March 2013 - galaxy-dev - lists.galaxyproject.org

Serving Galaxy behind apache mod_security
by Vipin TS 12 Mar '13

12 Mar '13

Hello members, On my new server machine I have configured apache server along with mod_security. Now I would like to place my Galaxy installation behind apache and is there any detailed explanation to describes the steps. I am following the galaxy wiki page<http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy#> and it is failing to invoke the page. Please share if you have an experience on the same. thanks in advance, --/Vipin

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Error Report contains STDERR from different job
by Eric Enns 12 Mar '13

12 Mar '13

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Updating help text for a tool shed repository
by Lance Parsons 11 Mar '13

11 Mar '13

I recently updated the htseq-count tool in the Galaxy toolshed to version 0.3. This version has some functional changes and thus the tool version was incremented. I installed this new version of the tool in my local Galaxy instance. However, I realized later that I missed updating one part of the help text. Today I fixed that text (but left the tool version the same), tarred up the file, and uploaded it to the toolshed. I then attempted to "Get Updates" from my local Galaxy instances for that tool got the following error: URL: http://galaxy-dev.princeton.edu/admin_toolshed/update_to_changeset_revision… File '/data/galaxy-dev/galaxy-dev/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/middleware/remoteuser.py', line 91 in __call__ return self.app( environ, start_response ) File '/data/galaxy-dev/galaxy-dev/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 206 in decorator return func( self, trans, *args, **kwargs ) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 1677 in update_to_changeset_revision update_repository( repo, latest_ctx_rev ) File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util_common.py', line 1428 in update_repository rev=ctx_rev ) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/commands.py', line 5661 in update rev = scmutil.revsingle(repo, rev, rev).rev() File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 515 in revsingle l = revrange(repo, [revspec]) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/scmutil.py', line 588 in revrange for r in m(repo, range(len(repo))): File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 1414 in mfunc return getset(repo, subset, tree) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 156 in getset return methods[x[0]](repo, subset, *x[1:]) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 171 in symbolset return stringset(repo, subset, x) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/revset.py', line 161 in stringset x = repo[x].rev() File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/localrepo.py', line 235 in __getitem__ return context.changectx(self, changeid) File '/data/galaxy-dev/galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs2.egg/mercurial/context.py', line 103 in __init__ _("unknown revision '%s'") % changeid) RepoLookupError: unknown revision '11' I believe this is because the revision I have installed (10) is not longer considered a valid revision by the toolshed (I presume since it is an older revision of with the same tool version). Any help would be appreciated. Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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How to Clean up Old Data
by greg 11 Mar '13

11 Mar '13

I'm trying to figure out how to reduce the data stored on the galaxy server. I came across this page and it looks like data will get deleted if the history element gets deleted but I can't tell if this happens automatically or if I need to cron these scripts: http://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20… Is there anything else I can do to clean up unused data? Also is there a way a user can keep her history around as a record of what was done and be able to rerun it later, but still delete the actual data? Thanks, Greg

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Server Error when creating Quota
by greg 11 Mar '13

11 Mar '13

My goal is that no user can upload or create a total of more than 100 gb. So I tried following the instructions here to set up a quota: http://wiki.galaxyproject.org/Admin/Disk%20Quotas I turned on these two things in universe_wsgi.ini: enable_quotas = True allow_user_dataset_purge = True And then tried to set up a quota like this: http://snag.gy/cf4CF.jpg When I clicked save i got a server error. I see this in the galaxy log file: WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x858b8d0> paste.cookies: (<SimpleCookie: galaxysession='040ae2dcc0761ad6d57d3a6c430f4cfc5d1d179e714a38e8623d7c662c791cc00a39bc01fe396534'>, 'galaxysession=040ae2dcc0761ad6d57d3a6c430f4cfc5d1d179e714a38e8623d7c662c791cc00a39bc01fe396534') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x858b550> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x2265950> paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_post_vars: (MultiDict([('name', 'General'), ('description', 'General User Quota'), ('amount', '100 gb'), ('operation', '='), ('default', 'registered'), ('create_quota_button', 'Save')]), <FakeCGIBody at 7f3c3ce18950 viewing MultiDict([('na...e')])>) webob._parsed_query_vars: (MultiDict([]), '') wsgi process: 'Multithreaded'

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Creating customized galaxy version for individual users
by Akshay Choche 10 Mar '13

10 Mar '13

Hello All, Is it possible to create a customized view of Galaxy server for individual user? To elaborate my question consider an example I have two users User A and User B, and I have deployed a new Galaxy server at http://customgalaxy.edu, User A and User B have accounts on this server. Is it possible to customized this version of Galaxy on user level (i.e., user A can have his own set of tools and user B can have his own set of tools, there may be some tools that only userA can access which user B can't) Thanks, -Akshay Choche

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Tool Shed examples defining datatype conversion
by Peter Cock 10 Mar '13

10 Mar '13

Hello all, I'd like to define 'blastxml' to 'tabular' conversion within Galaxy so that this can be used automatically (e.g. Tools expecting just tabular data would have converted BLAST XML files listed in the drop down). The functionality to do this exists in my Python tool 'blastxml_to_tabular' currently in the 'ncbi_blast_plus' repository, which might have to move into 'blast_datatypes' for this to work. http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus http://toolshed.g2.bx.psu.edu/view/devteam/blast_datatypes I've skimmed over the instructions here, but would like to look at a couple of real examples to make sure I've understood: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013434.html Are there any good examples of 3rd party Galaxy datatypes defining conversion like this? Thanks, Peter

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Re: [galaxy-dev] API - Status 403 Forbidden
by Rob Leclerc 08 Mar '13

08 Mar '13

Hi John, Thanks! I restarted the server, regenerated the API key, and can confirm that it's now working. As you mentioned, it's possible that I was missing a value on the end of the API key and was caught by the bug which allowed me to check find histories when I was logged out. Cheers! Rob On Fri, Mar 8, 2013 at 9:33 AM, John Chilton <chil0060(a)umn.edu> wrote: > I can confirm this is a Galaxy bug. Steps to reproduce: > > - Log into clean galaxy. > - Create an API key. > - Logout > - Got to localhost:8080/api/histories > > You should get a 403 and don't. > > This doesn't explain why the API isn't working for you, my best guess > would be the key is off by a character or you created a new one and > overwrote that one maybe. I think your instinct to try to diagnose > this outside of blend4j is a good one, if you can get the API working > without a browser session (perhaps from wget or curl) then I am > confident the blend4j part will work (or at least we can get it to). > > -John > > On Thu, Mar 7, 2013 at 9:09 PM, Rob Leclerc <robert.leclerc(a)gmail.com> > wrote: > > I'm trying to use the blend4j to access the Galaxy API, but I'm getting a > > 403 error, however when I pass the same request string through my > browser I > > get a json response (Status 200). > > > > //Here is the URL string being passed in both cases: > > http://localhost:8080/api/histories?key=c5954f0e726e52da297cdad5ad4aa249 > > > > > > //Below are the Galaxy logs emitted on my localhost: > > 127.0.0.1 - - [07/Mar/2013:21:12:01 -0400] "GET > > /api/histories?key=c5954f0e726e52da297cdad5ad4aa249 HTTP/1.1" 200 - "-" > > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/537.22 > (KHTML, > > like Gecko) Chrome/25.0.1364.155 Safari/537.22" > > > > 127.0.0.1 - - [07/Mar/2013:21:12:24 -0400] "GET > > /api/histories?key=c5954f0e726e52da297cdad5ad4aa249 HTTP/1.1" 403 - "-" > > "Java/1.6.0_41" > > > > > > I'm not sure if this is related or not, because I can logout in my > browser > > and still hit the local server without getting a 403, but how do I login > > (and logout) through the API to set up a session because I assume that > the > > API key is only valid for the logged in user? Is there an API request for > > the login? > > > > > > > > > > Cheers, > > Rob > > > > > > ___________________________________________________________ > > 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/ > -- Rob Leclerc, PhD <http://www.linkedin.com/in/robleclerc> <https://twitter.com/#!/robleclerc> P: (US) +1-(917)-873-3037 P: (Shanghai) +86-1-(861)-612-5469 Personal Email: rob.leclerc(a)aya.yale.edu

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Reminder: Galaxy Main & Test Server downtime for hardware relocation Thursday, March 14, 2013
by Jennifer Jackson 08 Mar '13

08 Mar '13

Original Notice Date: Thursday, March 7, 2013 Reminder NoticeDate: Friday, March 8, 2013 Greetings Galaxy *Main* & *Test* Users, The *Galaxy* *Public* *Main Galaxy Server* <http://wiki.galaxyproject.org/Main> at *http://main.g2.bx.psu.edu* (/usegalaxy.org/) and *Test Galaxy Server <http://wiki.galaxyproject.org/Test>* at *http://test.g2.bx.psu.edu* will be *down on Thursday, March 14, while the team _/relocates core hardware /to a new server room_*. Please note that_/jobs running at the time of the shutdown may be terminated/_. Once the move is complete, any terminated jobs can be easily restarted using the "re-run" function. dataset re-run The /yellow banner on //*Main*//and //*Test*//will provide updates/ (when the servers are up) as well our *@galaxyproject Twitter* posts. Don't use Twitter? See our *Twitter Wiki <http://wiki.galaxyproject.org/Galaxy%20on%20Twitter>*. *Galaxy's **Tool Shed <http://toolshed.g2.bx.psu.edu>**, **GalaxyProject.org <http://wiki.galaxyproject.org>**Wiki, and **Mailing list <http://wiki.galaxyproject.org/MailingLists>**services* will be /*unaffected*/ during this time. /Thanks for using Galaxy!!/ Galaxy team

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BioBlend: Problem Running Example file
by Rob Leclerc 08 Mar '13

08 Mar '13

I had trouble running blend4j, so I tried to jump into python (a language I have little experience with). I tried running the example run_import_workflow.py *% python run_imported_workflow.py http://localhost:80808c25bc83f6f9e4001dd21eb7b64f063f * but I get an error: Initiating Galaxy connection Importing workflow Creating data library 'Imported data for API demo' Traceback (most recent call last): File "run_imported_workflow.py", line 53, in <module> library_dict = gi.libraries.create_library(library_name) File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/libraries/__init__.py", line 27, in create_library File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/client.py", line 53, in _post File "build/bdist.macosx-10.6-intel/egg/bioblend/galaxy/__init__.py", line 132, in make_post_request File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/requests-1.1.0-py2.7.egg/requests/models.py", line 604, in json return json.loads(self.text or self.content) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/__init__.py", line 454, in loads return _default_decoder.decode(s) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py", line 374, in decode obj, end = self.raw_decode(s) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/simplejson-3.1.0-py2.7-macosx-10.6-intel.egg/simplejson/decoder.py", line 393, in raw_decode return self.scan_once(s, idx=_w(s, idx).end()) simplejson.scanner.JSONDecodeError: Expecting value: line 1 column 1 (char 0) Is there anything I am missing from the stock configuration which would cause this not to run out of the box? Cheers, Rob

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