Re: [galaxy-dev] TypeError with 'dict'
Hi again,
Has anyone had time to look into the traceback?
Best,
Martin
From: martinchristianse...@hotmail.com
To: jmchil...@gmail.com; n...@bx.psu.edu
Date: Tue, 12 Aug 2014 15:59:53 +0200
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] TypeError with 'dict'
Hi guys,
Thanks for the response.
I have been able to work around the from_work_dir option.
And here are the full traceback:
galaxy.tools ERROR 2014-08-12 15:55:35,298 Exception caught while attempting
tool execution:
Traceback (most recent call last):
File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2004, in
handle_single_execution
job, out_data = self.execute( trans, incoming=params, history=history,
rerun_remap_job_id=rerun_remap_job_id )
File /home/pcm692/galaxy-dist/lib/galaxy/tools/__init__.py, line 2535, in
execute
return self.tool_action.execute( self, trans, incoming=incoming,
set_output_hid=set_output_hid, history=history, **kwargs )
File /home/pcm692/galaxy-dist/lib/galaxy/tools/actions/__init__.py, line
238, in execute
data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation
).get( dataid )
File
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
line 767, in get
instance = self._get_from_identity(self.session, key, False)
File
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py,
line 2437, in _get_from_identity
instance = session.identity_map.get(key)
File
/home/pcm692/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/identity.py,
line 141, in get
state = dict.get(self, key, default)
TypeError: unhashable type: 'dict'
Best regards,
Martin
Date: Tue, 12 Aug 2014 08:58:38 -0400
From: jmchil...@gmail.com
To: n...@bx.psu.edu
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] TypeError with 'dict'
Nate is right - full traceback would help. I am not sure it is the
only problem - but these outputs do not look right:
outputs
data format=tabular name=Project label=Project
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
data format=tabular name=Samples label=Samples
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
/outputs
Galaxy isn't going to expand variables ($Project.input /
$Project.samples) in the from_work_dir attribute so those are going to
be taken as literal strings. That directory also really needs to be
relative to the tool directory and I believe this is enforced for
security reasons.
-John
On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor n...@bx.psu.edu wrote:
Hi Martin,
If there's a full traceback instead of just this fragment, that'd certainly
help with determining exactly where the problem is coming from.
--nate
On Aug 12, 2014, at 4:17 AM, bjoern.gruen...@googlemail.com
bjoern.gruen...@gmail.com wrote:
Hi,
Galaxy stores all information about a tool and it's parameters in a
database.
I suppose if something is wrong with your tool, under some circumstances, it
can't be stored in the database.
Cheers,
Bjoern
2014-08-12 9:23 GMT+02:00 Martin Christiansen
martinchristianse...@hotmail.com:
Hi Björn,
I'm using galaxy as a front-end to run a larger pipeline in the
background.
Originally I implemented the pipeline which had the same wrapper and was
running fine.
I have now begun to break it down into steps where this is the first step.
The only thing I've changed is the output.
How would this cause an error in the python egg?
Martin
Date: Tue, 12 Aug 2014 09:06:51 +0200
From: bjoern.gruen...@gmail.com
To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] TypeError with 'dict'
Hi Martin,
please keep galaxy-dev in the CC list.
Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
Hi Björn,
Most certainly. I have posted it below.
tool id=screen_reads name=Screen Reads
- add here a version number version=0.1
descriptionagainst hg19/description
command interpreter=bashscreen_reads.sh $Project.input
$Project.samples $Project $Samples /command
inputs
conditional name=Project
param name=input type=select label=Select project
option value=galaxy_test1galaxy_test1/option
option value=Untitled FolderUntitled Folder/option
- is the white space really needed? If so $Project.input will be two
words. Use ${Project.input} to convert it to onw argument
/param
when value=galaxy_test1
param name=samples type=select label=Select samples
display=checkboxes multiple=True
option value=147406386-700171390147406386-700171390/option
option value=158256496-700097688158256496-700097688/option
option value=158337416-700013715158337416-700013715/option
option
Re: [galaxy-dev] Question about composite blast datatypes
On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche rasche.e...@yandex.ru wrote: Hi Peter, I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using the blast datattype as reference material, I noticed that you had commented out files with variable names from the datatype. Is there rationale behind that? Are we ensured that the entire directory will always be transferred so it's not a problem to not specify files as part of the datatype? Reference: https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py#L232 Cheers, Eric Hi Eric, Edward Kirton wrote the original BLAST DB datatypes - I'm not sure how to nicely define open ended file lists for datatypes, but also the makeblastdb wrapper output does not have this problem (yet). If and when we try to support partitioned BLAST databases (with a *.nal or *.pal alias file) then this would be needed. I would think that the HTML composite datatype might be a better guide here, since you will order get lots of child files (images etc). My guess is the whole directory may be transferred anyway, but having undefined files could be a problem at some point... Regards, Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Providing BLAST db in a data library
On Mon, Jul 28, 2014 at 9:43 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Dear Nate, dear Peter Sorry for the delay in replying. I can import both HTML and blastdb from a history to a data library. If I try to get the data out of the library into anothre history, I am successful for the html but not for the blastdb. The problem seems to be that the primary data file (the /path/dataset_12345.dat) is empty for the blastdb, while the html primary file has something in it. OK. Can you tell where Galaxy thinks the library files are on disk, and check to see if the folder of BLAST database files is actually there? When I try to import the blastdb (from library to history) there is a message along the lines of can't import empty file. I hypothesise (admittedly without having looked at a line of code) that there is a test for file size 0 somewhere that is either altogether unnecessary or, more likely, does not take into account that for composite datatypes it might be completely legitimate for the primary file to be empty. This guess makes sense - but I've not yet tried to trace through the code either. Or is my primary blastdb file not supposed to be empty in the first place? I can blast against it just fine. The BLAST databases do not define/populate a primary file, so Galaxy seems to create a dummy empty file on its own. I have wondered about altering the BLAST database datatype definition to have a human readable text file as the primary file (i.e. the information currently saved as a text log file when creating a database). Correction: I actually implemented this late last year (included in BLAST+ wrapper version v0.0.22 onwards, and the Galaxy BLAST datatypes version v0.0.18 onwards): https://github.com/peterjc/galaxy_blast/commit/9b3f65cddcc60de26de63272c362c6ca53f6559d https://github.com/peterjc/galaxy_blast/commit/2ebfb790d5a1bbe310c3d7ccc2b953c2c37bccf2 The makeblastdb wrapper will send the stdout (log information) to the dummy index file, see the end of the command tag in: https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_makeblastdb.xml The display_data method for a BLAST database will show any makeblastdb log information held in the dummy index file, see https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py i.e. Only older BLAST databases in histories should have empty dummy index files, which will mitigate the library problem: https://trello.com/c/bNEKfOWR Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Workflow Loop
Hello All, I have a little issue. I want create workflow with loop but workflow's nodes must use different settings in each loop steps.How can i do this? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Workflow Loop
It's currently not possible to build loops into galaxy workflows. Major workflow engine enhancements are being worked on, but for an immediate solution you could drive something like this using the API if you wanted to. -Dannon On Thu, Aug 14, 2014 at 8:54 AM, Görkem Erdoğan gorkemerdoga...@gmail.com wrote: Hello All, I have a little issue. I want create workflow with loop but workflow's nodes must use different settings in each loop steps.How can i do this? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Announcing the UK Galaxy Community
Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: * To bring the Galaxy community in the United Kingdom closer together * Identify and address the needs of the community * Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: * UK based Galaxy training courses * UK based talks involving Galaxy * Information on the location of UK Galaxy servers * Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Announcing the UK Galaxy Community
Amazing! All the best from Germany! Bjoern 2014-08-14 15:21 GMT+02:00 graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk: Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: - To bring the Galaxy community in the United Kingdom closer together - Identify and address the needs of the community - Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: - UK based Galaxy training courses - UK based talks involving Galaxy - Information on the location of UK Galaxy servers - Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Announcing the UK Galaxy Community
Not to say 'exemplary' - really great :). @Björn: phone call within the next days? Cheers, Sebastian bjoern.gruen...@googlemail.com schrieb: Amazing! All the best from Germany! Bjoern 2014-08-14 15:21 GMT+02:00 graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk mailto:graham.ethering...@sainsbury-laboratory.ac.uk: Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: * To bring the Galaxy community in the United Kingdom closer together * Identify and address the needs of the community * Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: * UK based Galaxy training courses * UK based talks involving Galaxy * Information on the location of UK Galaxy servers * Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78178 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Announcing the UK Galaxy Community
I'm all in! :) 2014-08-14 17:11 GMT+02:00 Sebastian Schaaf sch...@ibe.med.uni-muenchen.de : Not to say 'exemplary' - really great :). @Björn: phone call within the next days? Cheers, Sebastian bjoern.gruen...@googlemail.com schrieb: Amazing! All the best from Germany! Bjoern 2014-08-14 15:21 GMT+02:00 graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk: Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: - To bring the Galaxy community in the United Kingdom closer together - Identify and address the needs of the community - Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: - UK based Galaxy training courses - UK based talks involving Galaxy - Information on the location of UK Galaxy servers - Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78178 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Question about composite blast datatypes
14.08.2014, 10:01, "Peter Cock" p.j.a.c...@googlemail.com:On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche rasche.e...@yandex.ru wrote: Hi Peter, I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using the blast datattype as reference material, I noticed that you had commented out files with variable names from the datatype. Is there rationale behind that? Are we ensured that the entire directory will always be transferred so it's not a problem to not specify files as part of the datatype? Reference: https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py#L232 Cheers, EricHi Eric,Edward Kirton wrote the original BLAST DB datatypes - I'm not surehow to nicely define open ended file lists for datatypes, but also themakeblastdb wrapper output does not have this problem (yet).If and when we try to support partitioned BLAST databases (with a*.nal or *.pal alias file) then this would be needed.I would think that the HTML composite datatype might be a betterguide here, since you will order get lots of child files (images etc).My guess is the whole directory may be transferred anyway, buthaving "undefined" files could be a problem at some point...Regards,PeterHi Peter, Okay, that generally answers that, I'm using the HTML datatype now, hopefully it'll accomplish what I want it to. Thanks for this information! Cheers,Eric -- Eric RascheProgrammer IICenter for Phage TechnologyTexas AM UnivesityCollege Station, TX 77843Ph: 4046922048 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Upload file not working with new install
Hi Team, I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Upload file not working with new install
No sure if this will help but you may want to check this. We just fixed a problem from uploading small files via the ftp directory. Our nfs mount was set to cache file meta data about every 30 sec. This proved problematic when uploading a small fasta file that previously uploaded. Every time we tried uploading, it finished with no errors but was empty. Turning the nfs caching off fixed this. From: Iry Witham iry.wit...@jax.orgmailto:iry.wit...@jax.org Date: Thursday, August 14, 2014 9:34 AM To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload file not working with new install Hi Team, I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)
Hi Jim Try setting it like this: default_cluster_job_runner = drmaa://-w n -l mem_free=16G/ I've just tried it and worked fine. Sorry for a delay in getting back to you, Enis On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker jmccus...@5amsolutions.com wrote: I have a galaxy/cloudman cluster where I would like to pass a -l mem_free=16G parameter when galaxy submits the job to SGE. I've tried adding it like this: default_cluster_job_runner = drmaa://-l mem_free=16G/ (it was: default_cluster_job_runner = drmaa:/// ) but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this? Thanks, Jim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)
thanks, I ended up doing subinvocations (submitting a job from within a job) because one tool in particular needs lots of memory. Is there a way to set these things on a per-tool basis (which would let me remove the subinvocation)? Jim On Thu, Aug 14, 2014 at 2:09 PM, Enis Afgan afg...@gmail.com wrote: Hi Jim Try setting it like this: default_cluster_job_runner = drmaa://-w n -l mem_free=16G/ I've just tried it and worked fine. Sorry for a delay in getting back to you, Enis On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker jmccus...@5amsolutions.com wrote: I have a galaxy/cloudman cluster where I would like to pass a -l mem_free=16G parameter when galaxy submits the job to SGE. I've tried adding it like this: default_cluster_job_runner = drmaa://-l mem_free=16G/ (it was: default_cluster_job_runner = drmaa:/// ) but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this? Thanks, Jim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Is anyone using composite datatype uploads?
Hello everyone, We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel Get Data Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet. Please let us know if you are using the composite file upload functionality of the former tool form. Thanks, Sam ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)
If I'm understanding your question correctly (ie, have the ability to specify SGE requirements on a per-tool basis), then yes. You'd do something like this in universe_wsgi.ini: [galaxy:tool_runners] bwa_wrapper = drmaa://-pe smp 2/ bowtie2 = drmaa://-pe smp 2/ On Thu, Aug 14, 2014 at 2:26 PM, Jim McCusker jmccus...@5amsolutions.com wrote: thanks, I ended up doing subinvocations (submitting a job from within a job) because one tool in particular needs lots of memory. Is there a way to set these things on a per-tool basis (which would let me remove the subinvocation)? Jim On Thu, Aug 14, 2014 at 2:09 PM, Enis Afgan afg...@gmail.com wrote: Hi Jim Try setting it like this: default_cluster_job_runner = drmaa://-w n -l mem_free=16G/ I've just tried it and worked fine. Sorry for a delay in getting back to you, Enis On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker jmccus...@5amsolutions.com wrote: I have a galaxy/cloudman cluster where I would like to pass a -l mem_free=16G parameter when galaxy submits the job to SGE. I've tried adding it like this: default_cluster_job_runner = drmaa://-l mem_free=16G/ (it was: default_cluster_job_runner = drmaa:/// ) but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this? Thanks, Jim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)
Perfect, thanks! That's in addition to the default arguments? On Thu, Aug 14, 2014 at 2:52 PM, Enis Afgan afg...@gmail.com wrote: If I'm understanding your question correctly (ie, have the ability to specify SGE requirements on a per-tool basis), then yes. You'd do something like this in universe_wsgi.ini: [galaxy:tool_runners] bwa_wrapper = drmaa://-pe smp 2/ bowtie2 = drmaa://-pe smp 2/ On Thu, Aug 14, 2014 at 2:26 PM, Jim McCusker jmccus...@5amsolutions.com wrote: thanks, I ended up doing subinvocations (submitting a job from within a job) because one tool in particular needs lots of memory. Is there a way to set these things on a per-tool basis (which would let me remove the subinvocation)? Jim On Thu, Aug 14, 2014 at 2:09 PM, Enis Afgan afg...@gmail.com wrote: Hi Jim Try setting it like this: default_cluster_job_runner = drmaa://-w n -l mem_free=16G/ I've just tried it and worked fine. Sorry for a delay in getting back to you, Enis On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker jmccus...@5amsolutions.com wrote: I have a galaxy/cloudman cluster where I would like to pass a -l mem_free=16G parameter when galaxy submits the job to SGE. I've tried adding it like this: default_cluster_job_runner = drmaa://-l mem_free=16G/ (it was: default_cluster_job_runner = drmaa:/// ) but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this? Thanks, Jim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] setting SGE arguments in galaxy (cloudman)
The default args will apply to all the tools. Tool-specific args will apply only for the tool you specify and those overwrite the default (ie, arguments will not add up). On Thu, Aug 14, 2014 at 2:53 PM, Jim McCusker jmccus...@5amsolutions.com wrote: Perfect, thanks! That's in addition to the default arguments? On Thu, Aug 14, 2014 at 2:52 PM, Enis Afgan afg...@gmail.com wrote: If I'm understanding your question correctly (ie, have the ability to specify SGE requirements on a per-tool basis), then yes. You'd do something like this in universe_wsgi.ini: [galaxy:tool_runners] bwa_wrapper = drmaa://-pe smp 2/ bowtie2 = drmaa://-pe smp 2/ On Thu, Aug 14, 2014 at 2:26 PM, Jim McCusker jmccus...@5amsolutions.com wrote: thanks, I ended up doing subinvocations (submitting a job from within a job) because one tool in particular needs lots of memory. Is there a way to set these things on a per-tool basis (which would let me remove the subinvocation)? Jim On Thu, Aug 14, 2014 at 2:09 PM, Enis Afgan afg...@gmail.com wrote: Hi Jim Try setting it like this: default_cluster_job_runner = drmaa://-w n -l mem_free=16G/ I've just tried it and worked fine. Sorry for a delay in getting back to you, Enis On Tue, Aug 5, 2014 at 6:44 PM, Jim McCusker jmccus...@5amsolutions.com wrote: I have a galaxy/cloudman cluster where I would like to pass a -l mem_free=16G parameter when galaxy submits the job to SGE. I've tried adding it like this: default_cluster_job_runner = drmaa://-l mem_free=16G/ (it was: default_cluster_job_runner = drmaa:/// ) but now the jobs don't even submit. Am I wiping out other important parameters? How should I do this? Thanks, Jim ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Packaging pycurl on toolshed
So far I have been trying to avoid this, but I would like to see packaged pycurl on the toolshed now. This is where my package sits: https://testtoolshed.g2.bx.psu.edu/repository?repository_id=534efefdbab02103 and this is the error: Traceback (most recent call last): File setup.py, line 563, in module ext = get_extension() File setup.py, line 368, in get_extension ext_config = ExtensionConfiguration() File setup.py, line 65, in __init__ self.configure() File setup.py, line 93, in configure_unix CURL_CONFIG = scan_argv(--curl-config=, CURL_CONFIG) File setup.py, line 42, in scan_argv assert p, arg AssertionError: --curl-config= and this is why it should be arising: python setup.py build --with-ssl --curl-config=$CURL amp;amp; $CURL being empty. A local installation with the commands as in the tool_dependencies.xml doe generate $INSTALL_DIR/install-destination/bin/curl-config which should then be set to $CURL. Is there a way to check the logs, something I attempted by doing this: action type=shell_commandecho $INSTALL_DIR/action action type=shell_commandecho $CURL/action Or any alternate way to debug? On 29 April 2014 14:25, Saket Choudhary sake...@gmail.com wrote: Thanks Greg Bjoern, I get your point now. I will reconfigure my tool to take into account the other dependencies. Thanks once again, Saket On 30 April 2014 02:30, Greg Von Kuster g...@bx.psu.edu wrote: Hello Saket, I'm not a system-level expert, so please ignore my attempt at helping if it is incorrect. Your recipe for installing and compiling pycurl may be assuming that certain dependencies exist in the Galaxy environment into which it is being installed for testing, but they do not. Galaxy tools and tool dependency recipes can only assume the following dependencies are available in the Galaxy environment into which they will be installed (this list is available in the Tool Shed wiki on this page: https://wiki.galaxyproject.org/InstallAndTestCertification). In your case, a recipe should probably also be installing the libcurl-devel package (and possibly others??). Recipes need to be created for dependencies that are not on the following list, and then relationships can be defined between repositories that contain them and repositories that contain tools that depend upon them. The reason the following list is short is because starting up a new Galaxy instance should be as simple as cloning it and starting it up with run.sh. autoconf automake autotools-dev build-essential cmake git-core libatlas-base-dev libblas-dev liblapack-dev libc6-dev mercurial python2.6 python2.6-dev pkg-config subversion python-dev python-pip Greg Von Kuster On Apr 29, 2014, at 4:34 PM, Saket Choudhary sake...@gmail.com wrote: Hi Bjoern, There is no script installed, I generally just do this on my local system $ python setup.py build --with-ssl $ python setup.py install The documentation mentions the following options: PycURL Unix options: --curl-config=/path/to/curl-config use specified curl-config binary --openssl-dir=/path/to/openssl/dir path to OpenSSL headers and libraries --with-ssl libcurl is linked against OpenSSL --with-gnutls libcurl is linked against GnuTLS --with-nss libcurl is linked against NSS Saket On 29 April 2014 23:31, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Saket, is there any script installed with that package? --install-scripts may be needed. Also I'm wondering if there is no dependency on curl-lib? Cheers, Bjoern Am 29.04.2014 19:16, schrieb Saket Choudhary: Any comments on this? http://testtoolshed.g2.bx.psu.edu/view/saketkc/package_pycurl_7_19_3_1 On 17 April 2014 19:54, Saket Choudhary sake...@gmail.com wrote: My attempt to 'package' pycurl on testtoolshed fails with the following error: src/pycurl.c: In function ‘do_multi_info_read’: src/pycurl.c:3549:15: warning: call to ‘_curl_easy_getinfo_err_string’ declared with attribute warning: curl_easy_getinfo expects a pointer to char * for this info [enabled by default] src/pycurl.c: In function ‘do_curl_getinfo’: src/pycurl.c:2888:19: warning: call to ‘_curl_easy_getinfo_err_curl_slist’ declared with attribute warning: curl_easy_getinfo expects a pointer to struct curl_slist * for this info [enabled by default] error: could not create '/usr/local/share/doc': Permission denied A local install worked fine. Is this because of libcurl-devel missing on toolshed instance? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
