galaxy-dev January 2014

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numpy and scipy
by David Hoover 21 Jan '14

21 Jan '14

Are numpy and scipy included with the standard python modules/eggs supplied by galaxy? David Hoover Helix Systems Staff

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casOT wrapper
by Shaun Webb 21 Jan '14

21 Jan '14

Hi, I was just wondering if anyone has put any work in to developing wrappers for casOT: http://eendb.zfgenetics.org/casot/index.php Couldn't see anything in the toolshed. If not I'll have a go myself. Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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toolshed image file location problem
by Eric Kuyt 21 Jan '14

21 Jan '14

Hi All, We are having some problems serving our toolshed images. We are using the notation below to embed images in our tools <help> tag set. .. image:: <some image file name> .. image:: $PATH_TO_IMAGES/<some image file name> The problem is, is that our galaxy instance runs on a proxy prefix while the link to the tool's help section doesn't include this prefix. example: http://galaxy/admin_toolshed/static/images/<rep_id>/<img>.png is the broken image in our help section. while the actual image is located at http://galaxy/<proxy_prefix>/admin_toolshed/static/images/<rep_id>/<img>.png Can anyone help me on this case? Thanks, Eric

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functional test errors when running behind proxy with authentication
by Luca Toldo 21 Jan '14

21 Jan '14

dear all, I am on Linux behind proxy with authentication. When I run the functional tests the following are "red" in the html output: functional.test_DNAse_flanked_genes.AnalysisDNAseHSSFlankedGenes.test_get_DNAseHSS_flanked_genes functional.test_get_data.UploadData.test_0150_upload_file functional.test_get_data.UploadData.test_0155_upload_file functional.test_get_data.UploadData.test_0160_url_paste according to my understanding all those tests are trying to get some data from the internet but are failing due to proxy with authentication. Shall I assume that my installation is now fine or shall I patch it somehow ? Will "regular users" encounter the same problems ? Thankyou for your advice.

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Re: [galaxy-dev] [galaxy-user] error:ordinary output of macs in stderr
by Bjoern Gruening 20 Jan '14

20 Jan '14

Hi Han, you can filter the output of every tool and react on it with the stdio tag in Galaxy. for more information please have a look at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C… Cheers, Bjoern > Hello, galaxy users and developers, > > I wrote a perl script conducting saturation analysis which called macs > several times. > > The tool's output was right but , > > error > An error occurred with this dataset:INFO @ Sat, 18 Jan 2014 21:46:33: > # ARGUMENTS LIST: # name > = /usr/local/galaxy-dist/database/job_working_directory/000/0.output # > format = BED # ChIP-seq file = 0.test.bed # control file = > 0.control.bed # effective genome size = 2.70e+09 # tag size = 2 > > > Tool execution generated the following error message: > > INFO @ Sat, 18 Jan 2014 21:46:33: > # ARGUMENTS LIST: > # name = /usr/local/galaxy-dist/database/job_working_directory/000/0.output > # format = BED > # ChIP-seq file = 0.test.bed > # control file = 0.control.bed > # effective genome size = 2.70e+09 > # tag size = 28 > # band width = 300 > # model fold = 16 > # pvalue cutoff = 1.00e-05 > # Ranges for calculating regional lambda are : peak_region,1000,5000,10000 > INFO @ Sat, 18 Jan 2014 21:46:33: #1 read tag files... > INFO @ Sat, 18 Jan 2014 21:46:33: #1 read treatment tags... > INFO @ Sat, 18 Jan 2014 21:46:37: #1.2 read input tags... > INFO @ Sat, 18 Jan 2014 21:46:39: #1 Background Redundant rate: 0.04 > INFO @ Sat, 18 Jan 2014 21:46:39: #1 finished! > INFO @ Sat, 18 Jan 2014 21:46:39: #2 Build Peak Model... > INFO @ Sat, 18 Jan 2014 21:46:47: #2 number of paired peaks: 11875 > INFO @ Sat, 18 Jan 2014 21:46:47: #2 finished! > INFO @ Sat, 18 Jan 2014 21:46:47: #2.2 Generate R script for model : /usr/local/galaxy-dist/database/job_working_directory/000/0.output_model.r > INFO @ Sat, 18 Jan 2014 21:46:47: #3 Call peaks... > INFO @ Sat, 18 Jan 2014 21:46:47: #3 shift treatment data > INFO @ Sat, 18 Jan 2014 21:46:47: #3 merge +/- strand of treatment data > INFO @ Sat, 18 Jan 2014 21:46:47: #3 call peak candidates > INFO @ Sat, 18 Jan 2014 21:46:48: #3 shift control data > INFO @ Sat, 18 Jan 2014 21:46:48: #3 merge +/- strand of control data > INFO @ Sat, 18 Jan 2014 21:46:48: #3 call negative peak candidates > INFO @ Sat, 18 Jan 2014 21:46:48: #3 use control data to filter peak candidates... > INFO @ Sat, 18 Jan 2014 21:46:48: #3 Finally, 2003 peaks are called! > INFO @ Sat, 18 Jan 2014 21:46:48: #3 find negative peaks by reversing treat and control > INFO @ Sat, 18 Jan 2014 21:46:49: #3 Finally, 120 peaks are called! > INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.xls > INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output bed file... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_peaks.bed > INFO @ Sat, 18 Jan 2014 21:46:49: #4 Write output xls file for negative peaks... /usr/local/galaxy-dist/database/job_working_directory/000/0.output_negative_peaks.xls > INFO @ Sat, 18 Jan 2014 21:46:49: #5 Done! Check the output files! > > > Just ordinary macs output, we see it in galaxy-macs report. The only > problem is that they're in stderr. With this error I cannot do other > works with the output of this tool. > > How can I deal with it? > > Thanks! > > > -Han > > > -------------------------------- > > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/

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Installation problems due to limited support for proxy with authentication.
by Luca Toldo 20 Jan '14

20 Jan '14

dear all, I'm trying to install galaxy locally, on a Linux Suse 11 SP1 with python 2.6 and mercurial 2.3.2. I am behind a proxy with user authentication. 1) Get the latest copy from the repository > hg clone https://bitbucket.org/galaxy/galaxy-dist/ > cd galaxy-dist > hgupdate stable after initial disconnects due to size of download, it worked well. 2) Start it up > sh run.sh > Some eggs are out of date, attempting to fetch... > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 37, in <module> > c.resolve() # Only fetch eggs required by the config > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, > in resolve > egg.resolve() > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, > in resolve > return self.version_conflict( e.args[0], e.args[1] ) > File "/home/galaxy/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 "/home/galaxy/galaxy-dist/lib/pkg_resources.py", line 565, in > resolve > raise DistributionNotFound(req) # XXX put more info here > pkg_resources.DistributionNotFound: mercurial==2.2.3 > Fetch failed. I've modified eggs.ini by modifying mercurial = 2.2.3 with mercurial = 2.3.2 I've then rerun it > sh run.sh > Some eggs are out of date, attempting to fetch... > Mako 0.4.1 couldn't be downloaded automatically. You can try > building it by hand with: > python scripts/scramble.py -e Mako > Fetch failed. I've then tried to follow scramble.py procedure however I got even more mistakes perhaps since scramble is using urllib instead of urllib3. > python scripts/scramble.py -e Mako > fetch_one(): Trying to fetch: > http://eggs.galaxyproject.org/Mako/Mako-0.4.1.tar.gz > Traceback (most recent call last): > File "scripts/scramble.py", line 50, in <module> > egg.scramble() > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 52, in > scramble > self.fetch_source() > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 112, > in fetch_source > self.source_path = self.fetch_one( urls ) > File "/home/galaxy/galaxy-dist/lib/galaxy/eggs/scramble.py", line 91, in > fetch_one > URLRetriever().retrieve( url, file + '.download' ) > File "/usr/lib64/python2.6/urllib.py", line 239, in retrieve > fp = self.open(url, data) > File "/usr/lib64/python2.6/urllib.py", line 207, in open > return getattr(self, name)(url) > File "/usr/lib64/python2.6/urllib.py", line 346, in open_http > h.endheaders() > File "/usr/lib64/python2.6/httplib.py", line 908, in endheaders > self._send_output() > File "/usr/lib64/python2.6/httplib.py", line 780, in _send_output > self.send(msg) > File "/usr/lib64/python2.6/httplib.py", line 739, in send > self.connect() > File "/usr/lib64/python2.6/httplib.py", line 720, in connect > self.timeout) > File "/usr/lib64/python2.6/socket.py", line 547, in create_connection > for res in getaddrinfo(host, port, 0, SOCK_STREAM): > IOError: [Errno socket error] [Errno -2] Name or service not known Needless to say, that wget worked fine wget http://eggs.galaxyproject.org/Mako/Mako-0.4.1.tar.gz However, I realised that it is going to give this same error message for any egg. I therefore followed the approach of downloading the eggs from a machine directly connected to the internet and it worked. I was wondering, if you have any plan to modify galaxy and making fetch_eggs supporting also proxy with authentication. thankyou and compliments. luca

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GATK2 Galaxy wrapper available, testing and help needed
by Björn Grüning 18 Jan '14

18 Jan '14

Hi all, over the last month we developed a new version of GATK2 wrappers and are now seeking for testers, users and overall feedback. We are currently targeting GATK 2.8. One of the big issues with GATK2 is the new licence. Because of that we can't install GATK2 with the wrappers, but we hope we have done it as easy as possible to plugin your local installed version. Furthermore, we made it easy to disable the 'call home feature' of GATK2 (if you have a GATK keyfile). Read more about it: https://github.com/bgruening/galaxytools/blob/master/gatk2/readme.rst The code is stored here: https://github.com/bgruening/galaxytools/tree/master/gatk2 The ToolShed wrappers can be found here: http://toolshed.g2.bx.psu.edu/view/iuc/gatk2 I would like to thank Jim Johnson, Nicola Soranzo, Dan Blankenberg and the Galaxy Team. If you like the wrappers you know what to do during the next GCC! If you have feedback or patches please let us know. Thanks, Bjoern

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DRMAA bug in galaxy-central
by Bjoern Gruening 17 Jan '14

17 Jan '14

Hi, since a few days there are frequent error messages popping up in my Galaxy log files. galaxy.jobs.runners ERROR 2014-01-17 13:11:17,094 Unhandled exception checking active jobs Traceback (most recent call last): File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 358, in monitor self.check_watched_items() File "/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 238, in check_watched_items if self.runner_params[ retry_param ] > 0: TypeError: 'RunnerParams' object has no attribute '__getitem__' Cheers, Bjoern

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Galaxy Reports link - registed users per month - does not work
by Liisa Koski 17 Jan '14

17 Jan '14

Hello, First..I love the Galaxy Reports tool...thanks so much for this. I did however come across an error when trying to few the Registered Users per month link. It would be really nice to have this working :) Thanks in advance, Liisa URL: http://domain:9001/users/registered_users_per_month Module paste.exceptions.errormiddleware:144 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.lint:170 in lint_app >> iterator = application(environ, start_response_wrapper) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.webapps.reports.controllers.users:29 in registered_users_per_month >> for row in q.execute(): Module sqlalchemy.sql.expression:2841 in execute Module sqlalchemy.engine.base:2453 in _execute_clauseelement Module sqlalchemy.engine.base:1584 in _execute_clauseelement Module sqlalchemy.engine.base:1698 in _execute_context Module sqlalchemy.engine.base:1691 in _execute_context Module sqlalchemy.engine.default:331 in do_execute Module MySQLdb.cursors:173 in execute Module MySQLdb.connections:36 in defaulterrorhandler OperationalError: (OperationalError) (1305, 'FUNCTION galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s, date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS num_users \nFROM galaxy_user GROUP BY date_trunc(%s, date(galaxy_user.create_time)) ORDER BY date DESC' ('month', 'month')

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Galaxy Australasia Workshop (GAW 2014), 24-25 March, Melbourne
by Dave Clements 17 Jan '14

17 Jan '14

Hello all, *We are pleased to announce the 1st Galaxy Australasia Workshop 2014 (GAW 2014) <https://wiki.galaxyproject.org/Events/GAW2014> will be held in Melbourne, Australia on 24 and 25th March 2014.* The Galaxy Australasia Workshop<https://wiki.galaxyproject.org/Events/GAW2014> is a great opportunity for you to participate in two full days of presentations, discussions, poster sessions, keynotes and lightning talks, all about ways of using Galaxy for high-throughput biology, imaging and other scientific applications. The workshop will also include Training Sessions taught by Galaxy developers and master users. GAW 2014 will run 24 and 25th March, immediately preceding Computational and Simulation Sciences and eResearch <http://wp.csiro.au/css/> in Melbourne. GAW 2014 will also include poster session, keynote speakers. *You should attend to:* - Present your work! - Learn best practices for deploying Galaxy, defining and installing resources, and managing and moving large datasets. - Network with others in the Galaxy community who are facing similar challenges and using Galaxy and other tools to address them. - Learn what the Galaxy Project's plans are, and contribute to Galaxy's future direction. - Learn - how to visualize your data in Galaxy and use visualization to guide your analysis (visual analytics) - how to share, publish, and reuse your analyses with Galaxy - how to perform and enable your users to perform common, yet complex, analyses using Galaxy - when and how to use Galaxy on the Cloud *Topics will potentially include:* - Image analysis and processing using Galaxy. - RNAseq/ChIPseq/Variant Calling/RNA Quality Control. - Galaxy on the Research Cloud. - CSIRO galaxy service - partnership between science and IT. - Identifying proteins from mass spec data with Galaxy. *Call For Abstracts* Participants who wish to give presentations or present posters (potentially with technical demonstrations) that showcase use of Galaxy should submit a brief one-page abstract and brief one-paragraph bio to the GAW2014 Organisers <gaw2014-org(a)groups.galaxyproject.org> *by February 15th, 2014.* Submitters will be notified by February 28th. Speakers, panelists, and poster presenters will be selected by the program committee based on relevance to symposium objectives and workshop balance. Submissions should clearly state whether they are for: poster or oral presentation. Looking forward to seeing you all in Melbourne! GAW 2014 Organising Committee<https://wiki.galaxyproject.org/Events/GAW2014#Organising_Committee> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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galaxy-dev January 2014