galaxy-dev September 2012

galaxy-dev@lists.galaxyproject.org

82 participants
160 discussions

markupsafe module conflicts
by Fenglou Mao 01 Oct '12

01 Oct '12

Galaxy imported a library which already existed in the python system folder. See the error message below. /home/xxxxx/work/galaxy-dist/lib/galaxy/__init__.py:79: UserWarning: Module markupsafe was already imported from /usr/lib64/python2.6/site-packages/markupsafe/__init__.pyc, but /home/xxxxx/work/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg is being added to sys.path self.check_version_conflict() The system package is python-markupsafe-0.9.2-4.el6.x86_64 Galaxy has a newer version, it is MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg Any idea how to resolve this problem? Thanks, Fenglou

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HYPHY tools
by Julian Pradinuk 01 Oct '12

01 Oct '12

Hi all, Could someone please point me to helpful ressources for installing HYPHY in Galaxy? - I've downloaded, compiled and installed HyPhy - I've copied the contents of the installation folder to .../galaxy-dist/tool-data/HYPHY - I've symlinked HYPHYMP in that folder to HYPHY - I uncommented the print statement in /usr/local/galaxy/develop/ galaxy-dist/tools/hyphy/hyphy_nj_tree_wrapper.py and the standard output from running in Galaxy now reads: Single Alignment Analyses > Error: > Could not read command file in ExecuteAFile. > Original path: '/usr/local/galaxy/develop/galaxy-dist/tool-data/HYPHY/ > TemplateBatchFiles/chooseDistanceFormula.def'. > Expanded path: '/usr/local/galaxy/develop/galaxy-dist/tool-data/HYPHY/ > TemplateBatchFiles/chooseDistanceFormula.def' > Function call stack > 1 : ExecuteAFile from file HYPHY_BASE_DIRECTORY+" > TemplateBatchFiles"+DIRECTORY_SEPARATOR+"chooseDistanceFormula.def" using > basepath /tmp/. > Standard input redirect: > 1 : TN93 > 2 : /galaxy_data/develop/files/000/dataset_285.dat > 3 : /tmp/tmpuKVPrQ > ------- > 2 : InferTreeTopology(0) > Standard input redirect: > 1 : TN93 > 2 : /galaxy_data/develop/files/000/dataset_285.dat > 3 : /tmp/tmpuKVPrQ > ------- > 3 : ExecuteAFile from file "/tmp/tmpdu4x8_" using basepath /tmp/. reading > input from _genomeScreenOptions > {"0":"/galaxy_data/develop/files/000/dataset_260.dat", > "1":"TN93", > "2":"/galaxy_data/develop/files/000/dataset_285.dat", > "3":"/tmp/tmpuKVPrQ"} > ------- Any help would be greatly appreciated! Thanks! Julian

2 1

Coupling the output of two tools
by Robert Chase 01 Oct '12

01 Oct '12

Hello, We added batch gfPcr as a tool in galaxy by writing a wrapper. We wrote another tool in python to modify the output of this tool (we increment the starts of the intervals by 1 to make the starting intervals 1 based) and wrote a wrapper for this other tool. Is is possible to couple these tools together as a single tool by writing a xml file? -Rob

2 1

collapse FASTA
by Deepthi Theresa 28 Sep '12

28 Sep '12

Hi Galaxy team, I tried to do collapse FASTA sequences for removing the duplicate reads. but error occured due to the lowercase letters at both the ends of the sequences. Is there any option available to clean my reads? some of my reads contains hyphen too. Thanks, D. -- ---------------------------------------------------------------------------------------------------------------- Deepthi Theresa Thomas Kannanayakal 1919 University Drive NW, Apt. No. E104 T2N 4K7 Calgary, Alberta Canada Ph: (403) 483 7409, (403) 618 5956 Email: deepthitheresa(a)gmail.com

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Migrating a galaxy installation?
by Fourie Joubert 28 Sep '12

28 Sep '12

Hi Folks Our current galaxy version is pretty old (git updates are causing problems), and we are running very low on space in our filesystem which hosts /xxx/galaxy/database/files. I need to start with a clean galaxy install (possibly on a new server) on a new file system (a large Lustre volume, which is also mounted on our cluster). I do need to migrate the shared data libs, histories, workflows, etc. from the old Galaxy installation. Most of the shared data lib stuff is symlinks, which will require a change to the root path. Would it possibly be feasible to use a schema-updated copy of our current database for the new install, and do a search-and-replace procedure on the file paths in the database to deal with the new root path for the files? Anyone know which tables are involved? Any tips and advice regarding a migration of Galaxy would be really appreciated. Best regards! Fourie -- -------------- Prof Fourie Joubert Bioinformatics and Computational Biology Unit Department of Biochemistry University of Pretoria fourie.joubert@.up.ac.za http://www.bi.up.ac.za Tel. +27-12-420-5802 Fax. +27-12-420-5800 ------------------------------------------------------------------------- This message and attachments are subject to a disclaimer. Please refer to www.it.up.ac.za/documentation/governance/disclaimer/ for full details.

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Re: [galaxy-dev] Automatic installation of third party dependancies
by Greg Von Kuster 28 Sep '12

28 Sep '12

Hi Lance, What is the changeset revision that you installed? It looks like you could only have installed one of the following 3 revisions: 1:14e18dc9ed13 2:f5d08224af89 4:14bec14f4290 Since you could not have installed 3:f7a5b54a8d4f, I'm not quite sure how you could be trying to update to 4. Did you install 4 and are trying to get updates? I've tried several things but am not able to reproduce this behavior, so it's difficult to determine what may be causing the problem Greg Von Kuster On Sep 12, 2012, at 3:08 PM, Lance Parsons wrote: > I've updated my development system now, and when I try to get updates for that particular tool (htseq_count) I run into the following error. Any ideas on how I can/should fix this? Thanks. > > 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 184 in decorator > return func( self, trans, *args, **kwargs ) > File '/data/galaxy-dev/galaxy-dev/lib/galaxy/web/controllers/admin_toolshed.py', line 1469 in update_to_changeset_revision > update_repository( repo, latest_ctx_rev ) > File '/data/galaxy-dev/galaxy-dev/lib/galaxy/util/shed_util.py', line 1655 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 '4' > > > Lance Parsons wrote: >> >> Thanks Greg. I used you're updated version and added numpy as a >> separate dependency. It seems to work in my development system. I >> haven't updated my qa or production versions yet, so I can't check >> there. Perhaps you could test it and let me know if there are issues, etc. >> >> Glad I can be of help. >> >> Lance >> >> Greg Von Kuster wrote: >>> >>> Hello Lance, >>> >>> See my inline comments. >>> >>> >>> On Sep 4, 2012, at 3:15 PM, Lance Parsons wrote: >>> >>>> >>>> I've put together a tool wrapper for the htseq-count script that is part of the HTSeq python package and uploaded that to the tool shed. However, I have discovered that the tool dependancies do not install properly. There are a couple of issues that I've run into. >>>> >>>> 1) The biggest issue is the inability to set both the PYTHONPATH and PATH environment variables as part of installation. If I put two separate<action type="set_environment"> tags, then the second overwrites the first in the env.sh file. If instead, I put two<environment_variable> tags within the action, only one (the second) gets executed during installation. >>> >>> >>> The above issues have been corrected in changeset 7621:108cda898646, which is currently available only in the Galaxy central repository. There is a new Galaxy distribution scheduled to go out today, but unfortunately this changeset will not be included. From here on, Galaxy releases are tentatively scheduled for every 2 weeks, so if you don't want to pull from the Galaxy central repository, the fix should be available in the next release 2 weeks from now. >>> >>> I've slightly altered your tool_dependencies.xml file (mostly because I've implemented support for a new "make_directory" tag. It is attached below - you should updated your tool_dependencies.xml file in your htseq_count repository with this updated version. >>> >>> >>>> >>>> 2) Another issue is the inability to install Numpy as a dependancy to HTSeq. I can get Numpy to install, but it won't be in the PYTHONPATH when HTSeq is installed (or executed). >>> >>> >>> Were you attempting to install numpy as another package defined in your tool-dependencies.xml file? If so, the fixes in the above changeset should allow you to do that now since you can install it before htseq and set PYTHONPATH to point to numpy as part of the installation. >>> >>> Let me know if you need additional help or bump into further problems. The tool dependency installation components are fairly immature, so adding enhancements for new tools like yours is very valuable. >>> >>> Thanks for your help on this, >>> >>> Greg Von Kuster >>> >>> >>>> >>>> Any thoughts on how to address these issues would be appreciated. >>>> >>>> -- >>>> Lance Parsons - Scientific Programmer >>>> 134 Carl C. Icahn Laboratory >>>> Lewis-Sigler Institute for Integrative Genomics >>>> Princeton University >>>> >>>> ___________________________________________________________ >>>> 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/ >>> >>> >> >> >> -- >> Lance Parsons - Scientific Programmer >> 134 Carl C. Icahn Laboratory >> Lewis-Sigler Institute for Integrative Genomics >> Princeton University >> >> ___________________________________________________________ >> 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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Can't create custom visualization
by Liisa Koski 27 Sep '12

27 Sep '12

Hello, I'm trying to create a custom visualization in Trackster. I am doing the following steps. Visualization -> New Visualization -> Add a Custom Build I get directed to the url below: http://galaxy.ca:8080/user/dbkeys?use_panels=True But the web page says: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) My paster.log file shows the following: WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0xf070d90> paste.cookies: (<SimpleCookie: __utma='99541067.1404064366.1320847925.1320847925.1320857512.2' galaxycommunitysession='eb142648ac45b770e95464ae1d51cc6457899dd48ca7f3e61a826ece0a2b5d2a65f4ac4aabb6e5e9' galaxyreportssession='c6ca0ddb55be603a922aa045b4afae662fca8487217f2ea25e5b488dcf5d52aefac5347681c8bf98' galaxysession='c6ca0ddb55be603a67ec94afb2c9a07cafdf91af0226f4689d096411ea1bc0c1004977df81ecca90' toolshedgalaxyurl='http://martin.dnalandmarks.ca:8080/'>, '__utma=99541067.1404064366.1320847925.1320847925.1320857512.2; galaxysession=c6ca0ddb55be603a67ec94afb2c9a07cafdf91af0226f4689d096411ea1bc0c1004977df81ecca90; galaxycommunitysession=eb142648ac45b770e95464ae1d51cc6457899dd48ca7f3e61a826ece0a2b5d2a65f4ac4aabb6e5e9; toolshedgalaxyurl="http://martin.dnalandmarks.ca:8080/"; galaxyreportssession=c6ca0ddb55be603a922aa045b4afae662fca8487217f2ea25e5b488dcf5d52aefac5347681c8bf98') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0xf0702d0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x2ae44714c0d0> paste.parsed_querystring: ([('use_panels', 'True')], 'use_panels=True') 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_query_vars: (MultiDict([('use_panels', 'True')]), 'use_panels=True') wsgi process: 'Multithreaded' ------------------------------------------------------------ Any help would be much appreciated. Thanks, Liisa

2 1

ToolShed README files, was: Blast2GO local instance
by Peter Cock 27 Sep '12

27 Sep '12

On Tue, Apr 3, 2012 at 12:16 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > > On Apr 3, 2012, at 6:07 AM, Peter Cock wrote: > >> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: >>> >>> On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: >>>> >>>> Have you seen the README file that comes with the >>>> Blast2GO wrapper? Perhaps the 'install from toolshed' >>>> could be tweaked to make this kind of documentation >>>> more visible... >>> >>> If you are installing a single repository that contains a file named one of >>> (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of >>> the file will be displayed on the "tool panel section selection page". An >>> example using the antismash repository on the main tool shed is below. This >>> new feature is available in change set revision 6945:5ea04ccb61e8, which is >>> currently running on the Galaxy tool shed and our central development >>> repository. It will be available in the next Galaxy distribution. >> >> Great. In this case I've actually called the file blast2go.txt (to match >> the use of blast2go.xml and blast2go.py). I didn't want to use a >> generic name like README since there could be other tools >> installed in the same folder (this predates the auto-install system). >> Is this naming pattern common used enough to justify including in >> the Galaxy Tool Shed code for spotting a README file? > > > Since the "read me" file contains instructions for installing the tools > in the repository, would it be better to assume only 1 installation file > that includes different instructions per contained tool if necessary? > If multiple "read me" files are allowed per repository, they would all > have to be merged together with the entire content displayed on > the tool panel section selection screen anyway, so allowing only > a single file would be better. The "read me" in your blast2go > repository is named blast2go.txt, so I suppose we could expand > the read me file name list to include <repository name>.txt. I'll do this. Hi Greg, Could you include <repository name>.txt on the list of README filenames looked for by the ToolShed as you said please? I've just checked and it isn't working at the moment. e.g. blast2go, seq_rename, clinod, venn_list, ... - in fact most of my tools :( Thanks, Peter

2 5

Fwd: problem installing blast_datatypes manually
by Peter Cock 27 Sep '12

27 Sep '12

Sorry, forgot to CC the list. ---------- Forwarded message ---------- From: *Peter Cock* Date: Tuesday, September 25, 2012 Subject: [galaxy-dev] problem installing blast_datatypes manually To: Liisa Koski <liisa.koski(a)basf.com> On Tuesday, September 25, 2012, Liisa Koski wrote: > Hello, > I followed the instructions below to manually install the blast_datatypes: > > Manual Installation > =================== > > Normally you would install this via the Galaxy ToolShed, which would move > the provided blast.py file into a suitable location and process the > datatypes_conf.xml entry to be combined with your local configuration. > > However, if you really want to this should work for a manual install. Add > the following line to the datatypes_conf.xml file in the Galaxy main > folder: > > <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" > mimetype="application/xml" display_in_upload="true"/> > > Also create the file lib/galaxy/datatypes/blast.py by moving, copying or > linking > the blast.py file provided in this tar-ball. Finally add 'import blast' > near > the start of file lib/galaxy/datatypes/registry.py (after the other import > lines). > > ========================= > > I restarted my local Galaxy instance but still get this error. > > *WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype > 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no > attribute 'BlastXml'* > > > Any help would be much appreciated. > Thanks, > Liisa > The error message sounds like your XML file is using the old location of the BlastXml class (it used to be in an xml.py file, now it is in blast.py instead). Can you grep the XML file for Blast? (Use -I for case insensitive) Sadly right now our Galaxy server is offline (suspected disk failure), so I may not be able to double check what is on our machine. I'll try to have a look at work tomorrow though. (Out of interest, was there a reason you didn't use the automatic install from the ToolShed?) Regards, Peter

3 4

Problem of running of galaxy
by Chebbi Mohamed Amine 27 Sep '12

27 Sep '12

Hi Galaxy-team ! I have uploaded the latest version of Galaxy of 05/09. However when I run run.sh I have the message below and I haven't found how to fix that: "TypeError: Invalid argument(s) 'server_side_cursors' sent to create_engine(), using configuration SQLiteDialect/SingletonThreadPool/TLEngine. Please check that the keyword arguments are appropriate for this combination of components." Thank you in advance Amine

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galaxy-dev September 2012