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install_tool_shed_repositories.py returns HTTP Error 400: Bad Request
by Mic 04 Aug '15

04 Aug '15

Hello, I found this shed_tool_conf.xml ( https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/c55aa042…) file on use galaxy-playbook. I copied information for snpSift_filter out of the xml file and pasted it to the command below: * $ python /Users/lorencm/galaxy/scripts/api/install_tool_shed_repositories.py -a 4bb8f6eb85efca463d2e60b9704d6caf -l http://localhost:8080 <http://localhost:8080> -n snpSift_filter -o pcingola -r c052639fa666 --panel-section-name 'snpEff' --repository-deps --tool-deps -u http://toolshed.g2.bx.psu.edu/ <http://toolshed.g2.bx.psu.edu/>* However, I received the following error massage: * HTTP Error 400: Bad Request* * {"traceback": "Traceback (most recent call last):\n File \"/Users/lorencm/galaxy/lib/galaxy/web/framework/decorators.py\", line 251, in decorator\n rval = func( self, trans, *args, **kwargs)\n File \"/Users/lorencm/galaxy/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py\", line 246, in install_repository_revision\n payload )\n File \"/Users/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py\", line 704, in install\n changeset_revision )\n File \"/Users/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py\", line 505, in __get_install_info_from_tool_shed\n raise exceptions.RequestParameterInvalidException( invalid_parameter_message )\nRequestParameterInvalidException: No information is available for the requested repository revision.\nOne or more of the following parameter values is likely invalid:\ntool_shed_url: http://toolshed.g2.bx.psu.edu/\nname <http://toolshed.g2.bx.psu.edu/\nname>: snpSift_filter\nowner: pcingola\nchangeset_revision: c052639fa666\n\n", "err_msg": "No information is available for * I also posted it on Github ( https://github.com/galaxyproject/usegalaxy-playbook/issues/8) How is it possible to fix the problem? Thank you in advance. Mic

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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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Call for Tool Shed Admins
by Martin Čech 03 Aug '15

03 Aug '15

Hi everybody, similar to the existing mailing list of Galaxy instance admins we are putting together a mailing list of admins of Tool Shed instances (especially the public ones) so if you administer one (or more) please respond to me privately and I will put you on it. Thank you very much. Martin, Galaxy Team

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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

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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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Bug on current history when using prefix in galaxy input file
by Ata Roudgar 30 Jul '15

30 Jul '15

Hi, I am using the most recent version of Galaxy. There seems to be a bug in viewing the current (active) history when I use prefix in galaxy input file. Here is the detail: When I do not use prefix, e.g., in /config/galaxy.in : prefix = / cookie_path = / and run galaxy server, I can upload a file and I can see my uploaded file in the current history even after I refresh the web browser (e.g., close and reopen the web browser) which seems to be working fine. However when I use prefix, e.g. in /config/galaxy.in : prefix = /galaxy-1/ cookie_path = /galaxy-1/ then after I upload a file and refresh the browser I do not see the uploaded file in the current (or active) history. It always shows me a new (clean history). This is a problem because I get a error which seems to be related to the history when I attempt to run any workflow. Any idea where the problem should be? Please note that I use external authentication but it shouldn't be matter because it is working when the prefix is "/". Thanks a lot, Cheers, Ata ---- Ata Roudgar Research Computing WestGrid Site IT Services Simon Fraser University Burnaby, British Columbia Canada V5A 1S6 phone: 778 782-8860 fax: 778 782-4242

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Problems installing pbs_python from scramble.
by Zuzanna K. Filutowska 30 Jul '15

30 Jul '15

Hello All, I am trying to setup job submission to pbs server running on our cluster. I have python 2.7 installed in /usr/local along with easy_install. But when trying to compile pbs_python I am getting following error: [galaxy@galaxy galaxy-dist]$ LIBTORQUE_DIR=/usr/lib python scripts/scramble.py -e pbs_python fetch_one(): Trying to fetch: http://eggs.galaxyproject.org/pbs_python/pbs_python-4.3.5.tar.gz fetch_one(): Fetched to: /home/galaxy/galaxy-dist/scripts/scramble/archives/pbs_python-4.3.5.tar.gz unpack_source(): Unpacked to: /home/galaxy/galaxy-dist/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python copy_build_script(): Using build script /home/galaxy/galaxy-dist/scripts/scramble/scripts/pbs_python.py run_scramble_script(): Beginning build run_scramble_script(): Executing in /home/galaxy/galaxy-dist/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python: /home/galaxy/galaxy-python/python scramble.py Traceback (most recent call last): File "scramble.py", line 14, in <module> from scramble_lib import * File "../../../lib/scramble_lib.py", line 146, in <module> from setuptools import * File "build/bdist.linux-x86_64/egg/setuptools/__init__.py", line 11, in <module> File "build/bdist.linux-x86_64/egg/setuptools/extension.py", line 8, in <module> File "build/bdist.linux-x86_64/egg/setuptools/dist.py", line 21, in <module> AttributeError: 'module' object has no attribute 'packaging' Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.3.5 I also tried setuptools-18.0.1 installed in user's local path but I am still getting the same error. It is Centos 6.6 OS. Any help would be appreciated. -- Regards, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating

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