June 2011 - galaxy-dev - lists.galaxyproject.org

Update of cufflinks
by Sarah Diehl 06 Jun '11

06 Jun '11

Hello everybody, I just found out that there was a major update to cufflinks on 5/5/2011. At least for us it now makes no sense anymore to use the old version, besides the fact that the cufflinks team highly recommends upgrading. Does anybody already have new wrappers for all the cuff... tools ready? Do you know if/when the Galaxy codebase will be updated to the new cufflinks version? Best regards, Sarah

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Compatible MACS version?
by Liisa Koski 03 Jun '11

03 Jun '11

Hi, I'm trying to use macs in my local Galaxy instance but am having difficulties. I have macs 1.4.0rc2 20110214 (Valentine) installed. I get macs: error: no such option: --lambdaset I checked documentation for Galaxy Dependencies but no version is mentioned for macs ( https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies) Thanks in advance for the help, Liisa

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Blast2GO in Galaxy
by Peter Cock 03 Jun '11

03 Jun '11

Hi all, As I mentioned on Twitter, at the end of last week I wrapped Blast2GO for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See http://blast2go.org/ Currently current code is on bitbucket under my tools branch, https://bitbucket.org/peterjc/galaxy-central/src/tools/ Specifically files tools/ncbi_blast_plus/blast2go.* viewable here: https://bitbucket.org/peterjc/galaxy-central/src/tools/tools/ncbi_blast_plu… I've using a Galaxy location file, tool-data/blast2go.loc, to offer one or more Blast2GO configurations (properties files), mapping this to the -prop argument. This way you could have for example the Spanish Blast2GO server with its current database (May 2010), and a local Blast2GO database. I want to setup a local database and try this before submitting the wrapper to the Tool Shed. The input to the tool is a BLAST XML file, specifically blasting against a protein database like NR (so blastp or blastx, not blastn etc). I want to try some very large BLAST XML files to confirm b2g4pipe copes with the current BLAST+ output files - I gather there were some problems in this area in the past, so having the wrapper script fragment the XML might be a workaround. Currently the only real function of the wrapper script is to rename the output file - b2g4pipe insists on using the *.annot extension. Right now the only output is a tabular three column *.annot file, which can be loaded into the Blast2GO GUI. For analysis within Galaxy, I'm wondering about an option to split the first column (which holds the original FASTA query's identifier and any description) in two. i.e. Split at the first white space to give the FASTA identifier, and any optional description as a separate column. That would make linking/joining/filtering on the ID much easier. If anyone has any comments or feedback now, that would be welcome. Yesterday Alex Bossers indicated on Twitter that Gerrit had also been looking at this (CC'd). Regards, Peter

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SMTP auth in galaxy?
by Holger Klein 03 Jun '11

03 Jun '11

Dear all, for our galaxy setup I have to use an SMTP server which requires authentication. Since I didn't find any documentation about galaxy's capabilities in that regard, I'd like to ask you either for pointers or a hint, if and how this can be handled. For the smtp_server variable in universe_wsgi.ini I saw that people used either a hostname or the path to a sendmail binary. Is something like user:pass@smtpserver.organisation.org possible as well? Cheers, Holger -- Dr. Holger Klein Core Facility Bioinformatics Institute of Molecular Biology gGmbH (IMB) http://www.imb-mainz.de/ Tel: +49(6131) 39 21511

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history export tool loading panic
by Louise-Amélie Schmitt 03 Jun '11

03 Jun '11

Hi I just blew everything up, I have no idea why. Galaxy doesn't start anymore. When I run the run.sh script, it stops after loading the converters and just crashes. Here's the traceback: Traceback (most recent call last): File "/home/galaxy/galaxy-dev/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dev/lib/galaxy/app.py", line 52, in __init__ load_history_imp_exp_tools( self.toolbox ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/imp_exp/__init__.py", line 34, in load_history_imp_exp_tools history_exp_tool = toolbox.load_tool( tmp_name.name ) File "/home/galaxy/galaxy-dev/lib/galaxy/tools/__init__.py", line 131, in load_tool tree = util.parse_xml( config_file ) File "/home/galaxy/galaxy-dev/lib/galaxy/util/__init__.py", line 104, in parse_xml tree = ElementTree.parse(fname) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 859, in parse tree.parse(source, parser) File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 584, in parse self._root = parser.close() File "/home/galaxy/galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py", line 1251, in close self._parser.Parse("", 1) # end of data ExpatError: no element found: line 1, column 0 Exception IOError: (28, 'No space left on device') in <bound method _TemporaryFileWrapper.__del__ of <closed file '<fdopen>', mode 'w+b' at 0x8539a50>> ignored Since the message is not really self-explanatory, I have no idea as to what's gone wrong. The only thing I know is that the file referred by tmp_name.name is empty. Do you have an idea where I should be looking? I really can't relate that to anything I did recently, I just modified some parameter labels in two tools, which should be really harmless, and the display name of a reference genome, which shouldn't make any difference either. Thanks, L-A

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Error when adding datasets
by Louise-Amélie Schmitt 03 Jun '11

03 Jun '11

Hello everyone I have an issue when trying to import new datasets or when putting a dataset into a history. I saw Edward Kirton had the same problem but he got no answer: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html Here is the error message I get when clicking the "Add datasets" button in a library, in the admin's "Manage data libraries" panel: UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped URL: http://manni/galaxy/library_common/upload_library_dataset?library_id=f2db41… File '/g/funcgen/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/g/funcgen/galaxy/lib/galaxy/web/framework/middleware/remoteuser.py', line 109 in __call__ return self.app( environ, start_response ) File '/g/funcgen/galaxy/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/g/funcgen/galaxy/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/g/funcgen/galaxy/lib/galaxy/web/controllers/library_common.py', line 907 in upload_library_dataset trans.sa_session.refresh( history ) File '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py', line 127 in do return getattr(self.registry(), name)(*args, **kwargs) File '/g/funcgen/galaxy/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py', line 925 in refresh raise exc.UnmappedInstanceError(instance) UnmappedInstanceError: Class '__builtin__.NoneType' is not mapped Now when does it occur: I have two databases. One test database I created a month ago which works fine, even now. The other one I created recently which is supposed to be the final database. But the latter keeps triggering the above message, even when I drop it and create it all over again. I even tried to create a third one, all clean and new but the problem remains. I tried to trash all the eggs so Galaxy gets fresh new eggs, with no effect at all. The error's still there. If you have any clue, I'll be forever grateful. Cheers, L-A

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Updates to Galaxy Community Conference website
by Peter Cock 03 Jun '11

03 Jun '11

Hi all, I have a couple of minor suggestions for improving the website http://galaxy.psu.edu/gcc2011/Home.html First, please fill in a meaningful HTML titles since that will be used as the default caption in a bookmark, tab or window title. Second, please add a link to the presentation slides and videos, e.g. from the programme page and main page? http://wiki.g2.bx.psu.edu/GCC2011 I realise this isn't complete yet, but it is already a useful resource. Also once you have all the slides, could the links in the wiki table be made to point straight to the file? Thanks, Peter

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Conventions for tool names and descriptions
by Peter Cock 03 Jun '11

03 Jun '11

Hi all, Are there any guidelines on tool names and lengths? There is a tendency due to the way the tool name and description are run together in the left hand pane listing to write the description as an extension of the name: e.g. Name: Select Description: lines that match an expression Many of the default tool's descriptions do not make sense without the name. I brought this up in in this thread at the end of last year, about how the tool shed showed these fields: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004012.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004017.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004019.html Again based on observation, the tool names are generally up to four words, short enough to fit on one line in the left hand pane. Description lengths vary from nothing (e.g. the "Indel Analysis" tool) to over four lines (e.g. the "Cuffcompare" tool). Note the line count depends on font settings and if the user has altered the left hand pane column width. Clearly there is a balance - shorter means more tools fit on screen at once making navigation easier, longer makes it less likely the user will have to click on each tool to read its more details description to find what they are looking for. This is also an issue for browsing the tool shed - I had an email exchange with Alex about this tool of mine: Name: Filter sequences by ID Description: from a tabular file I wrote it like this so that once installed the entry in Galaxy's left hand pane reads "Filter sequences by ID from a tabular file", where I mean the ID comes from a tabular file (not the sequences). This is however ambiguous, Alex interpreted it as meaning the sequences come from a tabular file. Including the words FASTA, FASTQ, or SFF in the text would help, but also makes the tool entry in the left hand pane bigger. Are there any guidelines for desirable name/description lengths? Having a tool mock-up in the Tool Shed would help when browsing potential tools of interest (enhancement issue 565), but that isn't likely to happen in the short term: https://bitbucket.org/galaxy/galaxy-central/issue/565 Thanks, Peter

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Separate histories between localhost and 127.0.0.1
by Lewis, Brian Andrew 02 Jun '11

02 Jun '11

For some odd reason, when I try to import data using the URL http://localhost:8081 or http://localhost:8081/galaxy none of my jobs will even show up. However if I go to http://127.0.0.1 or http://127.0.0.1/galaxy the jobs run fine. Here's a snip from my httpd.conf file: RewriteEngine on RewriteRule ^/static/style/(.*) /usr/local/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /usr/local/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /usr/local/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /usr/local/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /usr/local/galaxy-dist/static/robots.txt [L] RewriteRule ^(.*) http://localhost:8081$1 [P] The host lines are commented out in my universe_wsgi.ini files, so I'm guessing they should be set to the default "localhost." ~ Brian

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how can i get all the output file names in local.py file
by shashi shekhar 02 Jun '11

02 Jun '11

Hi All, I am using standalone system for galaxy and am doing some modification in galaxy .i need the all output file names in local.py .How can i get all the output file names in local.py file. Regards shashi shekhar

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