- galaxy-dev - lists.galaxyproject.org

possible to undelete a history?
by Edward Kirton 23 Jul '11

23 Jul '11

An unfortunate user emailed me and said he accidentally deleted his histories. :(( How can I help him recover these?

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Apache Configuration for Exporting Histories and Workflows
by John Chilton 23 Jul '11

23 Jul '11

Hello All, We have Galaxy behind an apache proxy, and apache is taking care of the authentication. If I want to enable exporting workflows and histories to other galaxy instances do I just need to disable the authentication checks for locations "/history/export_archive" and "/workflow/for_direct_import"? I assume this wouldn't also open a hole that would allow unpublished workflows or histories to be accessed by others (at my institution or else wise), is this correct? Thanks for your time, -John ------------------------------------------------ John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chilton(a)msi.umn.edu

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Re: [galaxy-dev] Newer Version of Cufflinks Wrapper
by Jeremy Goecks 23 Jul '11

23 Jul '11

Ilya, A patch is fine for a one-time fix; this is easy with Mercurial: % hg diff > my_patch.patch However, if you plan to contribute to Galaxy on a regular basis, we encourage you to fork Galaxy and maintain your own Bitbucket repository. Finally, please send all emails to our mailing lists rather than individual Galaxy developers or other list members. Sending email to the mailing lists ensures that everyone can see and contribute to questions and issues; in addition, emails to mailing lists are tracked and archived so that they are available in the future. Thanks, J. On Jul 21, 2011, at 5:16 PM, Chorny, Ilya wrote: > I would be happy to share any changes that I make. By patch do you mean a diff/patch share patch or just check in the code? > > From: Jeremy Goecks [mailto:jeremy.goecks@emory.edu] > Sent: Wednesday, July 20, 2011 4:55 PM > To: Chorny, Ilya > Cc: galaxy-user-bounces(a)lists.bx.psu.edu; galaxy-dev(a)lists.bx.psu.edu > Subject: Re: [galaxy-dev] Newer Version of Cufflinks Wrapper > > Ilya, > > Despite the wrapper version numbers (which I'll update shortly to avoid further confusion), the current Cufflinks wrapper in both galaxy-central and galaxy-dist supports Cufflinks v1.0.3 However, not all new options for v1.0.3 are implemented the current wrappers; should you decide to implement additional options in the Cufflinks/compare/diff wrappers, please consider submitting a patch that we could incorporate into Galaxy. > > Best, > J. > > On Jul 21, 2011, at 1:30 AM, Chorny, Ilya wrote: > > > Has anyone produced a newer version of the cufflinks wrapper? The current wrapper is for version 0.9.1. > > Thanks, > > Ilya > > > > Ilya Chorny Ph.D. > Bioinformatics – Intern > ichorny(a)illumina.com > 858-202-4582 > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ >

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Metadata in Galaxy Tool Shed
by Lance Parsons 23 Jul '11

23 Jul '11

I recently created a new repository in the galaxy tool shed for the cutadapt tool and "imported" my old hg repository into it. However, it doesn't seem to be picking up the metadata correctly. Does this take time, or is there something I need to do to get the metadata generated correctly? Also, any suggestions on how to organize the files in the repository are welcome. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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new data type.
by Luobin Yang 23 Jul '11

23 Jul '11

Hi, I created an XML file for a tool. This tool has an Nexus input. When I click the input field of the web interface for this tool, it shows all kinds of data that I can select. How do I restrict the list to show only data in nexus format? I added a line in the registration part and the sniffer part of the datatypes_conf.xml and I also created a class called Nexus which inherits the class galaxy.datatypes.Sequence, but this doesn't solve the problem. Thanks, Luobin

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Scroll bars not present using i.e.
by Chorny, Ilya 23 Jul '11

23 Jul '11

http://test.g2.bx.psu.edu/ Cheers, Ilya Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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error reading tool from path (epigraph.xml, epigraph_test.xml, access_libraries.xml)
by Leon Mei 23 Jul '11

23 Jul '11

Dear all, I installed a local galaxy using the latest codebase yesterday. During the startup, the loading of 3 tool wrappers are failed: epigraph.xml, epigraph_test.xml, access_libraries.xml. Similar errors were reported in http://www.mail-archive.com/galaxy-dev@lists.bx.psu.edu/msg01839.html Have other people experienced the same problem? Any suggested solutions? Thanks, Leon ==== paster.log below === ... galaxy.tools DEBUG 2011-07-22 16:02:47,084 Loaded tool: hbvar 1.0.0 galaxy.tools DEBUG 2011-07-22 16:02:47,088 Loaded tool: fix_errors 1.0.0 galaxy.tools DEBUG 2011-07-22 16:02:47,089 Loading section: Send Data galaxy.tools ERROR 2011-07-22 16:02:47,089 error reading tool from path: data_destination/epigraph.xml Traceback (most recent call last): File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get' galaxy.tools ERROR 2011-07-22 16:02:47,090 error reading tool from path: data_destination/epigraph_test.xml Traceback (most recent call last): File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get' ... galaxy.tools DEBUG 2011-07-22 16:02:50,556 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2011-07-22 16:02:50,587 Loaded tool: upload1 1.1.3 galaxy.tools ERROR 2011-07-22 16:02:50,587 error reading tool from path: data_source/access_libraries.xml Traceback (most recent call last): File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 77, in load_tool tool = self.load_tool( os.path.join( self.tool_root_dir, path ) ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 169, in load_tool return ToolClass( config_file, root, self.app ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 340, in __init__ self.parse( root ) File "/opt/galaxy/prog/galaxy-2011-7-21/lib/galaxy/tools/__init__.py", line 385, in parse self.interpreter = command.get("interpreter", None) AttributeError: 'NoneType' object has no attribute 'get' ... -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231

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Where to find the toolconfig parser code?
by Samuel Lampa 23 Jul '11

23 Jul '11

Quick question to you devs, I need to find the code where the tool configs are parsed ... especially the "free-text" if-else clauses in the command-tag. Could someone point me to the file? TIA // Samuel -- System Expert / Bioinformatician SNIC-UPPMAX / SciLifeLab Uppsala Uppsala University, Sweden -------------------------------------- E-mail: samuel.lampa(a)scilifelab.uu.se Phone: +46 (0)18 - 471 1060 WWW: http://www.uppmax.uu.se Uppnex: https://www.uppnex.uu.se

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Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes missing
by Bossers, Alex 23 Jul '11

23 Jul '11

Ross, I think I don't understand what you mean. Do you mean the actual reference to the files contained in the loc file? I have all non-relative paths to the bowtie indexes (snippet below). The last column is an additional column for some plotting tools to have a sensible short name and works fine in the original location. Separators are tabs. Alex {still confused} == Part of the bowtie_indices.loc -- Bos_taurus_ensembl Bos_taurus_ensembl Bos taurus ensembl 4.0.61 /share/bowtie/indexes/Bos_taurus_ensembl BosTaurus Homo_sapiens.GRCh37 Homo_sapiens.GRCh37 Homo sapiens ensembl GRch37 /share/bowtie/indexes/Homo_sapiens.GRCh37 Human Macaca_mulatta_NCBIdraft20110405 Macaca_mulatta_NCBIdraft20110405 Macaca mulatta (rhesus monkey draft NCBI) /share/bowtie/indexes/Macaca_mulatta_NCBIdraft20110405 Macaca Mus_musculus.NCBIM37 Mus_musculus.NCBIM37 Mus musculus NCBIM37 /share/bowtie/indexes/Mus_musculus.NCBIM37 Mouse -- -----Oorspronkelijk bericht----- Van: Ross [mailto:ross.lazarus@gmail.com] Verzonden: vrijdag 22 juli 2011 15:15 Aan: Bossers, Alex Onderwerp: Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes missing If those changes invalidate your loc files, you may need to adjust them? On Fri, Jul 22, 2011 at 11:02 PM, Bossers, Alex <Alex.Bossers(a)wur.nl<mailto:Alex.Bossers@wur.nl>> wrote: > On our up-to-date galaxy_central version I have successfully moved the > database/files directory to mounted storage. After adapting the > universe_wsgi.ini it works fine after galaxy restart. > > > > Now the tool-data dir becomes bigger and bigger and I wanted to move > that to mounted storage as well. > > I moved the tool-data dir to the other location, made sure file > permissions were ok and adapted the universe_wsgi.ini tool_data_path > to match the new tool-data location. > > > > Galaxy restarts and the loc files are read (since blast recognises its > databases). However, the bowtie indexes are not read since they do not > show up in the NGS bowtie mapper for illumina..... what could be wrong? > > > > When I restore the universe_wsgi.ini it works all fine. > > I am puzzled. > > > > > > Alex > > > > > > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this and other > Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

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Per-user tools permissions
by Assaf Gordon 22 Jul '11

22 Jul '11

Hi, I've noticed a ticket on the wiki for per-user tool permissions: https://bitbucket.org/galaxy/galaxy-central/issue/269/use-galaxy-security-t… If anyone is interested, the following patch implements such thing (but requires manual code changes whenever the access needs to be changed). The method "tool_allowed_for_user()" can of course be extended/rewritten to read access permissions from file or from a database. Comments are welcomed, -gordon

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