July 2015 - galaxy-dev - lists.galaxyproject.org

Rename output from a repeat
by Ulf Schaefer 27 Aug '15

27 Aug '15

Hi all We frequently use the syntax below to rename outputs of workflows that we run in batch. It is convenient to have sample names from fastqs carried over to sams, bams, vcfs, etc. #{input1 | basename}.bam This does not seem to be working for inputs that are in repeats, e.g. the VelvetOptimiser. Does anybody know if there is a syntax to make this work, maybe #{repeatname[0].input1 | basename}.bam ? Thanks a lot for your help Ulf ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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samtools dependency changes ?
by Wolfgang Maier 27 Aug '15

27 Aug '15

Dear all, with older Galaxies (prior to latest_15.03 I think), you could satisfy Galaxy's samtools dependence for indexing bam files by having a samtools executable in tool-dependencies/samtools/default/bin (with the tool-dependencies directory declared as tool_dependency_dir in galaxy.ini of course). Now (checked with latest_15.03 and .05), this is not working any more! The executable will still be used during bam uploads, but not when a bam file gets created by a tool. The reason is that before the job runner (tested this with the local job runner only) used to build the dependency shell command for dependency 'samtools' before finishing a job, but now the job wrapper finish method fails because it naively expects to find samtools on $PATH. Best, Wolfgang

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Slow repsonses viewing histories
by Poole, Richard 12 Aug '15

12 Aug '15

Hi all, I am having trouble right now with my own personal account on my production server. Grid refreshes are taking a huge amount of time (e.g. when viewing ‘saved histories’ or even generating the dataset list for a single history). My account is very full of data (1TB), could it be this? There are no obvious messages in the logs though so I am a bit stumped as to why.I do not have the same trouble when impersonating other users with fairly full accounts. Perhaps a database issue (I do not know how to ‘cleanup’ the database or indeed Galaxy user accounts). Any thoughts? Thanks, Richard Richard J Poole PhD Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)

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Externalizing Galaxy config in docker-galaxy-stable
by Oksana Korol 06 Aug '15

06 Aug '15

Hi, My question is to the docker-galaxy-stable community. I would like to use or extend this image with some Galaxy settings externalized. For instance, I would like to define my own GALAXY_UID and GALAXY_HOME environment variables. I have tried the -e setting when I build and run the container, but that doesn't work: > docker run -d -p 8080:80 -p 8021:21 -e "GALAXY_UID=1777" -e "GALAXY_HOME=/home/galaxy/env_test" --name galaxy-env-test bgruening/galaxy-stable ... > docker exec -ti galaxy-env-test bash ># getent passwd galaxy galaxy:x:1450:1450:Galaxy user:/home/galaxy: As you can see from above, GALAXY_UID is 1450, as hardcoded in the Dockerfile, and not 1777, as I've specified. Same goes for the home directory. Is there any other way that I can set those variables? If not, what would be the best way to proceed, since, ideally, I would like to extend the galaxy-stable Docker image, and not change the existing one. Currently, I don't see any other way but to fork https://github.com/bgruening/docker-galaxy-stable and change the Dockerfile to externalize those (and other) variables. I hope I can get better suggestions than this. Cheers, Oksana

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collection in workflow fail
by Alexander Vowinkel 03 Aug '15

03 Aug '15

Hi, I'm running cutadapt (from TS) on a collection with 96 datasets, started from a workflow as an intermediate step. About half of them fail with this message. Traceback (most recent call last): File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/__init__.py", line 590, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/__init__.py", line 1261, in finish ActionBox.execute(self.app, self.sa_session, pja.post_job_action, job) File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/actions/post.py", line 532, in execute ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict) File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/actions/post.py", line 405, in execute for input_dataset in [x.dataset for x in j2c.input_datasets if x.dataset.creating_job.workflow_invocation_step and x.dataset.creating_job.workflow_invocation_step.workflow_invocation == wfi]: AttributeError: 'NoneType' object has no attribute 'input_datasets' Running release 15.07 rev cf29f6c4a7 <https://github.com/galaxyproject/galaxy/commit/cf29f6c4a77a084bcf4732ddf1c5…> Is that Known? How to avoid? Best, Alexander

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migrated_tools_conf.xml propose
by Mic 03 Aug '15

03 Aug '15

Hello, I found this ( https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/8d1fe99e… ) file. If I would copy migrated_tools_conf.xml into the galaxy/config folder then would galaxy/run.sh script install all tools describe in that file? Thank you in advance. Mic

2 1

configuring job runner slurm on cloudman
by Alexander Vowinkel 31 Jul '15

31 Jul '15

Hi, I have adopted /mnt/galaxy/galaxy-app/config/job_conf.xml: I added a destination with following param: <param id="nativeSpecification">-N1 --cpus-per-task 1 --mem-per-cpu=4G</param> Galaxy service was restarted after chaning this. Now I get the error "Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator." when I try to run a job. Looking in the log gives: galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) submitting file /mnt/galaxy/tmp/job_working_directory/000/493/galaxy_493.sh > galaxy.jobs.runners.drmaa DEBUG 2015-07-06 22:50:40,187 (493) native specification is: -N1 --cpus-per-task 1 --mem-per-cpu=4G > galaxy.jobs.runners.drmaa ERROR 2015-07-06 22:50:40,187 (493) drmaa.Session.runJob() failed unconditionally > Traceback (most recent call last): > [...] > InvalidAttributeValueException: code 14: Invalid native specification: -N1 --cpus-per-task 1 --mem-per-cpu=4G Well. running this as galaxy user in the console with $ srun -N1 --cpus-per-task 1 --mem-per-cpu=4G > /mnt/galaxy/tmp/job_working_directory/000/494/galaxy_494.sh , it actually runs good. I was wondering if this is connected with the fact that the log states " galaxy.jobs.runners.drmaa" and not something like galaxy.jobs.runners.slurm, like defined in the job_conf.xml: <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner" /> So - What is going wrong here? Am I working on the wrong job_conf.xml? What does galaxy do here? Thanks for help!Alexander

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August 2015 Galactic News
by Dave Clements 31 Jul '15

31 Jul '15

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Galaxy Resource
by CHELSEA JU 30 Jul '15

30 Jul '15

Dear Galaxy Developer, As one of our data mining projects, we are trying to learn the metadata structure of different tool repositories. Since Galaxy provides a platform with a rich resource, we are wondering if there is an API service to retrieve all the tool information. So far, we have discovered that the list of tools can be found at https://toolshed.g2.bx.psu.edu/, and would like to know if there is an easier way to retrieve the information than crawling through the links in toolshed. Thank you, Chelsea

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if you consider switching from MySQL to PostgreSQL....
by Hans-Rudolf Hotz 30 Jul '15

30 Jul '15

Hi As you may know, over the last few months I undertook the challenge to switch from MySQL to PostgreSQL. If you are interested in my journey, you can read it here: https://wiki.galaxyproject.org/Community/Log/2015/MySQL2PostgreSQL It is probably not the best way to do it (and I am sure every PostgreSQL expert would smash her/his head to the desk while reading it), but it worked. Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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