- galaxy-dev - lists.galaxyproject.org

Galaxy News Page and RSS Feed
by Dave Clements 29 Jul '11

29 Jul '11

Hello all, The new Galaxy wiki features a Galaxy News page and RSS feed for items of interest to the Galaxy community. The news page is a good way to get information out to the community and is less intrusive than posting to the Galaxy mailing lists. Anyone can create a news items by following directions on the news page, or by sending the item to outreach(a)galaxyproject.org. News items automatically become items in the Galaxy News RSS feed, and are also automatically listed in the right bar on the wiki home page. The most recent posting is about the new Galaxy paper "Making whole genome multiple alignments usable for biologists" appearing in Bioinformatics. News Page http://wiki.g2.bx.psu.edu/News RSS Feed http://feed43.com/galaxynews.xml How to post a news item http://wiki.g2.bx.psu.edu/News#Add_a_News_Item Please let me know if you have any questions (or news items). Thanks, Dave C. -- http://getgalaxy.org http://usegalaxy.org/ http://galaxyproject.org/wiki

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Invalid job runner: drmaa
by remy d1 28 Jul '11

28 Jul '11

Hi, I try to configure Galaxy with SGE. It works one time yesterday but now I have the following message all the time : galaxy.jobs DEBUG 2011-07-26 16:50:54,002 dispatching job 118 to drmaa runner galaxy.jobs ERROR 2011-07-26 16:50:54,002 put(): (118) Invalid job runner: drmaa [ An error occurred running this job: *Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator.* ] On the web page.* * Here is my universe_wsgi.ini file : [server:main] port = 8000 host = X.X.X.X use_threadpool = True [filter:proxy-prefix] prefix = /galaxy [app:main] paste.app_factory = galaxy.web.buildapp:app_factory filter-with = proxy-prefix database_connection = mysql://galaxy:xxxxxx@localhost :3306/galaxy?unix_socket=/var/run/mysqld/mysqld.sock file_path = database/files new_file_path = database/tmp job_working_directory = database/users_space/user_galaxy cluster_files_directory = database/users_space/user_galaxy use_nglims = False nglims_config_file = tool-data/nglims.yaml static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue log_events = True log_actions = True debug = True use_interactive = True library_import_dir = /home/galaxy/galaxy-dist/tmpdir user_library_import_dir = True allow_library_path_paste = True admin_users = me@... enable_pages = True enable_api = True set_metadata_externally = True retry_metadata_internally = True outputs_to_working_directory = True start_job_runners = drmaa default_cluster_job_runner = drmaa:/// [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// [galaxy_amqp] I checked many things, but it did not change anything... Any help would gracefull. Regards.

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Re: [galaxy-dev] job runner error
by Peter Cock 28 Jul '11

28 Jul '11

On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar <meshashi29(a)gmail.com> >>> Hi all, >>> >>> I have added separate job runner in my galaxy instance. So far it was >>> running successfully from many months. >>> Now its giving error as below and i am unable to trace it. Please >>> suggest. >>> >>> Traceback (most recent call last): >>> ... >>> OperationalError: (OperationalError) database is locked None None >>> >>> Thanks >>> Shashi > On Wed, Jul 27, 2011 at 7:00 PM, Peter Cock <p.j.a.cock(a)googlemail.com> >> You're not using SQLite as the database are you? I've seen that kind of >> error message from locking problems (e.g. when the SQLite DB was on >> a CIFS mapped drive), and it wouldn't surprise me that with a separate >> thread for the job runner you get contention over the SQLite DB. >> >> If you are using PostgreSQL (or MySQL) as recommended for a production >> Galaxy server, then I'm not sure what could be wrong. On Wed, Jul 27, 2011 at 2:42 PM, shashi shekhar <meshashi29(a)gmail.com> wrote: > > I am using sqlite database . > I think that to avoid this database problem you will have to move to PostgreSQL (which is what the Galaxy team recommend), or possibly MySQL (not sure what the downsides are). This might be hard if you already have a number of users and datafiles. I've CC'd the list again so hopefully Nate or one of the other Galaxy Devs can confirm this. Peter

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Re: [galaxy-dev] Existing efforts to convert the QIIME pipeline to Galaxy?
by Amanda Zuzolo 28 Jul '11

28 Jul '11

Hello all, I'm working on a local instance of Galaxy at George Mason University. We'd been looking into integrating Qiime and I've found the toolkit very helpful, thanks! I did have one question, though: would you mind uploading the tool_conf file or chunk of text with the qiime functions in it? This would be helpful to myself, as well as others interested in the toolkit! Thank you, Amanda Zuzolo Bioengineering Major, George Mason University

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Re: [galaxy-dev] Regarding submitting jobs as actual user
by Chorny, Ilya 28 Jul '11

28 Jul '11

I put the wrong link in there. The link below is to pull the code. Ilya https://bitbucket.org/ichorny/galaxy-central/overview From: Chorny, Ilya Sent: Wednesday, July 27, 2011 1:22 PM To: galaxy-dev(a)lists.bx.psu.edu Cc: Wohlfrom, Tobias; Duddy, John Subject: Regarding submitting jobs as actual user I completed the changes to galaxy to submit DRMAA jobs (SGE) as the actual galaxy user. You can see the code at the fork below. Below is a brief description of how to turn it which is also described in the universe_wsgi.ini.sample. https://ichorny@bitbucket.org/ichorny/galaxy-central # Uncomment drmaa_external_runjob_script and drmaa_external_killjob_script pameters and have them point to the # absolute path for scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py. # The scripts directory is located in the top level galaxy directory. The parameters when # uncommented allow for submission to the drmaa queue with the user name of the user submitting # the job and not the galaxy user. In order for this to work the actual user must log into galaxy # and the galaxy authentication must be consistent with the authentication on the server in which the # drmaa queue is running (i.e. the username must have an account on the server and be allowed to # submit jobs to the queue). The galaxy user must also be given sudo permission to execute # scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py in /etc/sudoers # Example: # galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_runner.py # galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_killer.py # Also the # Defaults requiretty # in /etc/sudoers must be commented out #drmaa_external_runjob_script = None #drmaa_external_killjob_script = None Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Regarding submitting jobs as actual user
by Chorny, Ilya 28 Jul '11

28 Jul '11

I completed the changes to galaxy to submit DRMAA jobs (SGE) as the actual galaxy user. You can see the code at the fork below. Below is a brief description of how to turn it which is also described in the universe_wsgi.ini.sample. https://ichorny@bitbucket.org/ichorny/galaxy-central # Uncomment drmaa_external_runjob_script and drmaa_external_killjob_script pameters and have them point to the # absolute path for scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py. # The scripts directory is located in the top level galaxy directory. The parameters when # uncommented allow for submission to the drmaa queue with the user name of the user submitting # the job and not the galaxy user. In order for this to work the actual user must log into galaxy # and the galaxy authentication must be consistent with the authentication on the server in which the # drmaa queue is running (i.e. the username must have an account on the server and be allowed to # submit jobs to the queue). The galaxy user must also be given sudo permission to execute # scripts/drmaa_external_runner.py and scripts/drmaa_external_killer.py in /etc/sudoers # Example: # galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_runner.py # galaxy ALL = (root) NOPASSWD: SETENV: /opt/galaxy/scripts/drmaa_external_killer.py # Also the # Defaults requiretty # in /etc/sudoers must be commented out #drmaa_external_runjob_script = None #drmaa_external_killjob_script = None Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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Upload of images - jpg/png - "binary file contains inappropriate content"
by Jelle Scholtalbers 28 Jul '11

28 Jul '11

Hi all, I would like to be able to upload images to my Galaxy instance - in particular jpg/png to data libraries. I can't however find out how to overcome the problem of inappropriate content in binary file. How to go about? When I create a sniffer class in the galaxy.datatypes.images.py that always returns true (for testing purposes) I still don't get the jpg uploaded without an error (sniffer is incl. in the datatypes_conf.xml ). class Jpg( Image ): file_ext = "jpg" def sniff(self, filename): """Determine if the file is in jpg format. """ return True It seems I'm missing something obvious and could use some help. Cheers, Jelle

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problems with two coupled select menus using dynamic_options and refresh_on_change
by Leandro Hermida 28 Jul '11

28 Jul '11

Hi, I am trying to create a form where there are two select menus, both using dynamic_options, where one is the parent menu that is chosen first and based on the selection(s) there is a refresh and the second menu gets populated based on the first menu's choice(s). <param name="names" type="select" multiple="true" optional="true" dynamic_options="dyn_options('names')" refresh_on_change="true" label="Filter By Names"/> <param name="values" type="select" multiple="true" optional="true" dynamic_options="dyn_options('values', $names)" label="Filter by Values" /> There seems to be a problem when the form loads for the first time as $names is not selected yet. I get a syntax error like "Invalid string", when I remove $names as a parameters from my second dynamic_options function call everything is fine. Does someone know how to achieve the functionality I'm aiming for in Galaxy without having to use the deprecated <pages> tags? Is there a way in Cheetah to set a default value for $names and if so how would I do this in the tool xml? regards, Leandro

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Tool XML parameter options from locally stored files
by SHAUN WEBB 28 Jul '11

28 Jul '11

Hi, I am trying to write a tool xml file and want to do the following: I have a number of GTF files stored locally and referenced in a data table. I give the user a drop down list of those available using the following code: <param name="gtf" type="select" label="GTF File"> <options from_data_table="gtf_files"/> </param> I then want them to choose an annotation type based on those present in the selected gtf file above. It seems simple enough to do this if the gtf file is in your history already: <param name="feature" type="select" multiple="true" label="Extract features"> <options from_dataset="gtf"> <column name="name" index="2"/> <column name="value" index="2"/> <filter type="unique_value" name="unique" column="2"/> </options> </param> But is there a way to query locally stored files via datatables/.loc files to pull out options when the file is dynamically chosen by a different parameter? This code is also wrapped in a conditional, I'm not sure if that will affect anything. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Re: [galaxy-dev] set_metadata_externally =True
by Chorny, Ilya 28 Jul '11

28 Jul '11

Well I got all the rw permissions changed correctly except for the metadata files written to the temp directory (new_file_path). I still can't seem to track down where those are written. Any help would be greatly appreciated. Best, Ilya From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, July 25, 2011 4:29 PM To: galaxy-dev(a)lists.bx.psu.edu Subject: [galaxy-dev] set_matadata_externally =True I am still working on the patch to submit jobs as the actual user under SGE . I have it working for the default case but it fails for the case of set_metadata_externally = TRUE. Can someone point me to where the metadata files are created so that I can change the permissions for those files? Also, I have to addusers to the galaxy group in order for this to work because the galaxy_*.sh scripts are created as executable only by members of the galaxy group. I want to change this so that all users can execute these scripts. Any help on where in the code these scripts are created? Upon completion I will create a galaxy central fork and upload my changes to it. Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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