galaxy-dev March 2016

galaxy-dev@lists.galaxyproject.org

74 participants
98 discussions

Please help fix toolshed repository: trtr
by Lance Parsons 15 Mar '16

15 Mar '16

I was helping someone with their toolshed repository and we ran into an issue, there is an old folder "myTools" in the repository that we cannot delete. It has a second copy of the tool (inadvertently). However, when we upload a new version with Planemo, the directory remains. Attempts to delete it via the toolshed web interface result in internal server errors. Can an admin take a look? https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301 -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 136 Lewis-Sigler Institute for Integrative Genomics Princeton University

2 2

Help with dynamic job destination
by Lance Parsons 15 Mar '16

15 Mar '16

I'm trying to setup a dynamic job destination for bowtie2 so that it submits to a different destination if the `-a` option is set or the `-k` option is set to a high value. I've got things working, but the function I've written seems rather complicated and ugly. I was wondering if anyone had any advice on a better way to query job parameters. See the function here: https://gist.github.com/lparsons/a4724b51afd9027e3c0e Thanks in advance for any suggestions or comments. -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 136 Lewis-Sigler Institute for Integrative Genomics Princeton University

1 0

Job stuck in running state.
by Zuzanna K. Filutowska 15 Mar '16

15 Mar '16

Dear All, I am running newest version of Galaxy with PBS and I am observing strange behaviour: some jobs that were finished on the queue system are still shown as running on Galaxy Web interface. Communication with PBS server seems to work fine all the time. Nothing interesting seems to be in logs despite debug being on: sqlalchemy.pool.QueuePool ERROR 2016-03-13 11:36:02,544 Error closing cursor Any ideas, what can be a problem? -- Pozdrawiam, -- 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

2 1

Re: [galaxy-dev] Trackster in 16.01 broken
by Marius van den Beek 15 Mar '16

15 Mar '16

Hi Lubos, I opened a Pull Request on https://github.com/galaxyproject/galaxy/pull/1930, which should hopefully fix the problem. If you want to give it a try, you can do `git fetch origin pull/1930/head:more_bytestring_for_pysam` and `git checkout more_bytestring_for_pysam`. When the problem has been solved, you can switch back to release_16.01 by doing `git checkout release_16.01`. Thanks for reporting the error, Marius On 15 March 2016 at 19:25, Marius van den Beek <m.vandenbeek(a)gmail.com> wrote: > Yes, `git checkout release_16.01` should do it, but wait a second, there > might actually be a problem, > since ` File "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py", > line 892, in get_iterator`, > while the PR addresses 354-356! > > > On 15 March 2016 at 19:23, Lubos Klucar <klucar(a)embnet.sk> wrote: > >> >> >> On 15. 3. 2016 19:15, Marius van den Beek wrote: >> >>> Hi Lubos, >>> >>> hmm, I'm surprised about this. >>> Just to make sure, you are on the release_16.01 branch? >>> (`git branch` should highlight release_16.01) >>> This PR hasn't been merged into dev yet. >>> >>> >> Hi Marius, >> >> it seems I need more help with git, not the Galaxy!. ;-) My git branch >> gives me: >> >> dev >> * master >> >> How should I 'switch' to 16.01??.. >> >> regards >> >> Lubos >> >> Cheers, >>> Marius >>> >>> On 15 March 2016 at 19:08, Lubos Klucar <klucar(a)embnet.sk >>> <mailto:klucar@embnet.sk>> wrote: >>> >>> Dear Marius, >>> >>> thanks for help, but it looks our galaxy is up to date: >>> >>> remote: Counting objects: 111, done. >>> remote: Compressing objects: 100% (23/23), done. >>> remote: Total 111 (delta 82), reused 75 (delta 75), pack-reused 13 >>> Receiving objects: 100% (111/111), 39.85 KiB, done. >>> Resolving deltas: 100% (82/82), completed with 29 local objects. >>> >From https://github.com/galaxyproject/galaxy >>> 8423fe7..23c3300 dev -> origin/dev >>> 5a50a46..65a5b08 release_16.01 -> origin/release_16.01 >>> Already up-to-date. >>> >>> After Galaxy restart the problem still persist... >>> >>> all the best >>> >>> Lubos >>> >>> On 15. 3. 2016 18:59, Marius van den Beek wrote: >>> >>> Hello Lubos, >>> >>> this should be fixed with >>> https://github.com/galaxyproject/galaxy/pull/1897. >>> If you pull in the latest changes (git pull) on the >>> release_16.01 branch >>> things should work again. >>> >>> Cheers, >>> Marius >>> >>> On 15 March 2016 at 18:54, Lubos Klucar <klucar(a)embnet.sk >>> <mailto:klucar@embnet.sk> >>> <mailto:klucar@embnet.sk <mailto:klucar@embnet.sk>>> wrote: >>> >>> Hi, >>> >>> after upgrading from 15.10 to 16.01, the trackster >>> visualisation >>> tool is partly defective. It can successfully show e.g. GFF >>> tracks, >>> but after adding e.g. BAM track nothing is shown. The only >>> suspicious debug output I could get when loading >>> non-working-track is: >>> >>> galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 >>> 11:44:38,853 >>> Error in dataset API at listing contents: Expected bytes, >>> got >>> unicode: Expected bytes, got unicode >>> Traceback (most recent call last): >>> File >>> >>> >>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", >>> line 66, in show >>> rval = self._data( trans, dataset, **kwd ) >>> File >>> >>> >>> "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", >>> line 235, in _data >>> ref_seq=region, mean_depth=mean_depth, **kwargs ) >>> File >>> >>> >>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py", >>> line 192, in get_data >>> iterator = self.get_iterator( data_file, chrom, start, >>> end, >>> **kwargs ) >>> File >>> >>> >>> "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py", >>> line 892, in get_iterator >>> data = data_file.fetch( start=start, end=end, >>> reference=chrom ) >>> File "pysam/calignmentfile.pyx", line 868, in >>> pysam.calignmentfile.AlignmentFile.fetch >>> (pysam/calignmentfile.c:10170) >>> File "pysam/calignmentfile.pyx", line 787, in >>> pysam.calignmentfile.AlignmentFile.parse_region >>> (pysam/calignmentfile.c:9605) >>> File "pysam/calignmentfile.pyx", line 1576, in >>> pysam.calignmentfile.AlignmentFile.gettid >>> (pysam/calignmentfile.c:16665) >>> File "pysam/calignmentfile.pyx", line 640, in >>> pysam.calignmentfile.AlignmentFile.get_tid >>> (pysam/calignmentfile.c:8208) >>> File "pysam/cutils.pyx", line 106, in >>> pysam.cutils.force_bytes >>> (pysam/cutils.c:2170) >>> TypeError: Expected bytes, got unicode >>> >>> Any help to solve this problem would be highly appreciated! >>> >>> many thanks >>> -- >>> >>> Lubos Klucar >>> ___________________________________________________________ >>> 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/ >>> >>> >>> >>> -- >>> >>> Lubos Klucar >>> >>> Institute of Molecular Biology >>> Slovak Academy of Science >>> Dubravska cesta 21 >>> 845 51 Bratislava 45 >>> Slovakia >>> >>> Tel.: +421 2 5930 7413 >>> <tel:%2B421%202%205930%207413> >>> Fax.: +421 2 5930 7416 >>> <tel:%2B421%202%205930%207416> >>> >>> >>> >> -- >> >> Lubos Klucar >> >> Institute of Molecular Biology >> Slovak Academy of Science >> Dubravska cesta 21 >> 845 51 Bratislava 45 >> Slovakia >> >> Tel.: +421 2 5930 7413 >> Fax.: +421 2 5930 7416 >> > >

2 1

Trackster in 16.01 broken
by Lubos Klucar 15 Mar '16

15 Mar '16

Hi, after upgrading from 15.10 to 16.01, the trackster visualisation tool is partly defective. It can successfully show e.g. GFF tracks, but after adding e.g. BAM track nothing is shown. The only suspicious debug output I could get when loading non-working-track is: galaxy.webapps.galaxy.api.datasets ERROR 2016-03-15 11:44:38,853 Error in dataset API at listing contents: Expected bytes, got unicode: Expected bytes, got unicode Traceback (most recent call last): File "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line 66, in show rval = self._data( trans, dataset, **kwd ) File "/usr/local/galaxy-prod/lib/galaxy/webapps/galaxy/api/datasets.py", line 235, in _data ref_seq=region, mean_depth=mean_depth, **kwargs ) File "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py", line 192, in get_data iterator = self.get_iterator( data_file, chrom, start, end, **kwargs ) File "/usr/local/galaxy-prod/lib/galaxy/visualization/data_providers/genome.py", line 892, in get_iterator data = data_file.fetch( start=start, end=end, reference=chrom ) File "pysam/calignmentfile.pyx", line 868, in pysam.calignmentfile.AlignmentFile.fetch (pysam/calignmentfile.c:10170) File "pysam/calignmentfile.pyx", line 787, in pysam.calignmentfile.AlignmentFile.parse_region (pysam/calignmentfile.c:9605) File "pysam/calignmentfile.pyx", line 1576, in pysam.calignmentfile.AlignmentFile.gettid (pysam/calignmentfile.c:16665) File "pysam/calignmentfile.pyx", line 640, in pysam.calignmentfile.AlignmentFile.get_tid (pysam/calignmentfile.c:8208) File "pysam/cutils.pyx", line 106, in pysam.cutils.force_bytes (pysam/cutils.c:2170) TypeError: Expected bytes, got unicode Any help to solve this problem would be highly appreciated! many thanks -- Lubos Klucar

2 3

Problems uploading files to galaxy
by Lemley, Rob 15 Mar '16

15 Mar '16

Hi, I'm hoping you can help out with a problem we are experiencing uploading files to our own Galaxy instance. When a user tries to upload a file to Galaxy through their web browser, the job errors out: Traceback (most recent call last): File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", line 430, in <module> __main__() File "/gpfs/fs1/sfw/cibem_galaxy/app/galaxy/tools/data_source/upload.py", line 407, in __main__ for line in open( sys.argv[3], 'r' ): IOError: [Errno 13] Permission denied: '/scratch/XXXXXX/XXXXXX/galaxy/tmp/tmpSlG2pC' The permissions on the referenced file: -rw-------+ 1 rlemley rlemley 317 Mar 7 13:42 tmpSlG2pC As the Galaxy daemons run as XXXXXX_galaxy, it does not have permission to read the file. I tried modifying external_chown_script.py so that XXXXXX_galaxy has permission to read that file, but that caused problems elsewhere so I backed out the changes. Any suggestions? Many thanks, -Rob Rob Lemley Systems Administrator - CIRC University of Rochester

3 5

Galaxy tools for docking protein-compounds.
by Léo Biscassi 15 Mar '16

15 Mar '16

Hi folks, I've been developing Galaxy tools for docking protein-compounds. My docking program is Autodock Vina. In [1] is my repository. I'm writing here for two purpose: 1) Is there someone working in this way? I've found the project [2]. 2) I would like to share these tools to Galaxy project. Are they welcome for Galaxy project? Let me know the best practices for developing tools to be shared in Galaxy project. [1] https://github.com/leobiscassi/galaxy_tools [2] https://toolshed.g2.bx.psu.edu/ Thanks for any help. Att. -- *Léo Biscassi* Facebook - https://pt-br.facebook.com/lbiscassi Linkedin - https://br.linkedin.com/in/leobiscassi Skype - biscassi.leo Twitter - https://twitter.com/leobiscassi

4 19

Tool-install error with yaml file
by Rathert, Philipp, Dr. 15 Mar '16

15 Mar '16

Dear all, I want to install a bunch of tools using the install-tools function. In my yaml file tool.yml i have specified the url if my docker instance wit the ip adress i use in the web browser and the api_key is admin When i run install-tools tool.yml I get the error below and nothing happens. I attached my tool.yml file in case the error comes from there. Anybody has an idea whats wrong? root@galaxy:/galaxy-central# install-tools tool.yml * Starting PostgreSQL 9.3 database server [ OK ] starting Galaxy Activating virtualenv at .venv Ignoring indexes: https://pypi.python.org/simple /galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:315: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning. SNIMissingWarning /galaxy-central/.venv/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:120: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwar…. InsecurePlatformWarning Requirement already up-to-date: pip==8.0.2+gx2 in ./.venv/lib/python2.7/site-packages Requirement already satisfied (use --upgrade to upgrade): bx-python==0.7.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 2)) Requirement already satisfied (use --upgrade to upgrade): MarkupSafe==0.23 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 3)) Requirement already satisfied (use --upgrade to upgrade): PyYAML==3.11 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 4)) Requirement already satisfied (use --upgrade to upgrade): SQLAlchemy==1.0.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 5)) Requirement already satisfied (use --upgrade to upgrade): mercurial==3.4.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 7)) Requirement already satisfied (use --upgrade to upgrade): numpy==1.9.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 8)) Requirement already satisfied (use --upgrade to upgrade): pycrypto==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 9)) Requirement already satisfied (use --upgrade to upgrade): Paste==2.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 16)) Requirement already satisfied (use --upgrade to upgrade): PasteDeploy==1.5.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 17)) Requirement already satisfied (use --upgrade to upgrade): docutils==0.12 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 18)) Requirement already satisfied (use --upgrade to upgrade): wchartype==0.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 19)) Requirement already satisfied (use --upgrade to upgrade): repoze.lru==0.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 20)) Requirement already satisfied (use --upgrade to upgrade): Routes==2.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 21)) Requirement already satisfied (use --upgrade to upgrade): WebOb==1.4.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 22)) Requirement already satisfied (use --upgrade to upgrade): WebHelpers==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 23)) Requirement already satisfied (use --upgrade to upgrade): Mako==1.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 24)) Requirement already satisfied (use --upgrade to upgrade): pytz==2015.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 25)) Requirement already satisfied (use --upgrade to upgrade): Babel==2.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 26)) Requirement already satisfied (use --upgrade to upgrade): Beaker==1.7.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 27)) Requirement already satisfied (use --upgrade to upgrade): Cheetah==2.4.4 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 30)) Requirement already satisfied (use --upgrade to upgrade): Markdown==2.6.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 31)) Requirement already satisfied (use --upgrade to upgrade): bioblend==0.6.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 34)) Requirement already satisfied (use --upgrade to upgrade): boto==2.38.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 35)) Requirement already satisfied (use --upgrade to upgrade): requests==2.8.1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 36)) Requirement already satisfied (use --upgrade to upgrade): requests-toolbelt==0.4.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 37)) Requirement already satisfied (use --upgrade to upgrade): kombu==3.0.30 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 40)) Requirement already satisfied (use --upgrade to upgrade): amqp==1.4.8 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 41)) Requirement already satisfied (use --upgrade to upgrade): anyjson==0.3.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 42)) Requirement already satisfied (use --upgrade to upgrade): sqlalchemy-migrate==0.10.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 45)) Requirement already satisfied (use --upgrade to upgrade): decorator==4.0.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 46)) Requirement already satisfied (use --upgrade to upgrade): Tempita==0.5.3dev in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 47)) Requirement already satisfied (use --upgrade to upgrade): sqlparse==0.1.16 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 48)) Requirement already satisfied (use --upgrade to upgrade): pbr==1.8.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 49)) Requirement already satisfied (use --upgrade to upgrade): six==1.9.0 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 51)) Requirement already satisfied (use --upgrade to upgrade): Parsley==1.3 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 52)) Requirement already satisfied (use --upgrade to upgrade): nose==1.3.7 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 53)) Requirement already satisfied (use --upgrade to upgrade): SVGFig==1.1.6 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 54)) Requirement already satisfied (use --upgrade to upgrade): Fabric==1.10.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 57)) Requirement already satisfied (use --upgrade to upgrade): paramiko==1.15.2 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 58)) Requirement already satisfied (use --upgrade to upgrade): ecdsa==0.13 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 59)) Requirement already satisfied (use --upgrade to upgrade): Whoosh==2.4.1+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 66)) Requirement already satisfied (use --upgrade to upgrade): pysam==0.8.4+gx1 in ./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 69)) You are using pip version 8.0.2+gx2, however version 8.1.0 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Requirement already satisfied (use --upgrade to upgrade): psycopg2==2.6.1 in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 1)) Requirement already satisfied (use --upgrade to upgrade): drmaa in ./.venv/lib/python2.7/site-packages (from -r /dev/stdin (line 2)) You are using pip version 8.0.2+gx2, however version 8.1.0 is available. You should consider upgrading via the 'pip install --upgrade pip' command. Activating virtualenv at .venv Daemon is already running (PID: 323 from PID file galaxy_install.pid) Galaxy is running. PLAY ************************* TASK [galaxy_tools : include] **************** skipping: [localhost] TASK [galaxy_tools : include] **************** included: /home/galaxy/ansible/galaxy-tools-playbook/roles/galaxy_tools/tasks/tools.yml for localhost TASK [galaxy_tools : Create/invoke script virtualenv] ******** fatal: [localhost]: UNREACHABLE! => {"changed": false, "msg": "All items completed", "results": [{"item": "pyyaml", "msg": "Authentication or permission failure. In some cases, you may have been able to authenticate and did not have permissions on the remote directory. Consider changing the remote temp path in ansible.cfg to a path rooted in \"/tmp\". Failed command was: ( umask 22 && mkdir -p \"echo $HOME/.ansible/tmp/ansible-tmp-1457708936.13-72771790334072\" && echo \"echo $HOME/.ansible/tmp/ansible-tmp-1457708936.13-72771790334072\" ), exited with result 1", "unreachable": true}, {"item": "bioblend", "msg": "Authentication or permission failure. In some cases, you may have been able to authenticate and did not have permissions on the remote directory. Consider changing the remote temp path in ansible.cfg to a path rooted in \"/tmp\". Failed command was: ( umask 22 && mkdir -p \"echo $HOME/.ansible/tmp/ansible-tmp-1457708936.15-89736978480357\" && echo \"echo $HOME/.ansible/tmp/ansible-tmp-1457708936.15-89736978480357\" ), exited with result 1", "unreachable": true}]} to retry, use: --limit @tools.retry PLAY RECAP *********************** localhost : ok=1 changed=0 unreachable=1 failed=0

1 0

external_chown_script.py and the local job runner
by Peter Cock 15 Mar '16

15 Mar '16

On Mon, Jan 25, 2016 at 11:33 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > Hello all, > > We're currently looking at changing our Galaxy setup to link user accounts > with Linux user accounts for better cluster integration (running jobs as the > actual user on SGE). As part of this, we've tried setting up a fresh > installation on a new VM which has thrown up some issues. > > [snip] We eventually got Galaxy to talk to SGE and submit jobs successfully as the individual user's Linux account, with external_chown_script.py being called to handle ownership of the files. However, we would like to have some jobs (like the upload tool) configured to run on the Galaxy server itself - and the easiest way to do that is via the local job runner. We tried both the "upload1" and "Convert characters1" tools. These jobs would start and seem to run, but then fail with a file permission error (I don't have a stack trace to hand). From watching the Galaxy terminal output from run.sh we could see external_chown_script.py being called. As a test, when we disabled the external_chown_script setting in config/galaxy.ini then the local jobs would work. When using the local job runner, does Galaxy run the child process as the Galaxy user (my guess - no chown needed), or as the job owner's Linux account (calling chown would be needed)? Thanks, Peter

2 5

Mapping users to slurm
by Pardo Diaz, Alfonso 14 Mar '16

14 Mar '16

Hello, I have connected my galaxy to a Slurm cluster via DRMAA. Galaxy can send jobs to the cluster without problems. But then I configure galaxy to use “real users” I got this error: "User myuser(a)mydomain.es<mailto:myuser@mydomain.es> is not mapped to any real user, and not permitted to start jobs” Could you help me? Tanks!! This is my job_con.xml: <?xml version="1.0"?> <job_conf> <plugins workers="6"> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="2"> <param id="drmaa_library_path">/opt/slurm-drmaa/lib/libdrmaa.so</param> </plugin> </plugins> <handlers default="handlers"> <handler id="main" tags="handlers"/> </handlers> <destinations default="drmaa"> <destination id="drmaa" runner="drmaa"> <param id="galaxy_external_runjob_script">/opt/galaxy/scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">/opt/galaxy/scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">/opt/galaxy/scripts/external_chown_script.py</param> </destination> </destinations> </job_conf> this is my auth_conf.xml: <?xml version="1.0"?> <auth> <authenticator> <type>ldap</type> <options> <auto-register>True</auto-register> <allow-password-change>False</allow-password-change> <server>ldap://ldap.ceta-ciemat.es</server> <login-use-username>True</login-use-username> <continue-on-failure>False</continue-on-failure> <search-filter>(|(mail={email})(uid={username}))</search-filter> <search-fields>uid,mail,dn</search-fields> <search-base>ou=xxxxxx,dc=xxxxx,dc=xxxxx</search-base> <bind-user>{dn}</bind-user> <bind-password>{password}</bind-password> <auto-register-username>{uid}</auto-register-username> <auto-register-email>{mail}</auto-register-email> <login-use-username>True</login-use-username> </options> </authenticator> <authenticator> <type>localdb</type> <options>  <allow-password-change>true</allow-password-change> </options> </authenticator> </auth> And this is my galaxy.ini: [server:main] port = 8080 host = 0.0.0.0 use_threadpool = True threadpool_kill_thread_limit = 10800 [filter:gzip] [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory database_connection = postgres://xxxxxxxx:xxxxxx@xxxxx/galaxy_project database_engine_option_server_side_cursors = True database_engine_option_strategy = threadlocal new_file_path = database/tmp tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml tool_dependency_dir = dependency_dir cluster_files_directory = database/pbs smtp_server = localhost use_nglims = False nglims_config_file = tool-data/nglims.yaml debug = true use_interactive = True require_login = True allow_user_creation = False allow_user_deletion = True allow_user_impersonation = True allow_user_dataset_purge = True new_user_dataset_access_role_default_private = True auth_config_file = config/auth_conf.xml enable_quotas = True expose_dataset_path = False job_config_file = config/job_conf.xml enable_job_recovery = True outputs_to_working_directory = True drmaa_external_runjob_script = scripts/drmaa_external_runner.py drmaa_external_killjob_script = scripts/drmaa_external_killer.py external_chown_script = scripts/external_chown_script.py ---------------------------- Confidencialidad: Este mensaje y sus ficheros adjuntos se dirige exclusivamente a su destinatario y puede contener informaci�n privilegiada o confidencial. Si no es vd. el destinatario indicado, queda notificado de que la utilizaci�n, divulgaci�n y/o copia sin autorizaci�n est� prohibida en virtud de la legislaci�n vigente. Si ha recibido este mensaje por error, le rogamos que nos lo comunique inmediatamente respondiendo al mensaje y proceda a su destrucci�n. Disclaimer: This message and its attached files is intended exclusively for its recipients and may contain confidential information. If you received this e-mail in error you are hereby notified that any dissemination, copy or disclosure of this communication is strictly prohibited and may be unlawful. In this case, please notify us by a reply and delete this email and its contents immediately. ----------------------------

1 0

← Newer
1
2
3
4
5
6
7
8
9
10
Older →

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

galaxy-dev March 2016