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Tophat non Sanger input
by Stephen Taylor 09 Sep '11

09 Sep '11

Hi, Is there any plans to enhance the tophat wrapper to accept non Sanger fastqs, as for bowtie? https://bitbucket.org/galaxy/galaxy-central/changeset/7a9476924daf ? Kind regards and thanks, Steve

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upload files from file system
by shashi shekhar 08 Sep '11

08 Sep '11

Hi, In my local instance of Galaxy ,I want to make change in "upload files from file system" option which is used admin. in which file i have to make changes ? i want to attach some more features in that. Regards shashi

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Automatically removing items from history
by Kempenaar, M (med) 08 Sep '11

08 Sep '11

Hello, Is it possible to let a tool in a workflow manage the users history? For instance, I have a tool that takes a variable number of user-uploaded CSV files as input and merges them into one file. Before running this tool, the user thus has a number of CSV files in the history which I would like to 'replace' with the single merged file. I was hoping that when I remove a file from disk that it would also be removed from the history, but that only results in a 'The resource could not be found.' error. Alternatively, is it possible to create a composite datafile/history item from uploaded files? In any case, I would like to remove the separately uploaded files from the users history which makes selecting files for the next step(s) easier. (this is a bit of a followup for: http://gmod.827538.n3.nabble.com/Creating-new-datatype-with-variable-number…) One other question, is there (any) documentation available on the Galaxy API or a set of example files? Thanks for your input! Regards, Marcel. De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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Server down?
by Crystal Goh 08 Sep '11

08 Sep '11

Hi, I am user of Galaxy Test. I wonder is the Galaxy Test server down these 2 days? As the Tophat and Cufflinks job running take me a lot of time to run compared to previous? Thanks. Best regards, Crystal

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API: IDs standardized
by Nate Coraor 08 Sep '11

08 Sep '11

For those of you who've been keeping up with recent posts concerning confusion over the value of IDs returned by the API, the most recent commit to galaxy-central (5994:435e3f628e7d) addresses this issue. Here's the commit message: Do away with the encoding of 'file.<id>' and 'folder.<id>' in the API. All IDs in the API, with the exception of library folders, are now just the object's real encoded id. Library folders have an 'F' prepended to the id AFTER encoding. All real IDs (including the ldda ID of library datasets) can be seen in an item's element view. Workflows started from the API using the 'ld=' src should now use the new IDs as opposed to the old 'file.<id>' IDs. So: % ./display.py key http://foo/api/libraries/ebfb8f50c6abde6d/contents Collection Members ------------------ #1: /api/libraries/ebfb8f50c6abde6d/contents/Fa799d38679e985db name: / type: folder id: Fa799d38679e985db #2: /api/libraries/ebfb8f50c6abde6d/contents/4b187121143038ff name: /1.bed type: file id: 4b187121143038ff % ./display.py key http://foo/api/libraries/ebfb8f50c6abde6d/contents/Fa799d38679e985db Member Information ------------------ genome_build: hg18 item_count: 3 description: name: api3 id: a799d38679e985db % ./display.py key http://foo/api/libraries/ebfb8f50c6abde6d/contents/4b187121143038ff Member Information ------------------ ... id: 4b187121143038ff ldda_id: 4b187121143038ff model_class: LibraryDataset In this example the LibraryDatasetDatasetAssociation id and LibraryDataset id happen to be the same, this won't usually be the case on an established server. The API's run workflow method accepts LibraryDatasetDatasetAssociation, LibraryDataset, and HistoryDatasetAssocation ids. With this latest changeset, all of these can be obtained from the API. --nate

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Galaxy egg fetching error? Mac OS X 10.7 (Lion)
by Whyte, Jeffrey 08 Sep '11

08 Sep '11

Hi, I've been having trouble running a local instance of Galaxy on a Mac Pro after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed. The error I see after running the startup script is pasted at the end of this message. Thanks in advance for any help or advice. jjw ----- [~/galaxy-dist] myuserid 10:11 AM > ./run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be fetched Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 565, in resolve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed. [~/galaxy-dist] myuserid 10:12 AM >

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Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion)
by Whyte, Jeffrey 08 Sep '11

08 Sep '11

That worked, Nate! Thank you very much. I really appreciate your efforts. Jeff ________________________________________ From: Nate Coraor [nate(a)bx.psu.edu] Sent: Wednesday, September 07, 2011 10:33 AM To: Whyte, Jeffrey Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion) Hi Jeff, Could you try: % python ./scripts/fetch_eggs.py >From the top-level galaxy-dist directory? I have just placed eggs for py2.7-macosx-10.6-intel-ucs2 on http://eggs.g2.bx.psu.edu/ --nate Whyte, Jeffrey wrote: > Thanks, Nate! Much appreciated. > Jeff > > > > On Sep 7, 2011, at 7:54 AM, Nate Coraor wrote: > > > Whyte, Jeffrey wrote: > >> Nate, > >> > >> For some reason, ~/galaxy-dist wasn't in my PATH. Here is the output when the script is run from the ~/galaxy-dist directory: > >> > >> [~/galaxy-dist] myuserid 03:50 PM > python ./scripts/get_platforms.py > >> macosx-10.6-intel-ucs2 > >> [~/galaxy-dist] myuserid 03:50 PM > > >> > >> Looks like it is set for Mac OS X 10.6 Snow Leopard instead of 10.7 Lion. (?) > > > > This is normal since OS X has binary compatibility with older releases, > > the Python distributors build for an older platform rather than each > > individual platform. > > > > I see there's now an Intel-only build for 10.6+, I'll work on this ASAP. > > > >> > >> Thanks, > >> Jeff > >> > >> > >> On Sep 6, 2011, at 10:18 AM, Nate Coraor wrote: > >> > >>> Whyte, Jeffrey wrote: > >>>> Thanks for the information, Nate. > >>>> > >>>> I installed Python as you described, and the error I get now is pasted below. I appreciate your help. > >>>> > >>>> Jeff > >>>> > >>>> [~/galaxy-dist] myuserid 03:06 PM > ./run.sh > >>>> Some eggs are out of date, attempting to fetch... > >>>> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched > >>>> Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched > >>>> pysam 0.4.2 couldn't be downloaded automatically. You can try > >>>> building it by hand with: > >>>> python scripts/scramble.py -e pysam > >>>> Fetch failed. > >>>> [~/galaxy-dist] myuserid 03:06 PM > > >>> > >>> Could you report back with the output of: > >>> > >>> % python ./scripts/get_platforms.py > >>> > >>> ? > >>> > >>> Thanks, > >>> --nate > >>> > >>>> ________________________________________ > >>>> From: Nate Coraor [nate(a)bx.psu.edu] > >>>> Sent: Friday, September 02, 2011 1:16 PM > >>>> To: Whyte, Jeffrey > >>>> Cc: galaxy-dev(a)lists.bx.psu.edu > >>>> Subject: Re: [galaxy-dev] Galaxy egg fetching error? Mac OS X 10.7 (Lion) > >>>> > >>>> Whyte, Jeffrey wrote: > >>>>> Hi, > >>>>> > >>>>> I've been having trouble running a local instance of Galaxy on a Mac Pro after upgrading to OS X 10.7 (Lion). My Python version is 2.7.1 and Mercurial is 1.9.1 for MacOS X 10.7. I don't have any MacPorts installed. > >>>>> > >>>>> The error I see after running the startup script is pasted at the end of this message. Thanks in advance for any help or advice. > >>>>> jjw > >>>> > >>>> Hi Jeffrey, > >>>> > >>>> We haven't yet gotten our dependencies up to speed on Lion. Could you > >>>> grab a copy of Python from python.org and use this? It'll install under > >>>> /Library/Frameworks/Python.framework, just add the correct bin/ > >>>> directory to the front of your $PATH and start Galaxy as normal. > >>>> > >>>> Sorry for the inconvenience, > >>>> --nate > >>>> > >>>>> > >>>>> ----- > >>>>> > >>>>> [~/galaxy-dist] myuserid 10:11 AM > ./run.sh > >>>>> Some eggs are out of date, attempting to fetch... > >>>>> Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched > >>>>> Warning: decorator (a dependent egg of sqlalchemy-migrate) cannot be fetched > >>>>> Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched > >>>>> Traceback (most recent call last): > >>>>> File "./scripts/fetch_eggs.py", line 30, in <module> > >>>>> c.resolve() # Only fetch eggs required by the config > >>>>> File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve > >>>>> egg.resolve() > >>>>> File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, in resolve > >>>>> return self.version_conflict( e.args[0], e.args[1] ) > >>>>> File "/Users/myuserid/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, in version_conflict > >>>>> r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) > >>>>> File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 565, in resolve > >>>>> raise DistributionNotFound(req) # XXX put more info here > >>>>> pkg_resources.DistributionNotFound: numpy==1.6.0 > >>>>> Fetch failed. > >>>>> [~/galaxy-dist] myuserid 10:12 AM > > >>>>> > >>>>> > >>>>> > >>>>> ___________________________________________________________ > >>>>> 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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Tool Shed problems with browse repository files?
by Peter Cock 08 Sep '11

08 Sep '11

Hi all, I've been having a few server errors and other problems browsing files for tool shed repositories, for example clicking to expand a folder sometimes gives a red exclamation icon with the text "Load error! (error)". Other times it does load but seems to merge several entries into single lines, e.g. clustalw -- rgclustal/ ---- README rgClustal_testout.fasta rgClustalw.xml ---- rgClustal_testin.fasta rgClustal_testout.log Or, clustalomega -- clustalomega/ ----- clustal-omega-1.0.2/ README test-data/ ----- hide_stderr.py rgClustalOmega.xml Could someone take a look at this please? Thanks, Peter

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Path to tool designation in tool config xml
by Timothy Wu 07 Sep '11

07 Sep '11

Hi, I'm trying the add tool tutorial at http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial . It works, but how do I designate the path of the tool if it's not dropped into the same directory as the tool config xml? Some executable may not be in the directory. Surely it couldn't possiblely be the case with external tools like BLAST, isn't it?! But looking at the BLAST config xmls I couldn't make out the difference and I didn't find any documentation on how to designate the path of the tool. Help appreciated, thank you. Timothy

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value_label tool input param attribute doesn't work as documented
by Leandro Hermida 07 Sep '11

07 Sep '11

Hi, Looking at the example on the Tool Config Syntax wiki page: Example Assume that the tool includes an input parameter named "database" which is a select list ( e.g., assume the following inputs ): Toggle line numbers<http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#> 1 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b…> <inputs> 2 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b…> <param format="tabular" name="input" type="data" label="Input stuff"/> 3 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b…> <param type="select" name="database" label="Database"> 4 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b…> <option value="alignseq.loc">*Human (hg18)*</option> 5 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b…> <option value="faseq.loc">Fly (dm3)</option> 6 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b…> </param> 7 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-4197fe3d76b…> </inputs> Assume that the user selects the first option in the $database select list. Then the following will ensure that the tool produces a tabular data set whose associated history item has the label "Blat on *Human (hg18)*". Toggle line numbers<http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#> 1 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e…> <outputs> 2 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e…> <data format="input" name="output" label="Blat on ${database.value_label}" /> 3 <http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#CA-c1ccb05e35e…> </outputs> It shows that .value_label attribute should produce the string in between the <option> tags, not the actual value. Why does this not work? When I use it it produces the value, or am I doing something wrong? regards, Leandro

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