April 2017 - galaxy-dev - lists.galaxyproject.org

Groovy tool for galaxy
by Anshul Tak 22 Aug '17

22 Aug '17

Hi, I have a question regarding galaxy. Can I execute groovy scipts using galaxy? I installed groovy in galaxy docker image and all the dependencies. However, when I try to execute a tool which require groovy engine it says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh: line 9: groovy: command not found" So I understood the error that galaxy is not able to find groovy but ideally it should take the groovy engine as it is installed. Can you give me some pointers to solve this issue? -- With Regards, Anshul Tak

4 4

DeepTools installation error
by Timo Janßen 05 Jul '17

05 Jul '17

Hi all, trying to install the deeptools_suite from the toolshed I only get the following error: "500 Internal Server Error nginx/1.11.10" This happens as well for the dependencies, e.g. deeptools_bigwig_compare. I am currently using Galaxy 16.10 with nginx proxy. Also the installation of the dependency package_python_2_7_matplotlib_1_4 fails because of a missing dependency: "Error installing tool dependency python version 2.7.10: Unable to locate required tool shed repository named package_python_2_7_10 owned by iuc with revision 80931fb5f433." Has anyone seen these problems before and knows a solution? Best regards, Timo Janßen -- ------------------------------------------------------------------------ Timo Janßen Wissenschaftliche Hilfskraft Arbeitsgruppe "Anwendungs- und Informationssysteme" Tel.: +49(0)551/201-1791 E-Mail: timo.janssen(a)gwdg.de ------------------------------------------------------------------------ Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen (GWDG) Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: gwdg(a)gwdg.de Service-Hotline: Tel.: +49 551 201-1523, E-Mail: support(a)gwdg.de Geschäftsführer: Prof. Dr. Ramin Yahyapour Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau Sitz der Gesellschaft: Göttingen Registergericht: Göttingen, Handelsregister-Nr. B 598 ------------------------------------------------------------------------ Zertifiziert nach ISO 9001 ------------------------------------------------------------------------

6 9

cluster access
by Matthias Bernt 22 May '17

22 May '17

Dear list, I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username stored in the galaxy_user table is the name of the user (this is correctly generated by the LDAP login). The job runner script seems to get the user id, so I guess I need to dig deeper. So my question is: Where could I change this behavior? Thanks a lot. Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

2 4

Pulsar - running as real DRMAA user problems
by Poole, Richard 13 May '17

13 May '17

Hey John, So I’ve been happily using Pulsar to send all my Galaxy server jobs to our cluster here at UCL for several months now (I love it!). I am now exploring the ‘run-as-real-user’ option for DRMAA submissions and have run into a problem. The files are correctly staged, correctly chowned, successfully submitted to the queue and the job runs. However, at job end (collection?) fails with the following error message in Pulsar: Exception happened during processing of request from (‘*.*.*.*', 54321) Traceback (most recent call last): File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 1072, in process_request_in_thread self.finish_request(request, client_address) File "/opt/rocks/lib/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/opt/rocks/lib/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 446, in handle BaseHTTPRequestHandler.handle(self) File "/opt/rocks/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 441, in handle_one_request self.wsgi_execute() File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 291, in wsgi_execute self.wsgi_start_response) File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 39, in __call__ return controller(environ, start_response, **request_args) File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 144, in controller_replacement result = self.__execute_request(func, args, req, environ) File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 124, in __execute_request result = func(**args) File "/cluster/galaxy/pulsar/pulsar/web/routes.py", line 82, in status return status_dict(manager, job_id) File "/cluster/galaxy/pulsar/pulsar/manager_endpoint_util.py", line 12, in status_dict job_status = manager.get_status(job_id) File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 95, in get_status proxy_status, state_change = self.__proxy_status(job_directory, job_id) File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 115, in __proxy_status proxy_status = self._proxied_manager.get_status(job_id) File "/cluster/galaxy/pulsar/pulsar/managers/queued_external_drmaa_original.py", line 62, in get_status external_status = super(ExternalDrmaaQueueManager, self)._get_status_external(external_id) File "/cluster/galaxy/pulsar/pulsar/managers/base/base_drmaa.py", line 31, in _get_status_external drmaa_state = self.drmaa_session.job_status(external_id) File "/cluster/galaxy/pulsar/pulsar/managers/util/drmaa/__init__.py", line 50, in job_status return self.session.jobStatus(str(external_job_id)) File "build/bdist.linux-x86_64/egg/drmaa/session.py", line 518, in jobStatus c(drmaa_job_ps, jobId, byref(status)) File "build/bdist.linux-x86_64/egg/drmaa/helpers.py", line 299, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "build/bdist.linux-x86_64/egg/drmaa/errors.py", line 151, in error_check raise _ERRORS[code - 1](error_string) InvalidJobException: code 18: The job specified by the 'jobid' does not exist. With this corresponding error from my Galaxy server: galaxy.tools.actions INFO 2016-10-13 18:47:51,851 Handled output (279.421 ms) galaxy.tools.actions INFO 2016-10-13 18:47:52,093 Verified access to datasets (5.271 ms) galaxy.tools.execute DEBUG 2016-10-13 18:47:52,118 Tool [toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4] created job [25008<http://toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4]%20…>] (560.404 ms) galaxy.jobs DEBUG 2016-10-13 18:47:52,579 (25008) Working directory for job is: /Users/galaxy/galaxy-dist/database/job_working_directory/025/25008 galaxy.jobs.handler DEBUG 2016-10-13 18:47:52,591 (25008) Dispatching to pulsar runner galaxy.jobs DEBUG 2016-10-13 18:47:52,677 (25008) Persisting job destination (destination id: hpc_low) galaxy.jobs.runners DEBUG 2016-10-13 18:47:52,681 Job [25008] queued (90.231 ms) galaxy.jobs.handler INFO 2016-10-13 18:47:52,699 (25008) Job dispatched galaxy.tools.deps DEBUG 2016-10-13 18:47:53,138 Building dependency shell command for dependency 'samtools' galaxy.jobs.runners.pulsar INFO 2016-10-13 18:47:53,233 Pulsar job submitted with job_id 25008 galaxy.jobs DEBUG 2016-10-13 18:47:53,257 (25008) Persisting job destination (destination id: hpc_low) galaxy.datatypes.metadata DEBUG 2016-10-13 18:51:03,922 Cleaning up external metadata files galaxy.jobs.runners.pulsar ERROR 2016-10-13 18:51:03,945 failure finishing job 25008 Traceback (most recent call last): File "/Users/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pulsar.py", line 386, in finish_job run_results = client.full_status() File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 132, in full_status return self.raw_check_complete() File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 28, in replacement return func(*args, **kwargs) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 13, in replacement response = func(*args, **kwargs) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 146, in raw_check_complete check_complete_response = self._raw_execute("status", {"job_id": self.job_id}) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 215, in _raw_execute return self.job_manager_interface.execute(command, args, data, input_path, output_path) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/interface.py", line 96, in execute response = self.transport.execute(url, method=method, data=data, input_path=input_path, output_path=output_path) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", line 34, in execute response = self._url_open(request, data) File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", line 20, in _url_open return urlopen(request, data) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen return opener.open(url, data, timeout) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 437, in open response = meth(req, response) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 550, in http_response 'http', request, response, code, msg, hdrs) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 475, in error return self._call_chain(*args) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 409, in _call_chain result = func(*args) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 558, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error I am running 15.10 and Python 2.7.10 on my iMac for the server and the cluster submission node is running Pulsar 0.5.0 and Python 2.7.12 For these tests I run Pulsar in an interactive window so I have not set the sudoers file up, but rather enter sudo password when requested by Pulsar (at the first step of chowning the staging directory). Also have rewrites set up in Galaxy’s pulsar_actions.yml and I am using remote_scp for the file transfers rather than http - although I have also tried switching back to http (as I noticed caching, which I am also testing, does not work with scp transfers) but get an identical set of error messages. As I say, I have no troubles using a regular queued_drmaa manager in pulsar. Any ideas what the problem may be? Cheers, Rich Richard J Poole PhD Wellcome Trust Fellow Department of Cell and Developmental Biology University College London 518 Rockefeller 21 University Street, London WC1E 6DE Office (518 Rockefeller): +44 20 7679 6577 (int. 46577) Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133) https://www.ucl.ac.uk/cdb/academics/poole

2 5

Combine different resolvers for one tool
by Ignacio EGUINOA 30 Apr '17

30 Apr '17

Hi all, I'm setting up a Galaxy server which consists of a Galaxy head node and a Docker engine (swarm) running on top of an OpenNebula cloud. So, ideally I would like to run everything using this Docker engine. For tools that only have 1 dependency, the Docker resolver works perfectly. But, in the case of tools having more than 1 dependency, if I activate mulled containers (enable_beta_mulled_containers = True) it will just try to run the tool script using the container corresponding to the 1st dependency found, which of course fails. What is the correct approach for resolving several dependencies using Docker? I tried activating the involucro which (as far as I understood) builds the docker container on-the-go based on the conda environment which results from the merge of all the dependencies. I know it's a beta feature but still, couldn't make it work...besides setting the path and auto_init to True, what am I supposed to put in the containers_resolvers_config_file ? Beside this, would it be possible to combine the dependencies in another way? Is it possible in the current version to load the conda environment inside a I know it may sound redundant and unnecessary in terms of dependency resolution but in cases like I the one I described, where you have the Docker swarm already running. I tried this with a few tools, using one of the containers as base and loading the rest of the dependencies using conda environment. Would it be possible to do this in an automatic way, using a general base container? Anyway, the general question is where are things going regarding dependency resolution, so that I can get an idea of what to expect in the future and how to collaborate with development of these features. I found a thread on github about this ( [ https://github.com/galaxyproject/galaxy/issues/3299 | https://github.com/galaxyproject/galaxy/issues/3299 ] ) but don't know the resolutions taken about it (if any). Thanks in advance for the help. Ignacio Ignacio Eguinoa - Predoctoral fellow Applied Bioinformatics And Biostatistics VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 36 95 [ http://www.psb.ugent.be/ | www.psb.ugent.be ]

1 0

Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt 28 Apr '17

28 Apr '17

Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A

3 3

Environmental Variable in <version_command>
by D K 25 Apr '17

25 Apr '17

Is it possible to use environment variables within <version_command>? I'm trying to use git commit information as the version ID in galaxy where the path $GITREPO can change: e.g. <version_command>git --git-dir="$GITREPO/project.git" log -n 1 origin/master | grep -P "commit|Author|Date"</version_command> Thanks!

1 0

Additional Information about users in the API
by Milen Kouylekov 25 Apr '17

25 Apr '17

Dear Team, Hi, my name is Milen Kouylekov and I am working on the galaxy portal customized for natural language technology applications. http://lap.clarino.uio.no. I wrote an reporting script that uses Galaxy API to summarize the user activity. The idea of the script is to send regular reports with the information available to the reporting server as well as additional information like queries that failed to execute etc. I have managed to retrieve using the API most of the relevant information except the following: 1) User creation date. 2) User last access date. I have investigated that user object and see that information is part of it. My question is: Is there a way to access this information through the API? If not can I make a feature request? It is an information useful for administration of a galaxy instance. Cheers Milen

3 4

Galaxy User IDs and Group IDs
by Lemley, Rob 24 Apr '17

24 Apr '17

Hi everyone, This may seem like a silly question, but are user id's and group id's expected to be the "same"? For example: >>> gi.users.get_users() [{u'username': u'user1', u'model_class': u'User', u'id': u'f2db41e1fa331b3e', u'email': u'XXXXX'}, {u'username': u'user2', u'model_class': u'User', u'id': u'f597429621d6eb2b', u'email': u'XXXXX'}] >>> gi.groups.get_groups() [{u'url': u'/api/groups/f2db41e1fa331b3e', u'model_class': u'Group', u'id': u'f2db41e1fa331b3e', u'name': u'group1'}, {u'url': u'/api/groups/f597429621d6eb2b', u'model_class': u'Group', u'id': u'f597429621d6eb2b', u'name': u'group2'}] This is just a dev instance I set up really quick, so these are the first two users/groups I've created. If this is expected behavior I'll carry on, just seems odd to me. Thanks! -Rob -- Rob Lemley Systems Administrator - CIRC University of Rochester

2 1

conda path problem
by Matthias Bernt 20 Apr '17

20 Apr '17

Dear list, now that I got conda working I got a new error when installing tools (bot when installing via the web interface and via the galaxy-tools ansible role). There seems to be an update write on a nonexistent file ...../_condarc I guess an important point is that I needed to redefine the conda path in galaxy.ini (since I got warnings that the path name was to long). Maybe there are still some hard coded paths around? Best, Matthias Uncaught exception in exposed API method: Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/web/framework/decorators.py", line 282, in decorator rval = func( self, trans, *args, **kwargs ) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py", line 502, in install_repository_revision payload ) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 706, in install install_options File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 805, in __initiate_and_install_repositories return self.install_repositories(tsr_ids, decoded_kwd, reinstalling=False) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 852, in install_repositories tool_panel_section_mapping=tool_panel_section_mapping ) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/tool_shed/galaxy_install/install_manager.py", line 910, in install_tool_shed_repository [self._view.install_dependencies(r) for r in new_requirements] File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/views.py", line 59, in install_dependencies return self._dependency_manager._requirements_to_dependencies_dict(requirements, **{'install': True}) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/__init__.py", line 148, in _requirements_to_dependencies_dict dependencies = resolver.resolve_all(resolvable_requirements, **kwds) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/resolvers/conda.py", line 171, in resolve_all is_installed = self.install_all(conda_targets) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/resolvers/conda.py", line 126, in install_all return_code = install_conda_targets(conda_targets, env, conda_context=self.conda_context) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 405, in install_conda_targets conda_context.ensure_channels_configured() File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 136, in ensure_channels_configured self.save_condarc(conda_conf) File "/gpfs1/data/galaxy_server/galaxy-dev/lib/galaxy/tools/deps/conda_util.py", line 198, in save_condarc raise Exception(message) Exception: Failed to update write to path [/gpfs1/data/galaxy_server/galaxy-dev/database/dependencies/_condarc] while attempting to update conda configuration, please update the configuration to override the condarc location or grant this application write to the parent directory. -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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