March 2016 - galaxy-dev - lists.galaxyproject.org

Data removal after ftp import.
by Zuzanna K. Filutowska 14 Apr '16

14 Apr '16

Dear All, is there any option to not remove files that has been imported to Galaxy from FTP directory and to not remove files that haven't been imported since 3 days? -- Regards, -- Zuzanna K. Filutowska, HPC Systems Administrator Poznan Supercomputing and Networking Center Institute of Bioorganic Chemistry Polish Academy of Sciences Seize the day boys! Make your lifes extraordinary! --John Keating

2 2

Planemo test with SGE
by D K 11 Apr '16

11 Apr '16

Hi, I posted this question to biostars but didn't get an answer.... Is it possible to use "planemo test" functionality on an SGE cluster? I can correctly run a custom tool on an SGE cluster when I manually run a job through the galaxy interface. If I change the job_conf.xml so that the job is run locally, I can use "planemo test" successfully, but if I change the job_conf.xml so that Galaxy uses the SGE cluster, planemo fails: Traceback (most recent call last): File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py", line 289, in test_tool self.do_it( td ) File "/remote/home/galaxyd/galaxy-test-SGE/test/functional/test_toolbox.py", line 38, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 43, in stage_data_in_history upload_wait() File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 280, in wait while not self.__history_ready( history_id ): File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 298, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/remote/home/galaxyd/galaxy-test-SGE/test/base/interactor.py", line 361, in _state_ready raise Exception( error_msg ) Exception: History in error state. -------------------- >> begin captured stdout << --------------------- History with id 2891970512fa2d5a in error - summary of datasets in error below. -------------------------------------- | 1 - MTB_Genes.fasta (HID - NAME) | Dataset Blurb: | tool error | Dataset Info: | The cluster DRM system terminated this job | Dataset Job Standard Output: | *Standard output was empty.* | Dataset Job Standard Error: | *Standard error was empty.* | -------------------------------------- --------------------- >> end captured stdout << ---------------------- Is this a problem with my configuration or a limitation of planemo? Thanks!

2 2

2016 Galaxy Community Conference: June 25-29, Bloomington, Indiana
by Dave Clements 08 Apr '16

08 Apr '16

Hello all, Here's the official email announcement for the 2016 Galaxy Community Conference. Please redistribute to any of your communities that would benefit from attending. Also please note: * 1. Oral presentation abstracts are due March 25.* 2. The June 2016 GMOD Meeting <https://www.eventbrite.com/e/gmod-2016-community-meeting-tickets-22224544210> will be held immediately after GCC2016. Thanks, Dave C --------------- The *2016 Galaxy Community Conference *(*GCC2016*, *gcc2016.iu.edu <http://gcc2016.iu.edu/>*) features two days of presentations, discussions, poster sessions, lightning talks, computer demos, keynotes, and birds-of-a-feather meetups, *all about data-intensive biology and the tools that support it*. Keynote speaker Yoav Gilad <http://genes.uchicago.edu/directory/yoav-gilad-phd/>, a professor of human genetics at the University of Chicago, will kick-start the main conference with a discussion on the analysis of large gene regulatory data sets. Preconference events include data <https://gcc2016.iu.edu/hacks/hacks-data.php> and coding <https://gcc2016.iu.edu/hacks/hacks-coding.php> hackathons <https://gcc2016.iu.edu/hacks/index.php>, and *two days of training* <https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> in five concurrent tracks covering 26 topics. *GCC2016* will be held at *Indiana University* in Bloomington, Indiana, June 25-29, 2016. Since it started seven years ago, GCC has been a well-attended gathering of biologists, genome researchers, bioinformaticians, and others in data-intensive biomedical research around the world. Galaxy <https://galaxyproject.org/> is an open, web-based platform for data-intensive biomedical research and enables easy interactive analysis through the web on arbitrarily large data sets. The Galaxy framework is a major resource in achieving key research goals within the biological field. It provides next-generation sequencing (NGS) tools and workflows for short-read mapping, ChIP-seq, RNA-seq, metagenomics, variant analysis, visualization, and support for Galaxy in the cloud. There are hundreds of local installs, and *over 80 publicly accessible servers* around the world. *Abstract submission** for oral presentations closes March 25. *Abstract submission for posters and computer demonstrations closes May 20. *Early registration* is now open. Registration starts at less than $45/day for post-docs and students. Registering early assures you a place at the conference and also a spot in the training workshops <https://gcc16.sched.org/overview/type/Training+%E2%80%94+Any> you want to attend. You can also *book conference housing* when you register. *Registration and lodging scholarships* are available for attendees from underrepresented groups and developing countries. Thanks, and we hope to see you in Bloomington! The *GCC2016 Exec* -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 2

Galaxy Bare/Core and custom upload tool
by Suderman Keith 05 Apr '16

05 Apr '16

Dear Galaxy Team, Two questions. 1) Is there a bare-bones version of Galaxy available somewhere? That is, Galaxy with no tools pre-installed? We are creating Ansible play books for configuring Docker/Galaxy instances with our NLP tools installed. Currently we are using a fork of the Galaxy project with the bio tools removed, but this is less than ideal when we try to update to new versions of Galaxy. Alternatively, does anyone have an automated process to delete unwanted tools that we could run immediately after cloning the main Galaxy repo? 2) Is is possible to either a) modify the existing upload tool, or b) implement a new upload tool? Several options in the upload tool do not make sense in our domain (e.g. selecting a genome) and we would also like to do some post-processing to files after they have been uploaded. I've looked at the code for the existing upload tool and it seems quite tightly coupled to the Galaxy code base. I was hoping the "Downgrade upload tool" thread from a few weeks ago was going to help, but unfortunately for me (and good for the user) they found a solution that didn't involve installing a new upload tool. However, could I follow the approach suggested in that thread? I.E. go back in time and find an old upload.[py | xml] and use that as a starting point for my own custom upload tool? How far back in time would I have to go to find an upload.py that was a standalone tool? Cheers, Keith ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY

5 9

init scripts version 16.01
by Eric Kuyt 02 Apr '16

02 Apr '16

Hey guys, today I updated to the latest version of galaxy. No I noticed that because of the new virtualenv/wheel startup procedure, the init scripts as mentioned here https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28… are not working anymore. Whet is the new startup procedure? Thanks Eric Kuijt -- Central Veterinary Institute of Wageningen UR (CVI) Department of Infection Biology PO box 65, 8200 AB Lelystad, NL Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad Tel: +31-(0)320-293391 Fax: +31-(0)320-238153 E-mail: eric.kuijt(a)wur.nl Web: http://www.cvi.wur.nl

2 2

Galactic News! April Edition: GCC2016, DevOps, Hacks, events, papers, jobs, servers, hub entries, releases, tools
by Dave Clements 31 Mar '16

31 Mar '16

Hello all, The *April Galaxy News <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04>* brings more than the usual amount of *News of the Galaxy*. First, there are a plethora of events coming up around the world: - GCC2016 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#GCC2016>: - *Oral abstracts due April 8 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#GCC2016_Abstract_Deadl…>* - *Scholarship applications due May 1 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Scholarships:_Applicat…>* - Register now and save big <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#GCC2016_Early_Registra…> - Please welcome the the Indiana Health Industry Forum (IHIF) <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Sponsors> as a GCC2016 Sponsor - Two events sponsored by ELIXIR (and others) are coming up, both prominently featuring Galaxy: - Galaxy DevOps Workshop <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Galaxy_DevOps_Workshop…>, 6-7 April, Heidelberg, Germany. *And there is still space.* - Hackathon: Tools, Workflows and Workbenches <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Hackathon:_Tools.2C_Wo…>, 18-20 May, Paris, France - There is also a report from the RADSeq Tools and Workflows Hackathon <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Report:_IUC_Contributi…> held in March. - Plus 12 additional events <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Upcoming_Events> on three continents over the next three months. A lot of *new* - Papers <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#New_Papers> (86 of them, 6 highlighted) - Open positions <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Who.27s_Hiring> (10 of them) - Halogen Bonding <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#New_Public_Galaxy_Serv…> Galaxy server - Galaxy Community Hub <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Galaxy_Community_Hubs> entries (4 of them) - Releases <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Releases> (Planemo <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Planemo_0.24.0> and CloudMan <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#CloudMan_16.03>) - ToolShed Contributions <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#ToolShed_Contributions> And some other news <https://wiki.galaxyproject.org/GalaxyUpdates/2016_04#Other_News> too. Happy April, Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

1 0

Toolshed Question, In reference to https://toolshed.g2.bx.psu.edu/view/youngkim/ezbamqc/caed0168f704
by Molik, David 30 Mar '16

30 Mar '16

We're uploading a tool to the Galaxy Toolshed and were wondering about sample files: Should .loc.sample files refer to sample data ( test-data ) or should they be generalized for integration into other instances of Galaxy? Also, how should dependencies be noted? Best, Dave

2 1

file transference between different galaxy servers...
by Danilo Ceschin 30 Mar '16

30 Mar '16

hi, I have some big files uploaded at galaxy.ncgas-trinity.indiana.edu and I would like to use those file at https://usegalaxy.org/ Is there a way to transfer those files to avoid upload them again? My internet connection is very bad and it takes days just for one file. Thank in advance. sincerely yours, -- Danilo Ceschin PhD Fac. de Ciencias Agrarias IBAC - Instituto de Biotecnología Agropecuaria del Comahue Ruta 151 - Km 12,5 CP 8303 - Cinco Saltos - Río Negro Argentina

2 2

Warning: Incorrect datetime value in Galaxy 16.01
by SAPET, Frederic 30 Mar '16

30 Mar '16

Hello When I try to upload a file, I can see this error in the log file : /softs/bioinfo/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/engine/default.py:450: Warning: Incorrect datetime value: '2016-03-29 07:25:29.220Z' for column 'update_time' at row 32 On the interface, the upload job seems to be stuck. The history will never be refreshed. Otherwise, if I manually click on the "refresh history" icon, it works. The error is not shown again and my file appears in the history. Does anybody see this ? I hope it will be easy to debug because this is annoying. Thank you. Fred --- Frederic Sapet Bioinformatics Research Engineer BIOGEMMA - Upstream Genomics Group Centre de Recherche de Chappes CS 90126 63720 CHAPPES FRANCE Tel : +33 (0)4 73 67 88 54 Fax : +33 (0)4 73 67 88 99 E-mail : frederic.sapet(a)biogemma.com<mailto:frederic.sapet@biogemma.com>

2 2

Tool Visibility feature
by SAPET, Frederic 29 Mar '16

29 Mar '16

Hello I'm trying to set up this feature : https://wiki.galaxyproject.org/Admin/Config/Access%20Control it seems that some files have been moved from : lib/galaxy/tools/filters/ to lib/galaxy/tools/toolbox/filters/ by the way, when I uncomment " user_tool_filters = examples:restrict_upload_to_admins, examples:restrict_encode" in my galaxy.ini file, it does not work. When I click on "Manage your ToolBox filters" (/user/toolbox_filters?cntrller=user) in my User preferences panel, I'm facing this error : Internal Server Error Galaxy was unable to successfully complete your request URL: http://galaxy.biogemma.fr/user/toolbox_filters?cntrller=user sys.path: [ '/softs/bioinfo/galaxy-prod/eggs/Parsley-1.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Fabric-1.7.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/ssh-1.7.14-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/paramiko-1.11.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/SVGFig-1.1.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/drmaa-0.7.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Whoosh-2.4.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Beaker-1.4-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/MySQL_python-1.2.3c1_5.1.41_static-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/sqlalchemy_migrate-0.9.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Tempita-0.5.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/decorator-3.1.2-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/sqlparse-0.1.14-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/six-1.9.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Babel-1.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/pytz-2013.9-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/Mako-0.4.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/kombu-3.0.24-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/ordereddict-1.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/importlib-1.0.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/anyjson-0.3.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/PyYAML-3.10-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/WebHelpers-1.3-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/bx_python-0.7.2-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/SQLAlchemy-1.0.8-py2.6-linux-x86_64-ucs4.egg', '/softs/bioinfo/galaxy-prod/eggs/WebOb-0.8.5-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Routes-2.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/repoze.lru-0.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/amqp-1.4.6-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/wchartype-0.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/docutils-0.7-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/PasteDeploy-1.5.0-py2.6.egg', '/softs/bioinfo/galaxy-prod/eggs/Paste-1.7.5.1-py2.6.egg', '/softs/bioinfo/galaxy-prod/lib', '/usr/lib/python2.6/site-packages/pip-7.1.2-py2.6.egg', '/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg', '/usr/lib/python2.6/site-packages/bz2file-0.98-py2.6.egg', '/usr/lib64/python26.zip', '/usr/lib64/python2.6', '/usr/lib64/python2.6/plat-linux2', '/usr/lib64/python2.6/lib-tk', '/usr/lib64/python2.6/lib-old', '/usr/lib64/python2.6/lib-dynload', '/usr/lib64/python2.6/site-packages/gtk-2.0', '/usr/lib64/python2.6/site-packages', '/usr/lib/python2.6/site-packages'] Module galaxy.web.framework.middleware.error:151 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:143 in __call__ >> return self.app( environ, start_response ) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:133 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:191 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework.decorators:68 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.user:1331 in toolbox_filters >> tool_filters = get_filter_mapping( saved_user_tool_filters, trans.app.config.user_tool_filters ) Module galaxy.webapps.galaxy.controllers.user:1284 in get_filter_mapping >> module = __import__( module_name, globals(), fromlist=['temp_module'] ) ImportError: No module named examples Could you please provide me some help ? I have launched a git pull origin master before testing... Thank you. Fred

2 3