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

default quotas by mail domain
by Edward Kirton 09 Sep '11

09 Sep '11

with the new quotas, there's nothing to prevent a user from generating multiple accounts using assorted free email accounts. may i suggest the ability to have default quotas by mail domain? i would like to give gmail/yahoo or *.com users tiny quotas, larger quotas for *.edu, *.gov users, and largest quotas for users with our own mail domains e.g. @lbl.gov. alternatively i'd like to limit user registration by mail domain (disallow gmail, etc.). comments?

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Server Error
by Alex R Bigelow 09 Sep '11

09 Sep '11

Hi, I am a new developer interested in writing tools for Galaxy, but when I try to use the tool shed (http://toolshed.g2.bx.psu.edu) every link I click on gives me a Server Error. I have tried in both Google Chrome and Safari; does anyone know what is going on? Thanks, Alex Bigelow

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cuffcompare wrapper
by Chorny, Ilya 08 Sep '11

08 Sep '11

Hi Jeremy, The symlink in the cuffcompare wrapper was causing galaxy to crash because I run as the actual user and have to chmod the job_working directory at the end so Galaxy can clean it up. Turns out is seems like the symlink is not needed. Am I missing something. See below. Your code: for i, arg in enumerate( args ): input_file_name = "./input%i" % ( i+1 ) os.symlink( arg, input_file_name ) cmd += "%s " % input_file_name My code: for i, arg in enumerate( args ): cmd += arg Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Re: [galaxy-dev] galaxy-dev Digest, Vol 63, Issue 8
by Andrew Warren 08 Sep '11

08 Sep '11

I would also like to voice my support for this feature. I wrote a wrapper for bowtie that converts the SAM output to BAM after bowtie is finished just to avoid the hassle of letting galaxy "know" that the SAM file existed (didn't want to run Tophat). After thinking about how I would go about deleting an existing output it occurred to me that a "deleting tool" would require some extra logic since you would probably want to prevent the output port on a workflow node/tool from being connected to the input of another node if the output is going to be deleted. I was wondering if it might make sense to modify the "flagged output" feature (the asterisk) of the galaxy tools nodes to delete the non-flagged outputs instead of just hiding them? Or perhaps just mark them as deleted so they will be taken care of by the cleanup scripts? In this same line of thinking, it might make sense to have a flag for the input ports that specify that the input will be consumed/deleted after the tool has successfully run. This would address the case where you wanted to use the output of a tool before it is removed. Cheers, Andrew >I haven't had a chance to do anything on this yet, but I'll see if I can work something out in the near future.> > >-Dannon > >On Sep 7, 2011, at 9:34 PM, Glen Beane wrote: > > > On Sep 7, 2011, at 8:10 PM, Edward Kirton wrote: > >> i'm resurrecting this thread to see if there's any more support for the idea of deleting intermediate files in a workflow. i think this is an important feature to have. oftentimes a workflow creates many intermediate files no one will ever look at. and leaving it up to the user to cleanup their data files is asking too much. there's another ticket regarding allow users to still be able to preview the metadata of deleted workflow history items and together these would go together nicely. >> > > I am _very_ interested in this feature > > -- > Glen L. Beane > Senior Software Engineer > The Jackson Laboratory > (207) 288-6153 > > > ___________________________________________________________ > 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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Installation error
by IT Support 08 Sep '11

08 Sep '11

Greetings, I attempted to install Galaxy on a ROCKS 5.3 cluster. I checked out Galaxy to a location commonly accessible by all analysis nodes. I then set the path to Python 2.7 like so: export PATH=/opt/galaxy-python/python:$PATH However, executing run.sh gives me the error at the end of this message. The strange thing is that Galaxy runs fine on a CentOS 5.6 virtual machine. Any help would be much appreciated. Thanks! ----- Traceback (most recent call last): File "./scripts/paster.py", line 34, in ? command.run() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 84, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 123, in invoke exit_code = runner.run(args) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/command.py", line 218, in run result = self.command() File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 276, in command relative_to=base, global_conf=vars) File "/opt/galaxy-dist/eggs/PasteScript-1.7.3-py2.4.egg/paste/script/serve.py", line 311, in loadapp return loadapp( File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 225, in loadobj return context.create() File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 625, in create return self.object_type.invoke(self) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/loadwsgi.py", line 110, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/opt/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call val = callable(*args, **kw) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_controllers( webapp, app ) File "/opt/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_controllers module = __import__( module_name ) File "/opt/galaxy-dist/lib/galaxy/web/controllers/admin.py", line 310 link=( lambda item: (dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) if not item.default else dict( operation="Change amount", id=item.id, webapp="galaxy" )) ), -----

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Tophat non Sanger input
by Stephen Taylor 08 Sep '11

08 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 07 Sep '11

07 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 07 Sep '11

07 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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