date:20170124

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
>>  > > 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" > > 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
>>> 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  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
> 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/
>> 
>>
>> To search Galaxy mailing lists use the unified search at:
>> 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 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...@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" 
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 
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 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 
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 ___
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client.  To manage your subscriptions to this and other Galaxy lists,
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Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

2017-01-24 Thread bjoern.gruen...@googlemail.com

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"  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 
> wrote:
>
> 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  > 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/
>
> To search Galaxy mailing lists use the unified search at:
> 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 Lawrence, Cris W

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 
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 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 
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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Re: [galaxy-dev] Resource temporarily unavailable

2017-01-24 Thread Durdevic, Marija

Thank you Nicola,

it worked when I put retry_job_output_collection = 10, but only for some tools. 
For some of them is still the same. Especially if I run it on a data 
collections.
And if I run the tool locally , not over the Slurm, it worked well.

I am not sure if the problem is with Slurm maybe or some Galaxy-Slurm 
configuration?

Best,
Marija

Von: Nicola Soranzo [mailto:nicola.sora...@gmail.com] Im Auftrag von Nicola 
Soranzo
Gesendet: Montag, 23. Jänner 2017 17:17
An: Durdevic, Marija; 
galaxy-dev@lists.galaxyproject.org
Betreff: Re: [galaxy-dev] Resource temporarily unavailable

Hi Marija,
you can try to set

retry_job_output_collection = 3

in your config/galaxy.ini file and see if that helps.

Cheers,
Nicola
On 23/01/17 09:47, Durdevic, Marija wrote:
Dear developers,

From time to time I have issue on my Galaxy server. The problem is when job is 
done and results has to be written to the database something happened. The 
error message is: “/home/data/galaxy_database/files/024/dataset_24790.dat: 
Resource temporarily unavailable” where 
“/home/data/galaxy_database/files/024/dataset_24790.dat” is path to the output 
file. Although it produced reasonable output the job is shown as failed.

I am running galaxy over Slurm and we use NFS for connection with storage.

Do anyone have idea what can be possible reason for such error?

Thanks in advance.

Best,
Marija



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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,

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 > > 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/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> 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 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 
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/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


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[galaxy-dev] Which "upstream" Ansible Playbook to use for local galaxy instance?

2017-01-24 Thread Hendrickson, Curtis (Campus)

Dear Galatic Advisors,

We're building a new set of machines to replace our current local galaxy 
instance (prod, dev and db VMs running CentOS against a local SLURM cluster 
with local storage, want to start using wsgi), and are planning to start using 
Ansible, instead of doing everything by hand. Looking through the wikis and 
postings, we see many difference points of departure. Can anyone outline the 
pros and cons of these various choices or provide any recommendations?

Is it best to use an edited version of this:
https://github.com/galaxyproject/usegalaxy-playbook

Or this:
https://github.com/galaxyproject/ansible-galaxy

I also see a 3rd version that is linked from the "setting up your own galaxy" 
page
(wiki) https://wiki.galaxyproject.org/Admin/GetGalaxy
(Playbook) https://github.com/ARTbio/GalaxyKickStart

Ideally, we'd like to benefit from updates to the upstream package. All three 
seem to be actively supported.

Thanks
Curtis @ UAB.edu

PS - is it better to post this on galaxy-dev or on 
https://biostar.usegalaxy.org?

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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/
> 
> To search Galaxy mailing lists use the unified search at: 
> http://galaxyproject.org/search/mailinglists/
> 
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[galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

2017-01-24 Thread 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
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Re: [galaxy-dev] display at UCSC does not work

2017-01-24 Thread Hans-Rudolf Hotz


Dear All

I just wanna close this thread and shortly tell you how - with the help 
of Dannon - we solved the problem in the end:


The problem was at our side. Our Galaxy server is not visible from the 
out side. Only requests from the UCSC servers are allowed. Despite the 
claim by our IT department that the requests from UCSC are directly sent 
to our Galaxy server, they are not.


Dannon pointed me to the right position in the the sript:

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/web/framework/webapp.py

to insert a simple debug statement after line 533, like:

 " print('***',host) "


and this gave me the name of our proxy server. All I had to do was 
adding this name to the list of "UCSC_SERVERS" at the top of the script 
and it worked even when "require_login = True" is set.


With a big Thank You to Dannon Baker!

Regards, Hans-Rudolf





On 09/05/2016 11:44 AM, Hans-Rudolf Hotz wrote:

Hi


I am trying to set up the possibility to display data sets with the UCSC
genome browser for our new galaxy installation.

After clicking on "display at UCSC main", I get the UCSC genome browser,
opening in the right assembly, and at the correct location, but I get
the following Error:

Warning/Error(s):

 redirected to non-http(s): /login?redirect=%2Froot%2Fdisplay_as



In galaxy.ini, I did uncomment the line:

display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse. ...


We use the 'new' authentication method to connect to our LDAP server,
with the following changes in galaxy.ini:

require_login = True

auth_config_file = config/auth_conf.xml


Connection from UCSC to our galaxy server is working, since I can
display the data, when I switch to

require_login = False

it works, independent of whether I am logged in or not.



Is there a way to get it to work, even if I have "require_login = True"?


Thank you very much for your help
Regards, Hans-Rudolf






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Re: [galaxy-dev] Problem with 'galaxy_packages' dependency resolver in versionless mode

2017-01-24 Thread Peter Briggs


Hello Bjoern

Yes it looks like making the 'default' directory into a symlink makes 
this work.


Thanks for your help and sorry not to get back to you sooner!

Best wishes

Peter

On 20/01/17 16:56, Björn Grüning wrote:

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:



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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--
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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