August 2012 - galaxy-dev - lists.galaxyproject.org

Changing Install Directory
by SHAUN WEBB 08 Aug '12

08 Aug '12

Hi all, I would like to change the name of the directory where my Galaxy instance is installed. What is the best way to go about this without breaking any paths/links. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Galaxy and Toolshed issues
by SHAUN WEBB 08 Aug '12

08 Aug '12

Hi, I have been trying out the latest version of Galaxy and a newly installed local toolshed and I have a few questions/suggestions/bug reports: 1. Tool Versioning: a) As I understand from the wiki, when I create a new version of a tool in a tool shed I must then install the latest version in my Galaxy instance. This then shows up as two separate tools in my tool menu. Presumably it is best to change the xml description tag to reflect the version number and make tool versions distinguishable in the Galaxy tool menu? b) Would it make more sense to have a single entry for each tool in the tool menu and a drop down to choose which version to run in the tool gui? Similar to when I try to rerun a tool that is no longer installed I get a drop down option to use a derivative of that tool if it exists. d) Say I create a workflow then install a new version of a tool within the workflow. I would like to be able to run that workflow using either version of the tool without creating a new workflow. Is this possible? To me it would make sense to again provide a drop down to select tool versions on the workflow ui just before execution. c) The toolshed interface allows me to change the name of my tool. If I do this, then go to my Galaxy admin ui and try to get updates for my tool then it fails. Does it make sense to change a tools name after it is created? Is it possible to track previous tool names to avoid this happening? e) Email alerts: I could not find an option to receive email alerts about tool updates when installing via the Galaxy admin ui. Perhaps this should be an option during installation. Running toolshed tools: I have no problems installing tools from toolsheds via Galaxy admin interface, however I can't get these tools to run. They stay Grey forever and look like this in the manage jobs table: 65 xxxx(a)xxxx.xx.ac.uk 0 minutes ago toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools/bedtools_coveragebed_cou… new None None None Do I have to set a tool runner or some other option for shed_tools? Migrating tools: I upgraded to the latest dist release of galaxy and when I restarted the server I expected to get a message about migrating freebayes tools. I didn't see this message. Will this be because I restart using --daemon? Is it advisable to therefore restart without --daemon after an upgrade to see if there are any tools to be migrated? Genome indexing: 1. I realise this is just a beta feature and it will be great when fully integrated. I tried to generate bowtie2 indexes for an installed build. I can see the job appear below the table in yellow and it contains the message "...added to the job queue to be indexed with bowtie2". However it seems to just sit there, even after restarting. Should I be able to see the job under 'manage jobs'? 2. Where are the generated indexes stored and is the .loc file automatically updated? Workflow menus: Would it be possible to categorise workflows the way we do with tools. I have a long list of workflows and it is sometimes difficult to find the one I need. I realise that workflows are user specific so this is not as easy to implement as with tools. Perhaps it would be possible to have category menus for published workflows at least? Trackster: I have noticed a few bugs with trackster in the latest release (tested on Chrome and Firefox): 1. Overview button does not work 2. If I add tracks to a group and make a composite track, then showindividual tracks again I get new menu options (filters, tool, tool parameter space visualisation). None of these seem to work and trackster often stops working after doing this. Thanks for all the effort put in to these great new features. I hope this lengthy email is helpful! Shaun Webb Edinburgh University -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Error on database_connection statement in universe_wsgi.ini file
by Kenneth Auerbach 08 Aug '12

08 Aug '12

Hello, Galaxy runs fine 'out of the box' with the default universe_wsgi.ini initialization file. But when I change the "database_connection" statement to connect to my MySql database, I get the errors below. Can you please tell what the problem is? Thanks! -Wolf. Modification to universe_wsgi.ini file: ------------------------------------ #database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock ------------------------------------- Then when I type "sh run.sh" I get this: --------- wolf@linuxmint ~/Downloads/galaxy-galaxy-dist-ec29ce8e27a1 $ sh run.sh Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/command.py", line 218, in run result = self.command() File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteScript-1.7.3-py2.6.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 224, in loadobj global_conf=global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 248, in loadcontext global_conf=global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 413, in get_context section) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 458, in _context_from_explicit value = import_string(found_expr) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/loadwsgi.py", line 18, in import_string return pkg_resources.EntryPoint.parse("x="+s).load(False) File "/home/wolf/Downloads/galaxy-galaxy-dist-ec29ce8e27a1/lib/pkg_resources.py", line 1997, in parse src ValueError: ("EntryPoint must be in 'name=module:attrs [extras]' format", 'x=galaxy.web.buildapp:app_factory\ndatabase_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock') ----------------------------

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Adding column names to output
by Batsal Devkota 07 Aug '12

07 Aug '12

Hello, I am extracting data from a database and displaying the result in tabular format. I would like to have the header in the output as column names, so that when I do 'join' I know which columns I am referring to. Currently, it only displays as 1, 2, 3. How do I assign column names to the header? Whatever columns I search in the database can be the header in my output. I tried searching around but couldn't find the solution. Thank you. Batsal.

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Galaxy with hadoop
by bluesky8640 07 Aug '12

07 Aug '12

Hi all, As we all known, Galaxy can be configured to run jobs on a cluster with PBS, i'm wondering if Galaxy can run jobs on a Hadoop cluster. Does anyone have done some work to join Galaxy with Hadoop? Thanks, -Jin 2012-08-07 bluesky8640

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Job recovery of non existing job
by Sascha Kastens 07 Aug '12

07 Aug '12

Hi all, I?m running a local instance of Galaxy and every time I start it, Galaxy tries to recover some jobs. These jobs are not running anymore and I get the following information: galaxy.jobs DEBUG 2012-08-07 10:58:08,056 (418) Working directory for job is: /mnt/sec1/bioit/galaxy_working_dir/000/418 galaxy.jobs.handler DEBUG 2012-08-07 10:58:08,089 recovering job 418 in drmaa runner galaxy.jobs.runners.drmaa DEBUG 2012-08-07 10:58:08,090 (418/277560) is still in running state, adding to the DRM queue Is there a way to clean the job handler queue? I tried to start Galaxy with ?enable_job_recovery = False? but that did not solve the problem. Cheers, Sascha

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How to configure samtools in galaxy on cluster
by michael xu 07 Aug '12

07 Aug '12

Recently, I am trying to configure our galaxy on our cluster with PBS submission. I run galaxy locally very well on the head node, but I met one issue when I tried to configure galaxy on our cluster. In universe_wsgi.ini file, I added the following entries, start_job_runners = pbs default_cluster_job_runner = pbs:/// And then I run the command to generate an egg, LIBTORQUE_DIR=/usr/lib64/libtorque python scripts/scramble.py -e pbs_python --config=universe_wsgi.ini Then I run galaxy and submitted two jobs into the PBS queue. I checked the galaxy log and PBS queue and found these two jobs were submitted successfully. But after a while, galaxy told me that the two jobs were failed. I suspected I did not modify the galaxy:tool_runners section in the universe_wsgi.ini file. The node machines cannot find the 3rd party tools. Can anyone give me some advices? Thanks a lot!

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Different User with Torque
by Wood, James, D 06 Aug '12

06 Aug '12

I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the external scripts, but I haven't yet found a way to do it with torque. Is there a solution that you could suggest? I am guessing that the pbs runner process would have to be forked and use setuid to be able to run under the user. This would be great, because it would make it easier to keep track of user time utilization.

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Galaxy output not showing on tool success, indicating job failure.
by John Patterson 06 Aug '12

06 Aug '12

Hello. I am an undergraduate working on a tool very similar to Tophat. My question is probably very basic, but I am having issues displaying the output. I am assuming is giving me the failed run boxes, even though my tool completes execution and generates its files. Note that I am not working on a cluster, as I am simply trying out galaxy with this tool. I have modified universe_wsgi.ini "cleanup_job = onsuccess" to keep the output from being deleted due to the failure. Every file that is queued up in the history pane for each run appears in the working directory after execution, and I confirm successful runs with stdout and logs. If you click on the boxes in the history pane, you can download the output files correctly. I just cannot see previews of them or see them in the middle screen. output in my tool XML is specified as follows: <data format="sam" name="alignments" label="${tool.name} on ${on_string}: alignments" from_work_dir="mapsplice_out/alignments.sam" /> where mapsplice out is a sub directory created to contain all output of my command line tool. The reason I have it contained is because it runs its own combine and clean-up jobs before it is done executing, and you are left with logs. If you do not specify 'from_work_dir' in the output, the output files are there, but if you do specify, galaxy seems to be moving them into the database. stderr prints: (also I am aware stderr causes galaxy failures, I have nothing printing to stderr) "/home/XXXX/galaxy-dist/database/files/000/dataset_387.dat is fasta format" which suggests to me that galaxy is trying to copy the contents of the output files into this particular file which is not what needs to happen. If I do not include the optional "from_work_dir" in the <data> tag I am not able to download the files that are created. On the wiki, the output tag set says that " You specify the number and type of your output files using the contained<data>tags. You must pass them to your tool executable through using line variables just like the parameters described in the previous sections." For this, I have created variables to hold the output and pass them in the command string, but my tool takes no parameters to specify output. It simply creates various output files based on the parameters passed in. However it still runs regardless. The preview I get after execution is the print to stdout (exact copy of the log) that indicate a successful run. I apologize for the length, I am just trying to give most the helpful information. If more is needed, let me know. I am running my own instance of galaxy. John P - Undergraduate Research University of Kentucky Bioniformatics

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queue question
by Zwemer, Lillian 06 Aug '12

06 Aug '12

Hi There, I'm not sure if this is the correct address to email to, so apologies in advance if I am in error. I am using the Galaxy Main (publicly available) site. I am wondering if there is a way to tell where my job is in the queue - in other words, how long it will be until my job begins to run and also ,how long until the run is done. I submitted a Bowtie paired end alignment last night (8.5.12) and the history states that my job is still waiting to run (grey). Thank you, Lillian Zwemer Lillian Zwemer, PhD Mother Infant Research Institute Tufts Medical Center The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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