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

What is the suggested way of adding ones own eggs/modules?
by Alexander Rose 29 Apr '10

29 Apr '10

Hi, I have successfully added my own datatype but the code for it has dependencies for additional Python modules. For now have just added them to eggs.ini to satisfy the dependencies. This works in general though I occasionally stumble upon problems when scrambling these modules. I wonder what is the suggested way of adding your own Python modules for use your own datatypes inside of galaxy? Thanks in advance. Alexander Rose

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id to output path query
by Steve Taylor 28 Apr '10

28 Apr '10

Hi, I was wondering what the id refers to in the in the history of the galaxy web interface. So for example: http://domain/root/edit?id=96 which key does this refer to and in which table? I am trying to construct a query which will return the (user generated) name of the output, the command that ran it and the path of the .dat file. Can any one give some pointers and/or point me to a schema diagram? Thanks a lot! Steve

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'cookie_path' settings in reports
by Assaf Gordon 27 Apr '10

27 Apr '10

Hi, I think the cookie_path settings is missing from the reports application. The setting is created in 'config.py' of the main galaxy, but not in the 'config.py' of the reports. The following patch fixes it. -gordon

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NGS peak calling: MACS
by Claudia Cattoglio 27 Apr '10

27 Apr '10

Hi, I am trying to use MACS among your NGS peak-calling tools, but I can't work it out. I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu. Is this a problem of input file format, as I suspect? Thanks, -- Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204 phone: (510) 643-3762

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das2 server
by Davide Cittaro 26 Apr '10

26 Apr '10

Hi all, is it possible to configure galaxy to get data from a das2 server? d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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problem with getting the tables up in Profile Annotations
by CHAN Chee Seng 23 Apr '10

23 Apr '10

Hi, I have configured and built my own galaxy server. I have set up most of the genome databases but I have a problem with the getting the "Tables to Use" to be displayed on the web interface. I have looked at the following files. 1. annotation_profiler_options.xml 2. annotation_profiler_valid_builds.txt I did not change the annotation_profiler_options.xml file (used as is) and annotation_profiler_valid_builds.txt contains just one line, hg18 which is fine since I am starting with human. Where do I specify the location of my hg18? Please let me know if you need more information. Thanks for your help. Best regards, Chee Seng, Chan Genome Institute of Singapore 60 Biopolis Street, Genome #02-01 Singapore 138672 DID 64788065 ------------------------------- This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you. -------------------------------

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NGS peak calling: MACS
by Claudia Cattoglio 22 Apr '10

22 Apr '10

Hi, I am trying to use MACS among your NGS peak-calling tools, but I can't work it out. I have ELAND files; what should I specify as a file format when uploading them? There is no ELAND format in the 'upload file' window. If I choose BED as a format, after running MACS I get no results (empty) and a Strand Format Error message, although I am sure the strand information in my ELAND file is correct (9th column, F or R). If I choose TABULAR, instead, my files are not even visualized in the MACS dropdown menu. Is this a problem of input file format, as I suspect? Thanks, Claudia Cattoglio, PhD Tjian Lab University of California, Berkeley Department of Molecular & Cell Biology 16 Barker Hall # 3204 Berkeley, CA 94720-3204 phone: (510) 643-3762

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any plans to incorporate GSAssembler into Galaxy?
by Kevin Silverstein 21 Apr '10

21 Apr '10

Hi all, I was wondering if anyone has plans to incorporate GSAssembler for Roche 454 sequence assembly? If no one else is doing this, I will try my hand at it over the next couple months since I need this for my processing pipeline. But, obviously, if this is already in the works and will be done over the next two months horizon, there is no point in my reinventing the wheel. Thanks, Kevin

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Galaxy update problem
by Martin Paradesi 19 Apr '10

19 Apr '10

Hello, We have been running a local mirror of Galaxy on our cluster for few months now. Recently, I went ahead and updated the local repository using "hg pull -u". After attempting to run the latest version, I found out that SGE was updated to 6.2u5 (from 6.2u3). We compiled the DRMAA_python egg for Galaxy, but unfortunately we are unable to access it over the browser. The problem is that ToolRunner controller fails (as shown below) and Galaxy is not served via http. Here's the log: galaxy.jobs INFO 2010-04-09 13:19:28,003 job stopper started galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,056 Enabling 'admin' controller, class: Admin galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,063 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,265 Enabling 'cloud' controller, class: CloudController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,337 Enabling 'dataset' controller, class: DatasetInterface galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,342 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,354 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,367 Enabling 'history' controller, class: HistoryController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,371 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,376 Enabling 'library_admin' controller, class: LibraryAdmin galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,398 Enabling 'library_common' controller, class: LibraryCommon galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,402 Enabling 'mobile' controller, class: Mobile galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,407 Enabling 'page' controller, class: PageController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,411 Enabling 'requests' controller, class: Requests galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,440 Enabling 'requests_admin' controller, class: RequestsAdmin galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,445 Enabling 'root' controller, class: RootController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,449 Enabling 'tag' controller, class: TagsController galaxy.web.framework.base DEBUG 2010-04-09 13:19:28,453 Enabling 'tool_runner' controller, class: ToolRunner Traceback (most recent call last): File "./scripts/paster.py", line 34, in <module> command.run() File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/command.py", line 218, in run result = self.command() File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/LOCATION/galaxy/eggs/PasteScript-1.7.3-py2.5.egg/paste/script/serve.py", line 313, in loadapp **kw) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 188, in invoke filtered = context.next_context.create() File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/LOCATION/galaxy/eggs/PasteDeploy-1.3.3-py2.5.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/LOCATION/galaxy/lib/galaxy/web/buildapp.py", line 69, in app_factory add_controllers( webapp, app ) File "/LOCATION/galaxy/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/LOCATION/galaxy/lib/galaxy/web/controllers/tracks.py", line 27, in <module> from galaxy.visualization.tracks.data.bam import BamDataProvider File "/LOCATION/galaxy/lib/galaxy/visualization/tracks/data/bam.py", line 7, in <module> from pysam import csamtools File "/usr/lib/python-2.5.2/lib/python2.5/site-packages/PIL/__init__.py", line 1, in <module> # File "build/bdist.linux-x86_64-ucs2/egg/pysam/csamtools.py", line 7, in <module> File "build/bdist.linux-x86_64-ucs2/egg/pysam/csamtools.py", line 6, in __bootstrap__ ImportError: /HOME_LOCATION/.python-eggs/pysam-0.1.1_kanwei_90e03180969d-py2.5-linux-x86_64-ucs2.egg-tmp/pysam/csamtools.so: undefined symbol: deflateSetHeader Your help will be greatly appreciated. Thanks, Martin

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Problems with lims
by nsfox＠uwaterloo.ca 16 Apr '10

16 Apr '10

Hi, I just updated my galaxy instance and there is a few things that aren't working. 1. Whenever I try to transfer a file from a sequencing request I am getting the error Error.The user1(a)example.org user could not login to Galaxy 2. one of the update emails was "lims: required fields of samples are now enforced by submission" but I still don't seem to have this functionality 3. When importing the form fields from a csv file the fields are not being assigned to the grid level that they are specified for. This was true before I updated the instance. Let me know if you have any ideas for me to fix this issues. Thanks, Natalie

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