary for the path name and the tool wrapper "Tophat for 
Illumina". See the dependencies link. You probably need to install 
Tophat v1.3.3-1.4.0 or switch to using tool wrapper "Tophat2" and name 
the binary tophat2. The binary bowtie2 will also need to be correctly 
labeled if tophat2 is being used, to fully resolve the issue with locs.

>> which tophat
> /usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64/tophat

I think you will find that the problems you were having with "Tophat for 
Illumina" are linked to the above and if you correct the dependencies, 
the loc problems and errors will sort themselves out.



On 2/21/13 9:22 AM, greg wrote:

Ok, you're right, I did ask something similar before.

So is the simplest answer is to tell users to use Tophat2 instead of
"Tophat for Illumina"?  Or is there anything special in "Tophat for
Illumina" that they would be missing out on?


I am not sure if leaving tools with improper tool wrapper/binary/loc 
mapping in the tool menu is the best solution. If you don't want them, 
you can of course remove them from the tool config file.


Which is better? The updated tools are different and most users will 
probably want to use the new versions just like most updated tools, but 
it really depends on what they are doing (if they need to reproduce an 
older study or not, are using a datatype not supported by the new tool, 
or are in the middle of a project, etc.). You are pretty close to having 
all of it configured correctly, if you also have the indexes for both 
created. But this is entirely your call. Maybe the scientists you 
support can help you make the decision - the user manuals for each 
describe the changes between the software versions. The wrappers in 
Galaxy have most if not all of the core functions implemented and the 
tool form's describe this in detail.


Take care,

Jen
Galaxy team




-Greg

Here's some info I dug up in case it's useful:


which bowtie

/usr/local/galaxy/installs/bin/bowtie-0.12.8/bowtie

which tophat

/usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64/tophat

I do have all of these installed:

bowtie-0.12.8  bowtie2-2.0.2  bwa-0.6.2  cufflinks-2.0.2.Linux_x86_64
tophat-2.0.6.Linux_x86_64


Here's the PATH if it helps:


echo $PATH

/misc/local/galaxy/galaxy_python/bin:/sge/8.0.1p4/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/pinerog/bin:/usr/local.orig/bin:/usr/local/R-2.15.0/bin/:/usr/local/blast+:/usr/local/EMBOSS:/usr/local/galaxy/installs/bin/beam2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2/scripts:/usr/local/galaxy/installs/bin/bowtie-0.12.8:/usr/local/galaxy/installs/bin/bowtie-0.12.8/scripts:/usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64:/usr/local/galaxy/installs/bin/samtools-0.1.18:/usr/local/galaxy/installs/bin/samtools-0.1.18/misc:/usr/local/galaxy/installs/bin/samtools-0.1.18/bcftools:/usr/local/galaxy/installs/bin/cufflinks-2.0.2.Linux_x86_64:/usr/local/galaxy/installs/bin/express-1.2.2-linux_x86_64:/usr/local/galaxy/installs/bin/bwa-0.6.2:/usr/local/galaxy/installs/bin/fastx:/usr/local/galaxy/installs/bin/lastz-distrib-1.02.00:/usr/local/!

galaxy/ins
talls/bin/lastz-distrib-1.02.00/tools:/misc/local/galaxy/galaxy_python/bin


On Thu, Feb 21, 2013 at 11:40 AM, Jennifer Jackson  wrote:

Hi Greg,

The problem here and the confusion between the Bowtie loc files are likely
related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And
the tool wrappers for all versions are active? I though we resolved this
earlier but maybe you installed a new tool or updated?

The wrappers for the tools that have dependencies on bowtie vs bowtie2 (and
the associated indexes) are not interchangeable. You will need to chech your
paths to see which tool is being used for each - be sure to check any
symbolic paths that may have been created when the tools were installed
(these tools are known to create links such as bowtie -> bowtie2, that you
will want to get rid of).

Reviewing tool dependencies is the best way to troubleshoot:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

Hopefully this helps. Be sure to keep any followup on the mailing list so
the dev community can continue to have input,

Jen
Galaxy team


On 2/21/13 7:50 AM, greg wrote:


Hi guys,

On our local galaxy install I'm getting the error below when I run
tophat for illumina like this:

http://snag.gy/HsWyS.jpg

Any idea

Re: [galaxy-dev] Tabular file metadata - columns names

[Peter Cock]

On Thu, Feb 21, 2013 at 6:12 PM, Carlos Borroto
 wrote:
> On Wed, Feb 20, 2013 at 9:57 AM, Peter Cock  wrote:
>> [*] This is one reason why I've just switched the default BLAST+
>> output from the standard 12 column output to the extended 24
>> column output in v0.0.17 of the wrappers:
>> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
>
> Hi Peter,
>
> Would you consider adding the option to set a custom tabular output? I
> would like to be able to select exactly which fields to include. For
> example the alignment data I rarely need it and if I choose 24 column
> output I'll be wasting a lot of space by including it.
>
> I'll be happy to provide patch.
>
> And yes, I'll be very happy to be able to set custom column names in
> the workflow for tabular outputs.
>
> Regards,
> Carlos

Hi Carlos,

I had deliberately avoid letting users pick the columns - it is
doable, but has two major downsides. First a more complex
GUI (if we don't allow the order to change then it is still ~24
options), and then the worse problem of it being hard to know
what the output columns are in later work. If the columns are
consistent, it is much easier to write general instructions (e.g.
for filtering on percentage identity). If Galaxy let us label the
columns on the current 'tabular' format, then I'd be more
positive about this, but until that happens I would prefer not
to offer arbitrary columns in the BLAST tabular output.

In the mean time, would you prefer I revert the default to 12
column tabular output? Just how big are your BLAST files if
the extra disk space is a serious concern (compared to raw
sequencing data)?

(Separately I was asking about how to offer automatic datatype
conversion - that would allow easy conversion of BLAST XML
or even BLAST archive ASN.1 format into tabular on demand,
making them viable default output formats from a usability point
of view - but both of those are larger than the default 12 column
or even 24 column tabular formats.)

Regards,

Peter
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Re: [galaxy-dev] Tabular file metadata - columns names

[Carlos Borroto]

On Wed, Feb 20, 2013 at 9:57 AM, Peter Cock  wrote:
> [*] This is one reason why I've just switched the default BLAST+
> output from the standard 12 column output to the extended 24
> column output in v0.0.17 of the wrappers:
> http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/

Hi Peter,

Would you consider adding the option to set a custom tabular output? I
would like to be able to select exactly which fields to include. For
example the alignment data I rarely need it and if I choose 24 column
output I'll be wasting a lot of space by including it.

I'll be happy to provide patch.

And yes, I'll be very happy to be able to set custom column names in
the workflow for tabular outputs.

Regards,
Carlos
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Re: [galaxy-dev] KeyError ['tools'] on importing workflow from locally installed repository

[jorrit poelen]

Hi Dave,

Thanks for the quick reply.  Your fix worked like a charm!

-jorrit

> Date: Tue, 19 Feb 2013 12:54:23 -0500
> From: Dave Bouvier 
> To: galaxy-dev@lists.bx.psu.edu, closetic...@galaxyproject.org
> Subject: Re: [galaxy-dev] KeyError ['tools'] on importing workflow
>   from locally installed repository
> Message-ID: <5123bc4f.90...@bx.psu.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Jorrit,
> 
> Thank you for uncovering that issue, I've commited a fix in the stable 
> branch of galaxy-central at 8887:d5896e8a60fa. To apply that changeset, 
> you'll need to run the following commands from your Galaxy directory:
> 
> $ hg pull -b stable https://bitbucket.org/galaxy/galaxy-central/
> $ hg update stable
> 
>--Dave B.
> 
> On 2/18/13 21:57:18.000, jorrit poelen wrote:
>> Hey y'all,
>> 
>> I am testing how to best share a workflow through a tool shed.  I stumbled 
>> across a possible bug and am hoping that this is simply a configuration 
>> issue.
>> 
>> Steps to reproduce:
>> 
>> 1. In local galaxy instance goto . .  admin > search and browse tool sheds
>> 2. locate select "Galaxy test tool shed"
>> 3. search for "obo"
>> 4. preview and install repository "obo_test_workflows"
>> 5. in next screen click "install to Galaxy"
>> 6. in next screen click "install"
>> 7. in next screen click "obo_test_workflows"
>> 8. in next screen, under workflows, click "TestOboWorkflow1"
>> 9. in svg graphics page > repository actions > import workflow to galaxy
>> 
>> Expected results:
>> Workflow is installed and made available in workflow section in local Galaxy 
>> instance.
>> 
>> Actual results:
>> URL: 
>> http://galaxy:7474/admin_toolshed/import_workflow?repository_id=2d9035b3fc152403&workflow_name=0c2d739e4f60c1bed9e8e46f2f317141702ceb26%3A546573744f626f576f726b666c6f7731
>> File 
>> '/home/ubuntu/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
>>  line 364 in respond
>>   app_iter = self.application(environ, detect_start_response)
>> File 
>> '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', 
>> line 98 in __call__
>>   environ, self.app)
>> File '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', 
>> line 539 in intercept_output
>>   app_iter = application(environ, replacement_start_response)
>> File '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', 
>> line 80 in __call__
>>   return self.application(environ, start_response)
>> File 
>> '/home/ubuntu/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', 
>> line 632 in __call__
>>   return self.application(environ, start_response)
>> File '/home/ubuntu/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 
>> in __call__
>>   return self.handle_request( environ, start_response )
>> File '/home/ubuntu/galaxy-dist/lib/galaxy/web/framework/base.py', line 185 
>> in handle_request
>>   body = method( trans, **kwargs )
>> File '/home/ubuntu/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 
>> 216 in decorator
>>   return func( self, trans, *args, **kwargs )
>> File 
>> '/home/ubuntu/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>>  line 744 in import_workflow
>>   tools_metadata = metadata[ 'tools' ]
>> KeyError: 'tools'
>> 
>> Thanks in advance for suggestions on how to solve / work around this issue.
>> 
>> -jorrit
>> 
>> PS Note that the workflow can be installed using a url pointing to the 
>> workflow from a hg repository on bitbucket (ie. 
>> https://bitbucket.org/jhpoelen/obo_workflows/raw/25d386a50562d02e03fa821d96a831cf75edcbae/Galaxy-Workflow-TestOboWorkflow1.ga).
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> 
>>   http://lists.bx.psu.edu/
>> 
> 
> 


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Re: [galaxy-dev] Problem running Tophat for Illumina

[greg]

Ok, you're right, I did ask something similar before.

So is the simplest answer is to tell users to use Tophat2 instead of
"Tophat for Illumina"?  Or is there anything special in "Tophat for
Illumina" that they would be missing out on?

-Greg

Here's some info I dug up in case it's useful:

>which bowtie
/usr/local/galaxy/installs/bin/bowtie-0.12.8/bowtie
>which tophat
/usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64/tophat

I do have all of these installed:

bowtie-0.12.8  bowtie2-2.0.2  bwa-0.6.2  cufflinks-2.0.2.Linux_x86_64
tophat-2.0.6.Linux_x86_64


Here's the PATH if it helps:

>echo $PATH
/misc/local/galaxy/galaxy_python/bin:/sge/8.0.1p4/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/pinerog/bin:/usr/local.orig/bin:/usr/local/R-2.15.0/bin/:/usr/local/blast+:/usr/local/EMBOSS:/usr/local/galaxy/installs/bin/beam2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2/scripts:/usr/local/galaxy/installs/bin/bowtie-0.12.8:/usr/local/galaxy/installs/bin/bowtie-0.12.8/scripts:/usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64:/usr/local/galaxy/installs/bin/samtools-0.1.18:/usr/local/galaxy/installs/bin/samtools-0.1.18/misc:/usr/local/galaxy/installs/bin/samtools-0.1.18/bcftools:/usr/local/galaxy/installs/bin/cufflinks-2.0.2.Linux_x86_64:/usr/local/galaxy/installs/bin/express-1.2.2-linux_x86_64:/usr/local/galaxy/installs/bin/bwa-0.6.2:/usr/local/galaxy/installs/bin/fastx:/usr/local/galaxy/installs/bin/lastz-distrib-1.02.00:/usr/local/ga!
 
laxy/installs/bin/lastz-distrib-1.02.00/tools:/misc/local/galaxy/galaxy_python/bin

On Thu, Feb 21, 2013 at 11:40 AM, Jennifer Jackson  wrote:
> Hi Greg,
>
> The problem here and the confusion between the Bowtie loc files are likely
> related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And
> the tool wrappers for all versions are active? I though we resolved this
> earlier but maybe you installed a new tool or updated?
>
> The wrappers for the tools that have dependencies on bowtie vs bowtie2 (and
> the associated indexes) are not interchangeable. You will need to chech your
> paths to see which tool is being used for each - be sure to check any
> symbolic paths that may have been created when the tools were installed
> (these tools are known to create links such as bowtie -> bowtie2, that you
> will want to get rid of).
>
> Reviewing tool dependencies is the best way to troubleshoot:
> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
>
> Hopefully this helps. Be sure to keep any followup on the mailing list so
> the dev community can continue to have input,
>
> Jen
> Galaxy team
>
>
> On 2/21/13 7:50 AM, greg wrote:
>>
>> Hi guys,
>>
>> On our local galaxy install I'm getting the error below when I run
>> tophat for illumina like this:
>>
>> http://snag.gy/HsWyS.jpg
>>
>> Any ideas?
>>
>> Thanks,
>>
>> Greg
>>
>>
>> Error:
>>
>> Dataset generation errors
>>
>> Dataset 27: Tophat for Illumina on data 15: deletions
>>
>> Tool execution generated the following error message:
>>
>> Error in tophat:
>> tophat: option --no-closure-search not recognized
>>  for detailed help see http://tophat.cbcb.umd.edu/manual.html
>>
>> cp: cannot stat
>> `/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed':
>> No such file or directory
>> cp: cannot stat
>> `/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed':
>> No such file or directory
>> cp: cannot stat
>> `/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam':
>> No such file or directory
>> cp: cannot stat
>> `/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed':
>> No such file or directory
>>
>> The tool produced the following additional output:
>>
>> TopHat v2.0.6
>> tophat -p 4  -a 8 -m 0 -i 70 -I 50 -g 20 --library-type
>> fr-unstranded --max-insertion-length 3 --max-deletion-length 3
>> --coverage-search --min-coverage-intron 50 --max-coverage-intron 2
>> --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
>> --segment-length 25 --min-segment-intron 50 --max-segment-intron
>> 50
>> /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
>> /home/galaxy/000/dataset_306.dat
>> ___
>> 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:
>>
>>http://lists.bx.psu.edu/
>>
>
> --
> Jennifer Hillman-Jackson
> Galaxy Support and Training
> http://galaxyproject.org


On Thu, Feb 21, 2013 at 11:40 AM, Jennifer Jackson  wrote:
> Hi Greg,
>
> The problem here and the confusion between the Bowtie loc files are likely
> related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And
> the tool wrappers for all versions are active? I though we resolved this
>

Re: [galaxy-dev] Datatype display_in_upload not respected in upload1

[Carl Eberhard]

Good catch - thanks for reporting it:

https://trello.com/card/display-in-upload-not-respected-in-datatypes-conf-xml/506338ce32ae458f6d15e4b3/662

Carl



On Thu, Feb 14, 2013 at 12:50 PM, Nicola Soranzo  wrote:

> Hi all,
> I noticed that when I go in "Get Data" -> "Upload File from your
> computer" (i.e. upload1 tool) the "File Format" list contains also
> datatypes which have display_in_upload="false" in datatypes_conf.xml
> (e.g. "afg", "fli"), while the list does not contain datatypes which
> have no display_in_upload attribute at all (e.g. "bedstrict", "bed6").
> This sounds like a bug to me, but I have not found any reference around.
>
> Thanks,
> Nicola
> --
> Nicola Soranzo, Ph.D.
> CRS4
> Bioinformatics Program
> Loc. Piscina Manna
> 09010 Pula (CA), Italy
> http://www.bioinformatica.crs4.it/
>
> ___
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Re: [galaxy-dev] Installing Galaxy on ARM Architecture

[Nate Coraor]

On Feb 21, 2013, at 11:47 AM, Shun Liang wrote:

> Sorry just forgot to CC the mailing list.
> 
> 
> Hi James,
> 
> I followed the manual installation instruction on 
> "https://bitbucket.org/james_taylor/bx-python/wiki/HowToInstall";, and 
> surprisingly, bx-python seems to be built on the ARM server without any 
> problem:
> 
> Installed 
> /nfs/users/bx-python/lib/python/bx_python-0.7.1-py2.7-linux-armv7l.egg
> Processing dependencies for bx-python==0.7.1
> Finished processing dependencies for bx-python==0.7.1

Hi Shun.

I'm moving this over to galaxy-dev since it's about a local installation.

Galaxy's eggs lib isn't finding the egg you built because Galaxy adds the 
Mercurial revision to the egg version, and then expects the egg to be 
physically located in galaxy-dist/eggs/.  The library will be looking for:

bx_python-0.7.1_7b95ff194725-py2.7-linux-armv71.egg

If you are able to build it through scramble that would be ideal since it 
handles that naming for you, and there will be other C-Extension eggs to build 
under similar constraints.  There should have been an error earlier in the 
scramble output with more details on why building bx-python failed.  If you 
rerun scramble on just that egg, you should be able to recapture the output:

  % python ./scripts/scramble.py -e bx_python

--nate

> 
> 
> 
> Regards,
> Shun
> 
> From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
> [ja...@jamestaylor.org]
> Sent: 21 February 2013 16:07
> To: Shun Liang
> Cc: galaxy-u...@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Installing Galaxy on ARM Architecture
> 
> You are definitely in uncharted territory with an arm server. Can you
> try building just bx-python itself and let us know what the errors
> are?
> 
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
> 
> 
> On Thu, Feb 21, 2013 at 11:03 AM, Shun Liang  
> wrote:
>> Hi,
>> 
>> I am trying to install Galaxy on an ARMV7 architecture Linux server. I ran
>> "run.sh" and failed because some of the python eggs could not be fetched. I
>> then have a look at "http://eggs.galaxyproject.org/"; and I have realized
>> there aren't any armv7 builds for those eggs.
>> 
>> I then decided to build (or scramble) the eggs on my own. I ran
>> "scripts/scramble.py" and this also failed with the following message (after
>> building a lot of things):
>> 
>> scramble(): Copied egg to:
>>  /nfs/users/galaxy_dist/eggs/twill-0.9-py2.7.egg
>> Traceback (most recent call last):
>>  File "scripts/scramble.py", line 26, in 
>>eggs = c.scramble()
>>  File "/nfs/users/galaxy_dist/lib/galaxy/eggs/scramble.py", line 242, in
>> scramble
>>raise last_exc # only 1 failure out of the crate, be more informative
>> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
>> failed for bx_python 0.7.1
>> 
>> 
>> May I ask what may cause this problem? Have I done anything wrong? Or, is it
>> even possible to install Galaxy on ARM architecture Linux?
>> 
>> 
>> 
>> Many thanks,
>> Shun
>> 
>> 
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> 
>>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>>  http://lists.bx.psu.edu/
> 
> ___
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> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
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> 
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> 
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> please use the interface at:
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Re: [galaxy-dev] New release : display problem

[Carlos Borroto]

Hi Jeremy,

In my case the error went away by itself. Maybe at one point a did a
force reload (CTRL-SHIFT-R) I can't remember. I do think a cache issue
could be the culprit here, I normally use Chrome and only go to
Firefox when something is not working, Firefox would not have seen
this content before, so no cached content there.

Best,
Carlos

On Thu, Feb 21, 2013 at 11:04 AM, Jeremy Goecks  wrote:
> Clearing your browser's cache may solve the problem. Can you please try that 
> and let us know if it solves the problem?
>
> Thanks,
> J.
>
>
> On Feb 21, 2013, at 10:55 AM, MONJEAUD wrote:
>
>> Hello All,
>>
>> I've the same problem with Firefox (it works with Chrome).
>> With Firebug, I've got this message :
>>
>>> data.TabularDataset is not a constructor
>>
>> Firebug shows me the same lines of code than Carlos :
>>
>>> // Set up dataset and attributes.
>>> var dataset = new data.TabularDataset( {"misc_blurb": "33 lines", "name": 
>>> "Galaxy12-[Filtered_table__Remove_columns_on_data_11].tax.summary", 
>>> "data_type": "tabular", "metadata_columns": 4, "deleted": false, 
>>> "metadata_data_lines": 33, "metadata_column_names": null, "genome_build": 
>>> "?", "purged": false, "visible": true, "state": "ok", 
>>> "metadata_comment_lines": null, "file_size": 969, "model_class": 
>>> "HistoryDatasetAssociation", "metadata_column_types": ["int", "str", "str", 
>>> "int"], "id": 9664, "misc_info": "uploaded tabular file", "metadata_dbkey": 
>>> "?"} );
>>
>> Regards,
>> Cyril
>>
>>
>> On 02/15/2013 07:09 PM, Carlos Borroto wrote:
>>> On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker  
>>> wrote:
 Well, (un)fortunately this file works for me in both firefox and
 chrome on the current galaxy-dist.  Just to confirm -- when you click
 the eye, it doesn't download the file either, right -- nothing at all
 happens?

 In chrome, could you open the console (Tools ->  Javascript Console or
 Ctrl+Shift+J) and then try again, letting me know if there are any
 errors that show up?

>>> This is the error I see in Chrome Javascript Console:
>>> "Uncaught TypeError: undefined is not a function"
>>>
>>> And this is the code around the line causing the error:
>>> // Set up dataset and attributes.
>>> var dataset = new data.TabularDataset( {"misc_blurb": "8,024 lines",
>>> "name": "Join two Datasets on data 28 and data 36", "data_type":
>>> "tabular", "metadata_columns": 5, "deleted": false,
>>> "metadata_data_lines": 8024, "metadata_column_names": null,
>>> "genome_build": "build37.2", "purged": false, "visible": true,
>>> "state": "ok", "metadata_comment_lines": null, "file_size": 1569994,
>>> "model_class": "HistoryDatasetAssociation", "metadata_column_types":
>>> ["str", "float", "list", "str", "int"], "id": 110, "misc_info": "",
>>> "metadata_dbkey": "build37.2"} );
>>>
>>> dataset.set('chunk_url',
>>> "/datasets/f30a35c999095ed7/display");
>>>
>>> Please let me know if there is something else I can do to help solve this 
>>> issue.
>>>
>>> Regards,
>>> Carlos
>>> ___
>>> 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:
>>>
>>>   http://lists.bx.psu.edu/
>>
>>
>> --
>>
>> Cyril Monjeaud
>> Equipe Symbiose / Plate-forme GenOuest
>> Bureau D156
>> IRISA-INRIA, Campus de Beaulieu
>> 35042 Rennes cedex, France
>> Tél: +33 (0) 2 99 84 74 17
>>
>> ___
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>>
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>
>
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Re: [galaxy-dev] Problem running Tophat for Illumina

[Jennifer Jackson]

Hi Greg,

The problem here and the confusion between the Bowtie loc files are 
likely related. Do you have both bowtie/bowtie2 and tophat/tophat2 
installed? And the tool wrappers for all versions are active? I though 
we resolved this earlier but maybe you installed a new tool or updated?


The wrappers for the tools that have dependencies on bowtie vs bowtie2 
(and the associated indexes) are not interchangeable. You will need to 
chech your paths to see which tool is being used for each - be sure to 
check any symbolic paths that may have been created when the tools were 
installed (these tools are known to create links such as bowtie -> 
bowtie2, that you will want to get rid of).


Reviewing tool dependencies is the best way to troubleshoot:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

Hopefully this helps. Be sure to keep any followup on the mailing list 
so the dev community can continue to have input,


Jen
Galaxy team

On 2/21/13 7:50 AM, greg wrote:

Hi guys,

On our local galaxy install I'm getting the error below when I run
tophat for illumina like this:

http://snag.gy/HsWyS.jpg

Any ideas?

Thanks,

Greg


Error:

Dataset generation errors

Dataset 27: Tophat for Illumina on data 15: deletions

Tool execution generated the following error message:

Error in tophat:
tophat: option --no-closure-search not recognized
 for detailed help see http://tophat.cbcb.umd.edu/manual.html

cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed':
No such file or directory

The tool produced the following additional output:

TopHat v2.0.6
tophat -p 4  -a 8 -m 0 -i 70 -I 50 -g 20 --library-type
fr-unstranded --max-insertion-length 3 --max-deletion-length 3
--coverage-search --min-coverage-intron 50 --max-coverage-intron 2
--no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
--segment-length 25 --min-segment-intron 50 --max-segment-intron
50 
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
/home/galaxy/000/dataset_306.dat
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Galaxy Support and Training
http://galaxyproject.org
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Re: [galaxy-dev] where to announce transcript annotation file in local Galaxy install

[Jennifer Jackson]

Maxim,

Brad is correct - to supply a reference annotation file to Cufflinks, 
the file must in the active history at the time the tool is executed. 
Then when setting the options for "Use Reference Annotation:" on the 
tool form, the pull-down will select from datasets in the right history 
panel.


If you would like to keep these in a common area, using a "Shared Data 
-> Data Library" is a good choice. When users later import into a 
history to use, it would really just be a link to the original, saving 
disc space. An example is on the public Main Galaxy instance under 
"Shared Data -> Data Library -> iGenomes":

https://main.g2.bx.psu.edu/library

You could also put the reference files in a history, perhaps with other 
data, and then embed the dataset or history objects in a shared Page, 
along with text, graphics, etc. Importing this way creates links to 
originals as well, saving disc. An example of this is also on Main, in 
the RNA-seq tutorial under "Shared Data -> Published Pages -> Galaxy 
RNA-seq Analysis Exercise":

https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

Hopefully one of these options will work for you!

Jen
Galaxy team

On 2/21/13 4:05 AM, Langhorst, Brad wrote:

Hi Maxim:

I think you have to load your annotations into your history to do this.
I keep ours in the shared data area and have users import and provide it
as input to our workflows.


Brad
On Feb 21, 2013, at 6:53 AM, Maxim mailto:deeeperso...@googlemail.com>> wrote:


Hi,

I got my local instance of Galaxy running and most tools work
properly. Unfortunately I seem not to understand how to implement
cufflinks within Galaxy, in particular I do not know how to inform
Galaxy about the location of GTF annotation files.

I searched the archives for this and was not successful. Furthermore I
cannot find a preference file holding cufflinks specific information
nor a general place to keep annotation data.

Who can point me there?

Best regards and thanks for your effort!
Maxim
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--
Brad Langhorst
langho...@neb.com 







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Re: [galaxy-dev] New release : display problem

[Jeremy Goecks]

Clearing your browser's cache may solve the problem. Can you please try that 
and let us know if it solves the problem?

Thanks,
J.


On Feb 21, 2013, at 10:55 AM, MONJEAUD wrote:

> Hello All,
> 
> I've the same problem with Firefox (it works with Chrome).
> With Firebug, I've got this message :
> 
>> data.TabularDataset is not a constructor
> 
> Firebug shows me the same lines of code than Carlos :
> 
>> // Set up dataset and attributes.
>> var dataset = new data.TabularDataset( {"misc_blurb": "33 lines", "name": 
>> "Galaxy12-[Filtered_table__Remove_columns_on_data_11].tax.summary", 
>> "data_type": "tabular", "metadata_columns": 4, "deleted": false, 
>> "metadata_data_lines": 33, "metadata_column_names": null, "genome_build": 
>> "?", "purged": false, "visible": true, "state": "ok", 
>> "metadata_comment_lines": null, "file_size": 969, "model_class": 
>> "HistoryDatasetAssociation", "metadata_column_types": ["int", "str", "str", 
>> "int"], "id": 9664, "misc_info": "uploaded tabular file", "metadata_dbkey": 
>> "?"} );
> 
> Regards,
> Cyril
> 
> 
> On 02/15/2013 07:09 PM, Carlos Borroto wrote:
>> On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker  
>> wrote:
>>> Well, (un)fortunately this file works for me in both firefox and
>>> chrome on the current galaxy-dist.  Just to confirm -- when you click
>>> the eye, it doesn't download the file either, right -- nothing at all
>>> happens?
>>> 
>>> In chrome, could you open the console (Tools ->  Javascript Console or
>>> Ctrl+Shift+J) and then try again, letting me know if there are any
>>> errors that show up?
>>> 
>> This is the error I see in Chrome Javascript Console:
>> "Uncaught TypeError: undefined is not a function"
>> 
>> And this is the code around the line causing the error:
>> // Set up dataset and attributes.
>> var dataset = new data.TabularDataset( {"misc_blurb": "8,024 lines",
>> "name": "Join two Datasets on data 28 and data 36", "data_type":
>> "tabular", "metadata_columns": 5, "deleted": false,
>> "metadata_data_lines": 8024, "metadata_column_names": null,
>> "genome_build": "build37.2", "purged": false, "visible": true,
>> "state": "ok", "metadata_comment_lines": null, "file_size": 1569994,
>> "model_class": "HistoryDatasetAssociation", "metadata_column_types":
>> ["str", "float", "list", "str", "int"], "id": 110, "misc_info": "",
>> "metadata_dbkey": "build37.2"} );
>> 
>> dataset.set('chunk_url',
>> "/datasets/f30a35c999095ed7/display");
>> 
>> Please let me know if there is something else I can do to help solve this 
>> issue.
>> 
>> Regards,
>> Carlos
>> ___
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> 
> 
> -- 
> 
> Cyril Monjeaud
> Equipe Symbiose / Plate-forme GenOuest
> Bureau D156
> IRISA-INRIA, Campus de Beaulieu
> 35042 Rennes cedex, France
> Tél: +33 (0) 2 99 84 74 17
> 
> ___
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Re: [galaxy-dev] New release : display problem

[MONJEAUD]

Hello All,

I've the same problem with Firefox (it works with Chrome).
With Firebug, I've got this message :


data.TabularDataset is not a constructor


Firebug shows me the same lines of code than Carlos :


// Set up dataset and attributes.
var dataset = new data.TabularDataset( {"misc_blurb": "33 lines", 
"name": 
"Galaxy12-[Filtered_table__Remove_columns_on_data_11].tax.summary", 
"data_type": "tabular", "metadata_columns": 4, "deleted": false, 
"metadata_data_lines": 33, "metadata_column_names": null, 
"genome_build": "?", "purged": false, "visible": true, "state": "ok", 
"metadata_comment_lines": null, "file_size": 969, "model_class": 
"HistoryDatasetAssociation", "metadata_column_types": ["int", "str", 
"str", "int"], "id": 9664, "misc_info": "uploaded tabular file", 
"metadata_dbkey": "?"} );


Regards,
Cyril


On 02/15/2013 07:09 PM, Carlos Borroto wrote:

On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker  wrote:

Well, (un)fortunately this file works for me in both firefox and
chrome on the current galaxy-dist.  Just to confirm -- when you click
the eye, it doesn't download the file either, right -- nothing at all
happens?

In chrome, could you open the console (Tools ->  Javascript Console or
Ctrl+Shift+J) and then try again, letting me know if there are any
errors that show up?


This is the error I see in Chrome Javascript Console:
"Uncaught TypeError: undefined is not a function"

And this is the code around the line causing the error:
// Set up dataset and attributes.
var dataset = new data.TabularDataset( {"misc_blurb": "8,024 lines",
"name": "Join two Datasets on data 28 and data 36", "data_type":
"tabular", "metadata_columns": 5, "deleted": false,
"metadata_data_lines": 8024, "metadata_column_names": null,
"genome_build": "build37.2", "purged": false, "visible": true,
"state": "ok", "metadata_comment_lines": null, "file_size": 1569994,
"model_class": "HistoryDatasetAssociation", "metadata_column_types":
["str", "float", "list", "str", "int"], "id": 110, "misc_info": "",
"metadata_dbkey": "build37.2"} );

dataset.set('chunk_url',
"/datasets/f30a35c999095ed7/display");

Please let me know if there is something else I can do to help solve this issue.

Regards,
Carlos
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--

Cyril Monjeaud
Equipe Symbiose / Plate-forme GenOuest
Bureau D156
IRISA-INRIA, Campus de Beaulieu
35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 74 17

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[galaxy-dev] Problem running Tophat for Illumina

[greg]

Hi guys,

On our local galaxy install I'm getting the error below when I run
tophat for illumina like this:

http://snag.gy/HsWyS.jpg

Any ideas?

Thanks,

Greg


Error:

Dataset generation errors

Dataset 27: Tophat for Illumina on data 15: deletions

Tool execution generated the following error message:

Error in tophat:
tophat: option --no-closure-search not recognized
for detailed help see http://tophat.cbcb.umd.edu/manual.html

cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam':
No such file or directory
cp: cannot stat
`/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed':
No such file or directory

The tool produced the following additional output:

TopHat v2.0.6
tophat -p 4  -a 8 -m 0 -i 70 -I 50 -g 20 --library-type
fr-unstranded --max-insertion-length 3 --max-deletion-length 3
--coverage-search --min-coverage-intron 50 --max-coverage-intron 2
--no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
--segment-length 25 --min-segment-intron 50 --max-segment-intron
50 
/usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
/home/galaxy/000/dataset_306.dat
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Re: [galaxy-dev] tophat for illumina looking in wrong directory for bowtie2 indexes?

[greg]

Thanks, adding the genome did work!

But I still don't understand why bowtie2 is looking at the
bowtie_indices.loc file instead of the bowtie2_indices.loc file?
Could that be a bug somewhere?

Here's why I think I'm using bowtie 2:

[2013-02-20 16:31:10] Beginning TopHat run (v2.0.6)
---
[2013-02-20 16:31:10] Checking for Bowtie
 Bowtie version: 2.0.2.0

-Greg

On Wed, Feb 20, 2013 at 5:44 PM, Jeremy Goecks  wrote:
> But this is what's in my galaxy-dist/tool-data/bowtie2_indices.loc file:
>
>
> mm10mm10mm10
>
> /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index
>
>
> You need:
>
> /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome
>
> J.
>
>
>
> Why isn't it looking in that directory for the bowtie2 files?  It's
>
> almost as if it's reading my bowtie_indices.loc file instead?
>
>
> Thanks,
>
>
> Greg
>
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Re: [galaxy-dev] Problem with saving workflows

[Dannon Baker]

Hi Alex,

Could you open the javascript console in your browser and tell me
what, if any, errors you see when you try to save?

-Dannon


On Thu, Feb 21, 2013 at 5:48 AM, Alexander Kurze
 wrote:
> Hello,
>
> I am running a local server of Galaxy. I have a problem with editing and
> then saving already created workflows. The "saving workflow" bar just does
> not disappear anymore. I can hit the save on an unaltered workflow, the
> saving workflow bar appears for 2 secs and then it disappears how it should
> do.
>
> Does anyone now how I can fix it?
>
> Thanks,
>
> Alex
>
> --
> Alexander Kurze, DPhil
> University of Oxford
> Department of Biochemistry
> South Parks Road
> Oxford, OX1 3QU
> United Kingdom
>
> Tel: +44 1865 613 230
> Fax:+44 1865 613 341
>
> ___
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[galaxy-dev] Problem with saving workflows

[Alexander Kurze]

Hello,

I am running a local server of Galaxy. I have a problem with editing and
then saving already created workflows. The "saving workflow" bar just does
not disappear anymore. I can hit the save on an unaltered workflow, the
saving workflow bar appears for 2 secs and then it disappears how it should
do.

Does anyone now how I can fix it?

Thanks,

Alex

-- 
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United Kingdom

Tel: +44 1865 613 230
Fax:+44 1865 613 341
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Re: [galaxy-dev] Submitting jobs as a real user without using chown, please

[Nate Coraor]

On Feb 20, 2013, at 2:37 PM, Anthonius deBoer wrote:

> Ah...Found what root squashing is and yes, that is turned on our isilon 
> system...
> 
> So out of luck I take it? We need to chown? we cannot fake the submission 
> name in another way ;)

Galaxy must have a way to make the job working directory writable for the user 
that the job is running as.  If this means logging in to another system via ssh 
that *does* have the ability to change ownership, then you can do that.  The 
method is completely customizable because you can set the chown script to 
anything that works for you.

However, some means of doing this that is appropriate for your environment has 
to exist for Galaxy to perform it.  That said, you might be able to get away 
with having the script make the working directory world-writeable instead of 
owned by the real user.

--nate

> 
> Thanks
> 
> Thon
> 
> On Feb 20, 2013, at 10:32 AM, Anthonius deBoer  wrote:
> 
>> I cannot run chown even as a sudo command...Same error...
>> What is root squashing? I am reading on the internet that it is very common 
>> not to allow users to change the ownership of files...
>> 
>> 
>> Thon
>> On Feb 20, 2013, at 05:52 AM, Nate Coraor  wrote:
>> 
>>> On Feb 19, 2013, at 11:02 PM, Thon de Boer wrote:
>>> 
>>> > Hi,
>>> > 
>>> > I am trying to setup my galaxy system to allow jobs to be submitted as 
>>> > the real user, since people want to keep an eye on their job on the 
>>> > cluster sometimes and they have no ideas which ones are theirs…
>>> > 
>>> > I tried the approach on the wiki here:
>>> > 
>>> > http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?highlight=%28submit%29%7C%28jobs%29%7C%28as%29%7C%28user%29#Submitting_Jobs_as_the_Real_User
>>> > 
>>> > but unfortunately, the CHOWN command is not allowed, not even as a sudo 
>>> > user…
>>> > Probably has to do with the fact that we run our cluster from an isilon 
>>> > system, which I assume is pretty typical…
>>> > 
>>> > The job was actually successfully submitted as the intended user, so that 
>>> > part works, but if we can just get it to work without having to rely on 
>>> > chown that would be awesome…
>>> > 
>>> > Can someone point me in the right direction?
>>> 
>>> Hi Thon,
>>> 
>>> If you run the command from the command line, what results do you get?
>>> 
>>> /usr/bin/sudo -E scripts/external_chown_script.py 
>>> /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148
>>>  svcgalaxy 1
>>> 
>>> Note that external_chown_script.py can be modified as necessary to allow 
>>> you to change ownership in whatever way is appropriate for your site. Since 
>>> it should just be an NFS mount, as long as root squashing is not enabled 
>>> and your svcgalaxy user has sudo permission to run this script, it should 
>>> succeed.
>>> 
>>> --nate
>>> 
>>> > 
>>> > Here’s the error…
>>> > 
>>> > galaxy.jobs.runners.local DEBUG 2013-02-19 19:35:31,524 execution of 
>>> > external set_meta for job 148 finished
>>> > galaxy.jobs DEBUG 2013-02-19 19:35:31,576 (148) Changing ownership of 
>>> > working directory with: /usr/bin/sudo -E scripts/external_chown_script.py 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148
>>> >  svcgalaxy 1
>>> > galaxy.jobs ERROR 2013-02-19 19:35:31,653 (148) Failed to change 
>>> > ownership of 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148,
>>> >  failing
>>> > Traceback (most recent call last):
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", 
>>> > line 343, in finish
>>> > self.reclaim_ownership()
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", 
>>> > line 916, in reclaim_ownership
>>> > self._change_ownership( self.galaxy_system_pwent[0], str( 
>>> > self.galaxy_system_pwent[3] ) )
>>> > File 
>>> > "/mnt/ngs/analysis/svcgalaxy/galaxy-test/lib/galaxy/jobs/__init__.py", 
>>> > line 902, in _change_ownership
>>> > assert p.returncode == 0
>>> > AssertionError
>>> > galaxy.jobs DEBUG 2013-02-19 19:35:31,722 fail(): Moved 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/job_working_directory/000/148/galaxy_dataset_332.dat
>>> >  to 
>>> > /mnt/ngs/analysis/svcgalaxy/galaxy-test/database/files/000/dataset_332.dat
>>> > galaxy.datatypes.metadata DEBUG 2013-02-19 19:35:31,924 Cleaning up 
>>> > external metadata files
>>> > 
>>> > Thanks
>>> > 
>>> > Thon
>>> > ___
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>>> > in your mail client. To manage your subscriptions to this
>>> > and other Galaxy lists, please use the interface at:
>>> > 
>>> > http://lists.bx.psu.edu/
>>> 
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Re: [galaxy-dev] where to announce transcript annotation file in local Galaxy install

[Langhorst, Brad]

Hi Maxim:

I think you have to load your annotations into your history to do this.
I keep ours in the shared data area and have users import and provide it as 
input to our workflows.


Brad
On Feb 21, 2013, at 6:53 AM, Maxim 
mailto:deeeperso...@googlemail.com>> wrote:

Hi,

I got my local instance of Galaxy running and most tools work properly. 
Unfortunately I seem not to understand how to implement cufflinks within 
Galaxy, in particular I do not know how to inform Galaxy about the location of 
GTF annotation files.

I searched the archives for this and was not successful. Furthermore I cannot 
find a preference file holding cufflinks specific information nor a general 
place to keep annotation data.

Who can point me there?

Best regards and thanks for your effort!
Maxim
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--
Brad Langhorst
langho...@neb.com





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[galaxy-dev] where to announce transcript annotation file in local Galaxy install

[Maxim]

Hi,

I got my local instance of Galaxy running and most tools work properly.
Unfortunately I seem not to understand how to implement cufflinks within
Galaxy, in particular I do not know how to inform Galaxy about the location
of GTF annotation files.

I searched the archives for this and was not successful. Furthermore I
cannot find a preference file holding cufflinks specific information nor a
general place to keep annotation data.

Who can point me there?

Best regards and thanks for your effort!
Maxim
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Re: [galaxy-dev] History not updating for multiple instances of Galaxy

[Ross]

maybe the cookie path for each instance defined in universe_wsgi.ini needs
to be distinguishable if you're swapping between authenticated instances ?


# If proxy-prefix is enabled and you're running more than one Galaxy
instance
# behind one hostname, you will want to set this to the same path as the
prefix
# in the filter above.  This value becomes the "path" attribute set in the
# cookie so the cookies from each instance will not clobber each other.
cookie_path = /galaxy


On Thu, Feb 21, 2013 at 7:07 PM, Peter Cock wrote:

> On Thursday, February 21, 2013, wrote:
>
>>  Further, when I try “register” I add an email address and password, but
>> the system still doesn’t log me in
>>
>> ** **
>>
>> Maybe this is a database configuration issue?
>>
>> ** **
>>
>> I didn’t think I’d need to state any specific entries in universe as I am
>> using physically separate directories
>>
>> ** **
>>
>> i.e. /home/galaxy/galaxy-cte/ 
>>
>> i.e. /home/galaxy/galaxy-Newcastle/ 
>>
>> ** **
>>
>> Cheers
>>
>> Neil
>>
>>
>>
> The logging in problem sounds like a cookie path issue to me,
> I had something similar when I added second public Galaxy
> to our server (in my case, a live on and a dev one).
>
> Peter
>
>
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-- 
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4J
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Re: [galaxy-dev] History not updating for multiple instances of Galaxy

[Peter Cock]

On Thursday, February 21, 2013, wrote:

>  Further, when I try “register” I add an email address and password, but
> the system still doesn’t log me in
>
> ** **
>
> Maybe this is a database configuration issue?
>
> ** **
>
> I didn’t think I’d need to state any specific entries in universe as I am
> using physically separate directories
>
> ** **
>
> i.e. /home/galaxy/galaxy-cte/ 
>
> i.e. /home/galaxy/galaxy-Newcastle/ 
>
> ** **
>
> Cheers
>
> Neil
>
>
>
The logging in problem sounds like a cookie path issue to me,
I had something similar when I added second public Galaxy
to our server (in my case, a live on and a dev one).

Peter
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