November 2015 - galaxy-dev - lists.galaxyproject.org

IUC Contribution Fest - Metagenomics Tools and Workflows
by Björn Grüning 30 Nov '15

30 Nov '15

Hi everyone, I'm ready to start the 2nd IUC Contribution Fest! Please feel free to join our Hangout: https://hangouts.google.com/call/iems2ffkpd4s7cyjoq4mi3hgwma our IRC channel: https://wiki.galaxyproject.org/News/IRCPublicLogProposal and add yourself to the map! https://www.google.com/maps/d/edit?mid=zQipez5uCQ8I.khoUIhze9Fek&usp More information is here: https://github.com/galaxyproject/tools-iuc/issues/299 I'm excited! Bjoern

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Bx-python and numpy eggs
by Jose Juan Almagro Armenteros 27 Nov '15

27 Nov '15

Hello, I am in the master branch and I recently pull all the changes to my local Galaxy. However, when I run one tool I obtained this error: Fatal error: Matched on Error: Traceback (most recent call last): File "/steno-internal/projects/galaxy/galaxy-dist/database/job_working_directory/024/24973/set_metadata_GULyCa.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 27, in <module> import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/model/mapping.py", line 21, in <module> from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/model/custom_types.py", line 15, in <module> from galaxy import app File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/app.py", line 14, in <module> from galaxy.visualization.data_providers.registry import DataProviderRegistry File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py", line 2, in <module> from galaxy.visualization.data_providers import genome File "/steno-internal/projects/galaxy/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py", line 16, in <module> from bx.bbi.bigbed_file import BigBedFile File "bigbed_file.pyx", line 1, in init bx.bbi.bigbed_file (lib/bx/bbi/bigbed_file.c:6272) File "numpy.pxd", line 155, in init bx.bbi.bbi_file (lib/bx/bbi/bbi_file.c:12669) ValueError: numpy.dtype has the wrong size, try recompiling I suppose there is a problem with the bx-python or numpy egg but I am not really sure if is this. I run check_eggs.py and it did nothing and I also try to update numpy for the system, which didn't work neither. Do you know which numpy should I recompile in order to get this to work? Regards, Jose

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Potential Hackathon proposal: RADSeq
by Tiago Antao 27 Nov '15

27 Nov '15

Dear all, This is an email to inquire about the potential community interest in having a RADSeq hackathon. There has been quite some interest in analyzing RADSeq with Galaxy. As far as I know there are essentially only two tools dedicated to this, wrapping stacks and prada. I have been exchanging emails with the authors of the stacks tool (Yvan is Cced here) and they seem to have interest in pursuing this also. Where I am based now, we have quite a few RADSeq users that can advise on needs of the RADSeq community (obviously if others have any ideas, those would be most welcome). We also have good connections to some of the researchers involved with creating the technology, whom I believe could provide some advice on what we need to implement. RADSeq is a cheap sequencing technology that is used by many resource-limited groups and they would potentially benefit a lot from easy-to-use galaxy tools. Any interest in this? Tiago

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RAD-Seq Hackathon: Doodle pool
by Tiago Antao 27 Nov '15

27 Nov '15

Hi, I have created a doodle pool for the Hackathon: http://doodle.com/poll/hcc83a4yzgnecq4w It spawns 2-days across the month of March (Starting on Mondays or Thrusdays). It has the If-Need-Be option. A note (probably to Yvan and maybe others): Note that this doodle is only going out to people on the galaxy-dev mailing. Feel free to forward this to anyone else that you might think may be interested. Thanks, Tiago

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Re: [galaxy-dev] tool data_column param issue under workflow mode
by Christian Brenninkmeijer 25 Nov '15

25 Nov '15

Hi If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs so the data appears in one column. This is especially the case for tab separated files that do not have row names and therefore the same number of tabs in the header row as the next row. Manually change the type to tabular which will solve the problem. One possible solution which add a stricter csv sniff method is in: https://github.com/galaxyproject/galaxy/pull/1156 regards Christian University of Manchester ________________________________ From: Christian Brenninkmeijer Sent: Wednesday, November 25, 2015 9:23 AM To: FGiacomoni INRA Subject: RE: [galaxy-dev] tool data_column param issue under workflow mode Hi If you load a tabular table with type auto there is a possibility that it incorrectly sniffed as a csv file. With type csv the columns are split on commas and not tabs. This is especially the case for tab separated files that do not have row names and therefor the same number of tabs in the header row as the next row. Manually change the type to tabular which will solve the problem. One possible solution which add a stricter csv sniff is in: https://github.com/galaxyproject/galaxy/pull/1156 regards Christian ________________________________ From: galaxy-dev [galaxy-dev-bounces(a)lists.galaxyproject.org] on behalf of FGiacomoni INRA [franck.giacomoni(a)clermont.inra.fr] Sent: Tuesday, November 24, 2015 2:16 PM To: galaxy-dev(a)lists.galaxyproject.org Subject: [galaxy-dev] tool data_column param issue under workflow mode Dears, We observed this issue under galaxy release 15.07. Tools with a param tag and type="data_column" in their xml file are impossible to set on a workflow "run" mode. The value of the column stay at "column 1" or void even if your tabular file has more than one column. The setting of the tool is ok in the "analyze data" mode : you can change the value of the column. We tested this issue with home made tools but also with Merge Columns (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. and we detected the issue on the galaxy main instance too... Any idea ? Thanks Marion & Franck

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tool data_column param issue under workflow mode
by FGiacomoni INRA 24 Nov '15

24 Nov '15

Dears, We observed this issue under galaxy release 15.07. Tools with a param tag and type="data_column" in their xml file are impossible to set on a workflow "run" mode. The value of the column stay at "column 1" or void even if your tabular file has more than one column. The setting of the tool is ok in the "analyze data" mode : you can change the value of the column. We tested this issue with home made tools but also with Merge Columns (version 1.0.1) tool - "text manipulation" section on our Galaxy instance. and we detected the issue on the galaxy main instance too... Any idea ? Thanks Marion & Franck

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Unable to up Planemo against latest dev
by Christian Brenninkmeijer 23 Nov '15

23 Nov '15

Hi All, I am unable to run Planemo against the latest dev branch. 1. import twill error I was able to fix this by adding to requirements.txt twill==1.8.0 lxml==3.5.0 cssselect==0.9.1 But then I get functional_tests.py: error: no such option: --with-nosehtml functional_tests.py ERROR 2015-11-20 09:57:23,066 Failure running tests Traceback (most recent call last): File "./scripts/functional_tests.py", line 494, in main success = _run_functional_test( ) File "./scripts/functional_tests.py", line 454, in _run_functional_test test_config.configure( sys.argv ) File "/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/nose/config.py", line 281, in configure options, args = self._parseArgs(argv, cfg_files) File "/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/nose/config.py", line 269, in _parseArgs return parser.parseArgsAndConfigFiles(argv[1:], cfg_files) File "/home/christian/galaxy_new/.venv/local/lib/python2.7/site-packages/nose/config.py", line 138, in parseArgsAndConfigFiles return self._parser.parse_args(args, values) File "/usr/lib/python2.7/optparse.py", line 1402, in parse_args self.error(str(err)) File "/usr/lib/python2.7/optparse.py", line 1584, in error self.exit(2, "%s: error: %s\n" % (self.get_prog_name(), msg)) File "/usr/lib/python2.7/optparse.py", line 1574, in exit sys.exit(status) SystemExit: 2 Christian University of Manchester

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Clustered heatmap bug?
by Tiago Antao 20 Nov '15

20 Nov '15

Hi, One of my users is trying to use the clustered heatmap feature and we are getting the following error: /data/homes/galaxy/galaxy/dependencies/R/3.0.3/iuc/package_r_3_0_3/a8438aa1207c/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.1: cannot open shared object file: No such file or directory If I understand well, this is a bug on Galaxy as the library should be bundled with the dependency? In any case libgfortran1 seems to be very very old, the proper dependency maybe is libgfortran3... Tiago

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Re: [galaxy-dev] Error installing tools from toolshed
by Nicola Soranzo 20 Nov '15

20 Nov '15

Hi Scott, please always reply to the mailing list, because I may not be able to solve your issues. I was able to install the latest revision of Trimmomatic without issues, so we may need some more information from the Galaxy logs to understand what is your issue. Same for the other repositories. Cheers, Nicola On 20/11/15 16:09, Scott Szakonyi wrote: > Hi Nicola, > > I was able to switch over to GitHub without issue. Thanks for pointing > me in the right direction. > > I have installed Trimmomatic successfully, although I wasn't able to > install the latest version. If I try to install the "2015-09-23" > revision, I get "Internal Server Error Galaxy was unable to > successfully complete your request". The "2015-04-22" revision > installs without issue. > > However, I'm still having problems with the Picard tool. I've tried > sever of the revisions, and have similar issues with all. Dependencies > are not installing correctly, and I'm unable to repair them or > otherwise resolve the problem. Three of the tools that install with > Picard end up missing dependencies: package_cairo_1_12_14, > package_pixman_0_32_4, and package_readline_6_2. The underlying errors > do not seem to have a definite pattern, as was the case when I was > having problems before the GitHub switch. Is this something that I > should take up with whoever provides the Picard tool? > > Thanks! > > Scott > > On Fri, Nov 20, 2015 at 9:39 AM, Scott Szakonyi > <Scott.B.Szakonyi.1(a)nd.edu <mailto:Scott.B.Szakonyi.1@nd.edu>> wrote: > > Hi Nicola, > > Thank you, that's very helpful. I'll switch over to the GitHub > repository and get the latest revision, then we'll see if that > doesn't solve the problem. > > Best, > > Scott > > On Fri, Nov 20, 2015 at 9:33 AM, Nicola Soranzo > <nsoranzo(a)tiscali.it <mailto:nsoranzo@tiscali.it>> wrote: > > Hi Scott, > the mercurial mirror is not up to date unfortunately, see this > previous discussion: > > http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-t… > > Cheers, > Nicola > > > On 20/11/15 13:13, Scott Szakonyi wrote: >> Hi Nicola, >> >> I'm not entirely sure which version... but I am still using >> the mercurial mirror, which says I'm up to date. Would this >> be a wise time, then, to change over to the Git repository >> directly? >> >> Thanks! >> >> Scott >> >> On Thu, Nov 19, 2015 at 8:15 PM, Nicola Soranzo >> <nsoranzo(a)tiscali.it <mailto:nsoranzo@tiscali.it>> wrote: >> >> Hi Scott, >> which Galaxy release are you using? >> This is a bug which should be fixed in an updated >> release_15.07 git branch. >> >> Cheers, >> Nicola >> >> ---- Scott Szakonyi ha scritto ---- >> >> >> Hello all, >> >> I'm having issues installing Trimmomatic and Picard tools >> from the toolshed. The errors are of the following form >> (Trimmomatic used for the example). >> >> Trimmomatic 0.32 package shows an installation error. >> >> Error details: >> File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric >> tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) >> File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 136, in install_and_build_package >> dir = tmp_dir >> File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ >> self.gen.throw(type, value, traceback) >> File "/vectorbase/web/Galaxy/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv >> yield >> File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package >> initial_download=True ) >> File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step >> initial_download=initial_download ) >> File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step >> dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) >> File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download >> extraction_path = archive.extract( install_dir ) >> File "/vectorbase/web/Galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract >> os.chmod( absolute_filepath, unix_permissions ) >> >> [Errno 2] No such file or directory: '/data/galaxy/tmp/tmp-toolshed-mtdeqJvts/Trimmomatic-0.32/Trimmomatic-0.32/' >> >> I've tried several version of the tool with no success. >> Any thoughts? I've searched project website but haven't >> come up with anything definitive. >> >> Thanks for any help you can offer, >> >> -- >> Scott B. Szakonyi >> Research Programmer >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> <http://crc.nd.edu/>http://crc.nd.edu >> >> >> >> >> -- >> Scott B. Szakonyi >> Research Programmer >> >> *Center for Research Computing* >> 107 Information Technology Center >> Notre Dame, IN 46556 >> <http://crc.nd.edu/>http://crc.nd.edu > > > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu <http://crc.nd.edu/> > > > > > -- > Scott B. Szakonyi > Research Programmer > > *Center for Research Computing* > 107 Information Technology Center > Notre Dame, IN 46556 > http://crc.nd.edu <http://crc.nd.edu/>

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Planemo 0.20.0 and xunit
by Tiago Antao 20 Nov '15

20 Nov '15

Hi, I have recently upgraded to planemo 0.20.0 and I am getting an error that I cannot resolve: Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown. The output from the tool_test_output.json is empty {} I am using planemo t --install_galaxy I am a bit lost here, can anyone offer a suggestion please? I am afraid this might be too trivial... As a further note, I have this on the log: functional_tests.py: error: no such option: --with-nosehtml Many thanks, Tiago

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