May 2010 - galaxy-dev - lists.galaxyproject.org

Bioscope Tools in Galaxy
by Ryan Golhar 14 May '10

14 May '10

Has anyone tried integrating ABI's Bioscope tools within Galaxy?

1 0

problem when running Histogram
by zong-pei.han＠imm.ox.ac.uk 13 May '10

13 May '10

We have problem to run Histogram, and the problem is the same for both python 2.4 and 2.5. Dataset 46: Histogram on data 16 Tool execution generated the following error message: Traceback (most recent call last): File "/wwwdata/galaxy-dist/tools/plotting/histogram.py", line 5, in from rpy import * File "/usr/lib64/python2.5/site-packages/rpy.py", line 248, in start_r_eventloop() File "/usr/lib64/python2.5/site-packages/rpy.py", line 238, in start_r_eventloop _r_thread.start() File "/usr/lib64/python2.5/threading.py", line 434, in start _start_new_thread(self.__bootstrap, ()) thread.error: can't start new thread Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib64/python2.5/site-packages/rpy.py", line 244, in stop_r_eventloop _r_thread.join() File "/usr/lib64/python2.5/threading.py", line 549, in join assert self.__started, "cannot join thread before it is started" AssertionError: cannot join thread before it is started Error in sys.exitfunc: Traceback (most recent call last): File "/usr/lib64/python2.5/atexit.py", line 24, in _run_exitfuncs func(*targs, **kargs) File "/usr/lib64/python2.5/site-packages/rpy.py", line 244, in stop_r_eventloop _r_thread.join() File "/usr/lib64/python2.5/threading.py", line 549, in join assert self.__started, "cannot join thread before it is started" AssertionError: cannot join thread before it is started

1 1

interoperabilty between Galaxy and other workflow environments
by Loraine Brillet 12 May '10

12 May '10

Dear galaxy devs, Is there any possibility (tool, script) to easily _convert a program description from a xml format into another_ (Mobyle to Galaxy, or Taverna to Galaxy for example) ? And I wonder as well how is the interoperability between these different tools for the _workflows_ (export - import). Thanks for your help, Loraine -- Loraine Brillet Service Informatique et Genomique Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29682 Roscoff Cedex tel: ++33 (0)2 98 29 25 50 fax: ++33 (0)2 98 29 23 24 email: loraine.brillet(a)sb-roscoff.fr http://www.sb-roscoff.fr http://www.sb-roscoff.fr/abims/

8 10

Problem uploading local data
by Roy Weckiewicz 11 May '10

11 May '10

I have a local galaxy installation running on OSX and have been testing it with genomes: hg18 and sacCer2. I've added these to builds.txt, and added paths to the appropriate files in alignsec.loc and faseq.loc. When I go to the upload tab in galaxy and select one of these genomes from the pull-down menu, I get the following error after execution: Error Traceback: View as: Interactive <http://localhost:8081/tool_runner/index#> | Text<http://localhost:8081/tool_runner/index#> | XML <http://localhost:8081/tool_runner/index#> (full)<http://localhost:8081/tool_runner/index#> ⇝ ValueError: too many values to unpack URL: http://localhost:8081/tool_runner/index Module weberror.evalexception.middleware:*364* in respond <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>app_iter *=* self*.* application*(*environ*,* detect_start_response*)* Module paste.debug.prints:*98* in __call__ <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>environ*,* self*.*app*)* Module paste.wsgilib:*539* in intercept_output <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>app_iter *=* application*(* environ*,* replacement_start_response*)* Module paste.recursive:*80* in __call__ <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>*return* self*.*application*( *environ*,* start_response*)* Module paste.httpexceptions:*632* in __call__ <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>*return* self*.*application*( *environ*,* start_response*)* Module galaxy.web.framework.base:*126* in __call__ <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>body *=* method*(* trans*,* * ***kwargs *)* Module galaxy.web.controllers.tool_runner:*68* in index <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>template*,* vars *=* tool*.* handle_input*(* trans*,* params*.*__dict__ *)* Module galaxy.tools:*835* in handle_input <http://localhost:8081/tool_runner/index#> view <http://localhost:8081/tool_runner/index#> >> <http://localhost:8081/tool_runner/index#>_*,* out_data *=* self*.* execute*(* trans*,* incoming*=*params *)* *ValueError: too many values to unpack* URL: http://localhost:8081/tool_runner/index File '/Library/WebServer/galaxy/galaxy-central/eggs/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/Library/WebServer/galaxy/galaxy-central/eggs/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/Library/WebServer/galaxy/galaxy-central/eggs/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/Library/WebServer/galaxy/galaxy-central/eggs/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/Library/WebServer/galaxy/galaxy-central/eggs/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/Library/WebServer/galaxy/galaxy-central/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/Library/WebServer/galaxy/galaxy-central/lib/galaxy/web/controllers/tool_runner.py', line 68 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/Library/WebServer/galaxy/galaxy-central/lib/galaxy/tools/__init__.py', line 835 in handle_input _, out_data = self.execute( trans, incoming=params ) ValueError: too many values to unpack Any idea as to why this is happening? Rgds, Roy W. -- Roy Weckiewicz Texas A&M University

2 1

Changes to builds.txt
by Nate Coraor 10 May '10

10 May '10

Folks, r3765:dd6d09de392e introduces a change to builds.txt that may cause a source control conflict if you modified this file locally. tool-data/shard/ucsc/builds.txt is consulted to populate the list of available builds you can associate a dataset with. In the past, changes to this file in our repository could cause conflicts with your local version if you had made changes to the file. To prevent this from happening in the future, we have removed builds.txt from source control and added builds.txt.sample. If you have not changed builds.txt, this should be transparent to you. If you have, you will probably get this message from Mercurial (it may differ by version): % hg update local changed tool-data/shared/ucsc/builds.txt which remote deleted use (c)hanged version or (d)elete? As explained in the message, enter 'c' to keep your version, or 'd' to remove it and allow it to be recreated from builds.txt.sample. --nate

1 0

Source control commits
by Nate Coraor 10 May '10

10 May '10

Folks, Due to the large number of commit messages that come in a burst when we move source commits from our development repository to the stable repository, we've moved these emails to a new list. To subscribe, please visit this URL: http://lists.bx.psu.edu/listinfo/galaxy-commits --nate P.S., a bunch of commits are coming in a few minutes, check the stable bitbucket[1] repository or galaxy-commits archive[2] to see these. [1] http://bitbucket.org/galaxy/galaxy-dist [2] http://lists.bx.psu.edu/pipermail/galaxy-commits/

1 0

adding tools to galaxy - restart galaxy
by Loraine Brillet 07 May '10

07 May '10

Hello, I would like to add a new tool to my local Galaxy install but I fail. I have put the script and the xml description file in the tools/ directory and modified the tool_conf.xml file. I type sh run.sh and the end of the message on the screen is : socket.error: (98, 'Address already in use') galaxy.jobs INFO 2010-05-07 11:19:20,397 sending stop signal to worker thread galaxy.jobs INFO 2010-05-07 11:19:20,397 job queue stopped galaxy.jobs.runners.local INFO 2010-05-07 11:19:20,397 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2010-05-07 11:19:20,398 local job runner stopped galaxy.jobs INFO 2010-05-07 11:19:20,398 sending stop signal to worker thread galaxy.jobs INFO 2010-05-07 11:19:20,398 job stopper stopped and the new tool was not available on the refreshed page of the browser. The script being already running , I thought that could be problem (Am I right ?) and tried "run.sh --stop-daemon", which returned me "No PID file exists in paster.pid". What is the right thing to do ? Thanks for your help, Loraine -- Loraine Brillet Service Informatique et Genomique Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29682 Roscoff Cedex tel: ++33 (0)2 98 29 25 50 fax: ++33 (0)2 98 29 23 24 email: loraine.brillet(a)sb-roscoff.fr http://www.sb-roscoff.fr http://www.sb-roscoff.fr/abims/

3 2

bwa
by Ryan Golhar 05 May '10

05 May '10

I noticed in the public site, bwa is listed as a mapping tool. Where can I download the tool files to include it in my local install? -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

2 1

Re: [galaxy-dev] [galaxy-user] MACS input format
by Steve Taylor 05 May '10

05 May '10

On 30/04/2010 15:37, Daniel Blankenberg wrote: > Hi Steve, > > The latest version in the repository and on the test server accepts bed, sam, bam, eland and elandmulti for single-end and elandmulti only for paired-end. The version currently on the main public server accepts bed, sam, and bam for single-end with paired-end not functioning. The newest version of MACs will be available on the main public server the next time it is updated. > > Strange. On our local Galaxy instance I got ERROR:root:Format "SAM" cannot be recognized! and the bowtie (SAM) format was generated from within Galaxy. Any ideas why? Steve

3 3

Workflow annotations and history peek problem
by SHAUN WEBB 05 May '10

05 May '10

Hi, I'm wondering if it would be possible to make workflow annotations visible when running a workflow, currently they are only visible when a shared workflow is viewed. We create workflows for various galaxy users and it would be useful to provide instructions next to each step where user input is required. Required input is not always clear in the context of a workflow. Also, since the last update of galaxy I am having issues with the peek view on history items. The dataset expands to show the extra information but immediately collapses again. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1