- galaxy-dev - lists.galaxyproject.org

JBrowse on dev branch: progress
by Peter van Heusden 22 Feb '16

22 Feb '16

Hi there Eric and others I tried to install the JBrowse tool on a dev branch server running on an Ubuntu 14.04 VM. It got stuck at the package_gnu_coreutils_8_22 dependency (revision ac64dfe4b1fb) - this ended up in "Installing tool dependencies" state. If I go look at the tool details it highlights errors in package_perl_5_18 which in turn refers to errors in gnu_coreutils (just "Error" state) and then this more informative failure for perl: "tar (child): local-lib-1.008009.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now" I wonder if this is a sign of a download error? Digging a bit more I find the error "Shutting down process id 21094 because it generated no output for the defined timeout period of 3600.0 seconds." for gnu_coreutils. I'm trying to do a reinstall of the gnu_coreutils and perl packages to see if I can get further. Peter

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It would be nice to know that labels can only be lowercase in format tags
by rbrown1422＠comcast.net 20 Feb '16

20 Feb '16

Good evening, Having wasted multiple hours it would be helpful to see in the documentation that only LOWERCASE is allowed for defining unique file extensions to link specific files output by one tool as a particular input to another tool. <datatype extension="LOWER CASE ONLY-prog1_output" type="galaxy.datatypes.data:Text" sub display_in_upload="True"/> outgoing tool's xml <datatype format="LOWER CASE ONLY-prog1_output" name="output1" label="xxxx"/> Accepting tool's xml <datatype format="LOWER CASE ONLY-prog1_output" type="data" name="input1" label="xxxx" /> It would be great to know up-front the format can only be LOWER CASE -- no error message, no ignoring upper or lower and treating the same. Just failure when trying to run it.

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Bypassing Data Managers?
by Raymond Wan 19 Feb '16

19 Feb '16

Dear all, I'm a bit new at being a Galaxy administrator, so apologies for the basic question. I need to install some bowtie and bowtie2 indices. I have the indices already but came across this page: https://wiki.galaxyproject.org/Admin/DataPreparation which says the steps mentioned on that page have been replaced with Data Managers. I'm having problems with installing Data Managers (accessing ToolShed right now and some errors which I guess I need to sort out later) and was wondering if there was a way to bypass Data Managers? Are Data Managers the only way of installing reference data? With the indices already pre-calculated, can I install them without having to go through re-calculating them within Galaxy? Thank you! Ray

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18 February GalaxyAdmins Meetup: Ansible, Python Wheels
by Hans-Rudolf Hotz 19 Feb '16

19 Feb '16

Hello all, The next GalaxyAdmins online meetup is next week, on Thursday, February 18 at 5PM CET (see your local time to know when to connect: http://bit.ly/1nDGAkZ) https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2016_02_18 The featured topics are: - Automating Galaxy deployment @ artbio.fr: the pros and cons of Ansible, presented by Marius van den Beek - The Wheels on the Galaxy go round and round: Python Wheels in Galaxy, presented by Nate Coraor The meetup will use the same Adobe Connect technology used on previous calls. The 'Meeting Room Link' will be provided on the wiki page in time. It takes a couple of minutes to connect, so you are encouraged to start connecting a few minutes early. Looking forward to our first gathering in 2016 Dave C and Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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GCC2016 Registration & Lodging Scholarships
by Dave Clements 19 Feb '16

19 Feb '16

We are pleased to offer scholarships <https://docs.google.com/forms/d/1IbMoNcA6z31a8hvqjSdfQRIQ92wo-HxXvA5uk0Uiln…> for the 2016 Galaxy Community Conference <http://gcc2016.iu.edu/>, being held in Bloomington, Indiana, United States, June 25-29. Scholarships are available to students and post-docs in historically under-represented groups, and to those from or based in Low and Lower-Middle Income Economies, as defined by the World Bank <http://bit.ly/1nO82wD>. If this describes you or one of your students then we hope to receive an application. *Scholarships cover registration <http://gcc2016.iu.edu/registration> and lodging <http://gcc2016.iu.edu/location> during the GCC Meeting, and for any Training or Hackathon events the applicant chooses to attend.* Scholarships do not cover travel or other expenses. Applicants are required to 1. Either • Submit a poster and/or demo abstract <http://bit.ly/gcc2016abssub>. Or, • Submit a 200-250 word essay on how attending GCC2016 will benefit your research and career. *Poster/demo abstracts are strongly preferred.* The essay option should only be used by those who are starting their research careers. 2. Have a faculty member / PI send a letter of recommendation to community-fund(a)lists.galaxyproject.org no later than May 10 or March 27 (depending on your deadline). 3. Submit an application form <https://docs.google.com/forms/d/1IbMoNcA6z31a8hvqjSdfQRIQ92wo-HxXvA5uk0Uiln…> . 4. Have sufficient funds to cover your own travel and other expenses If you are submitting a poster or demo, please do so *before* submitting an application <https://docs.google.com/forms/d/1IbMoNcA6z31a8hvqjSdfQRIQ92wo-HxXvA5uk0Uiln…>. You also need to identify and ask a faculty member to write a letter of recommendation prior to applying. *The application deadline is May 1 for members of historically underrepresented groups and March 20 for those from Low and Lower-Middle Income Economies*. Applicants will be notified of their scholarship status no later than two weeks after the deadline. Dave Clements on behalf of the Galaxy Community Fund Board -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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copy/import shared history
by Le-Shin Wu 18 Feb '16

18 Feb '16

Hi, I’ve recently installed a new galaxy server and I found some weird behaviors of admin jobs. First, a shared history can not be copied as a new history. For example, user A shared one of his history with user B. User B can see this shared history through “histories shred with me” link, but when user B clicks “copy” of this history nothing happened. However, user B can view this history if he clicks “view” but if he then clicks “import history”, a new galaxy home page will be displayed on the center panel (as shown in the attached screenshot). Second, the administer can only delete groups but he can not purge those deleted groups. In other words, when the administer clicks the “purge” button of a deleted group, nothing will happen on this group. It still shows on the table with status as “deleted” Third, when installed the “package_fontconfig_2_11_1” through tool shed, the status of this package always shows as “installing tool dependencies”. We restarted our galaxy server several times but this message never went away (it always shows on the “monitor installing repositories” page). We really have no idea how to fix these strange behaviors and the web log file also don’t have any error message. Any suggestion? Thank you. Best LW

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Fwd: [GMOD-devel] Google Summer of Code - Open Genome Informatics group
by Dave Clements 18 Feb '16

18 Feb '16

Hello all, I know it's late in the game (I meant to email about this last week) but *Galaxy is applying to the 2016 Google Summer of Code as part of the Open Genome Informatics group*. That group includes GMOD, Reactome, Wormbase, OICR, and if we get some ideas in, Galaxy. *The application goes in on Friday, which means ideas are due by the end of Thursday* (which may be today, by the time you read this). If you have ideas, please post 'em. Details and links are below. Thanks, and again I apologize for the late notice, Dave C ---------- Forwarded message ---------- From: Robin Haw <Robin.Haw(a)oicr.on.ca> Date: Tue, Feb 16, 2016 at 1:25 PM Subject: [GMOD-devel] Google Summer of Code - Open Genome Informatics group To: "gmod-devel(a)lists.sourceforge.net" <gmod-devel(a)lists.sourceforge.net> Dear All, I’ve updated the Open Genome Informatics page: http://gmod.org/wiki/GSoC., in preparation for applying for this year’s Google Summer of Code. If you are interested in participating, please 1. Let me, Scott and Marc (cc’d) know. 2. Post your project ideas on http://gmod.org/wiki/GSOC_Project_Ideas_2016 over the next week; the application process has started. Last year’s project idea page is http://gmod.org/wiki/GSOC_Project_Ideas_2015 Scott, Marc and I will work on the application. Please take a look over the pages and provide any feedback? Questions? Please let me know! Thanks, Robin

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Error sorting tophat accepted hits BAM file by name
by Raphenya, Amogelang 18 Feb '16

18 Feb '16

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stage_data_in_history ValueError: No JSON object could be decoded
by Peter Cock 17 Feb '16

17 Feb '16

Hi all, Occasionally I've seen TravisCI tool tests fail with an exeception ValueError: No JSON object could be decoded, e.g. https://travis-ci.org/peterjc/galaxy_blast/jobs/107255016 ... galaxy.jobs INFO 2016-02-16 14:17:41,118 Collecting metrics for Job 139 galaxy.jobs DEBUG 2016-02-16 14:17:41,143 job 139 ended (finish() executed in (1049.363 ms)) galaxy.model.metadata DEBUG 2016-02-16 14:17:41,154 Cleaning up external metadata files ... ====================================================================== ERROR: NCBI BLAST+ blastn ( ncbi_blastn_wrapper ) > Test-2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py", line 291, in test_tool self.do_it( td ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/functional/test_toolbox.py", line 40, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py", line 41, in stage_data_in_history upload_wait() File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py", line 278, in wait while not self.__history_ready( history_id ): File "/home/travis/build/peterjc/galaxy_blast/galaxy-dev/test/base/interactor.py", line 297, in __history_ready history_json = self._get( "histories/%s" % history_id ).json() File "/home/travis/virtualenv/python2.6.9/lib/python2.6/site-packages/requests/models.py", line 805, in json return complexjson.loads(self.text, **kwargs) File "/opt/python/2.6.9/lib/python2.6/json/__init__.py", line 307, in loads return _default_decoder.decode(s) File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 319, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/opt/python/2.6.9/lib/python2.6/json/decoder.py", line 338, in raw_decode raise ValueError("No JSON object could be decoded") ValueError: No JSON object could be decoded -------------------- >> begin captured stdout << --------------------- ... On this run there was no sign of an SQLite locking issue. This JSON problem went away on a re-run, sadly instead the test-set failed further on with an SQLite locking problem, see: https://github.com/galaxyproject/galaxy/issues/1158#issuecomment-168714547 Does this "No JSON object could be decoded" point at a file system issue (perhaps a race condition)? From searching the email archive this exception (although not necessarily from the same area of the code) seems to occur most often where Galaxy is being used with a cluster. But here this is all running on a single TravisCI VM with the local job runner. I appreciate there probably isn't enough information here to solve this, but perhaps we need better logging here - are the JSON files simply empty for example? Regards, Peter

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Gemini installation error
by Sebastian Schaaf 16 Feb '16

16 Feb '16

Hey all, I am currently trying to install Gemini (v0.18.1) via the test toolshed. It finally fails in dependencies as 'package_gemini_0_18_1' finds dependency 'gemini' to end in error state. There the message looks like the following: --- 2016-02-11 16:34:47 (72.4 MB/s) - `Miniconda-latest-Linux-x86_64.sh' saved [25416725/25416725] Python 2.7.11 :: Continuum Analytics, Inc. Traceback (most recent call last): File "gemini_install.py", line 190, in <module> main(parser.parse_args()) File "gemini_install.py", line 80, in main gemini = install_conda_pkgs(anaconda, remotes, args) File "gemini_install.py", line 97, in install_conda_pkgs urllib.urlretrieve(remotes["requirements_conda"], filename=req_file) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 98, in urlretrieve return opener.retrieve(url, filename, reporthook, data) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 245, in retrieve fp = self.open(url, data) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 213, in open return getattr(self, name)(url) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/urllib.py", line 443, in open_https h.endheaders(data) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 1049, in endheaders self._send_output(message_body) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 893, in _send_output self.send(msg) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 855, in send self.connect() File "/home/galaxy/tool_libs/python2.7/lib/python2.7/httplib.py", line 1274, in connect server_hostname=server_hostname) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 352, in wrap_socket _context=self) File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 579, in __init__ self.do_handshake() File "/home/galaxy/tool_libs/python2.7/lib/python2.7/ssl.py", line 808, in do_handshake self._sslobj.do_handshake() IOError: [Errno socket error] [SSL: UNKNOWN_PROTOCOL] unknown protocol (_ssl.c:590) --- Some browsing at Google brought hints on three common cases where this could appear *plus* a fourth one which looks by error code pretty much what I got: http://blog.techstacks.com/2010/03/3-common-causes-of-unknown-ssl-protocol-… So, may I be right that there is a typo in an URL needed for downloading during the setup process? Or is it, according to http://stackoverflow.com/questions/10667960/python-requests-throwing-up-ssl… due to some failed SSL certificate check? Some help (or ideas for targeted checking) would be great :). Cheers, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich DKTK Munich Marchioninistr. 15, K U1 808 D-81377 Munich (Germany) Tel: +49 89 4400 77499

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