galaxy-dev August 2017

galaxy-dev@lists.galaxyproject.org

29 participants
35 discussions

Galaxy Conda resolver install Issue
by evan clark 17 Aug '17

17 Aug '17

I just ran across an issue when attempting to load galaxy. I am not sure how to fix this issue or what could be causing it. Conda is installed properly. File "/var/web_services/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 58, in paste_app_factory app = galaxy.app.UniverseApplication( global_conf=global_conf, **kwargs ) File "/var/web_services/galaxy/lib/galaxy/app.py", line 113, in __init__ self._configure_toolbox() File "/var/web_services/galaxy/lib/galaxy/config.py", line 935, in _configure_toolbox self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) File "/var/web_services/galaxy/lib/galaxy/tools/__init__.py", line 205, in __init__ app=app, File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line 1044, in __init__ self._init_dependency_manager() File "/var/web_services/galaxy/lib/galaxy/tools/toolbox/base.py", line 1057, in _init_dependency_manager self.dependency_manager = build_dependency_manager( self.app.config ) File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 41, in build_dependency_manager dependency_manager = DependencyManager( **dependency_manager_kwds ) File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 84, in __init__ self.dependency_resolvers = self.__build_dependency_resolvers( conf_file ) File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 193, in __build_dependency_resolvers return self.__default_dependency_resolvers() File "/var/web_services/galaxy/lib/galaxy/tools/deps/__init__.py", line 201, in __default_dependency_resolvers CondaDependencyResolver(self), File "/var/web_services/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 134, in __init__ self.disabled = not galaxy.tools.deps.installable.ensure_installed(conda_context, install_conda, self.auto_init) File "/var/web_services/galaxy/lib/galaxy/tools/deps/installable.py", line 77, in ensure_installed return ensure_installed(installable_context, auto_init) TypeError: ensure_installed() takes exactly 3 arguments (2 given)

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Job output not returned from Cluster Error
by Yip, Miu ki 17 Aug '17

17 Aug '17

Hi, We’re having a bit of an error where the GUI shows that a job had an error. When the user submits the job, the job is seen to have run via terminal and uge. The job working directory exists and the out and error file is in there. Once the job completes, it seems like the GUI will say that it works. But then several minutes later, the GUI shows the job turning from green to red and giving the error that the “Job output not returned from the Cluster” error. I tried setting the retry_job_output_collection but it did not work (we’re using a local file system): http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-failed… This seems to happen randomly for different jobs. Some jobs receive errors but others do not receive this error. Does anybody have any suggestions on how to fix this? There is no error that appears in the paster.log file and we are using SGE. Thanks in advance!

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Data manager for ncbi_blast_plus in the main tool shed?
by David Kovalic 15 Aug '17

15 Aug '17

Peter, Thanks. Dan, What is your opinion (what work needs to be done to make this production-worthy)? Maybe if my chops are up to it I can take a crack… David David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail: kovalic(a)analome.com On Fri, Aug 11, 2017 4:58 AM, Peter Cock p.j.a.cock(a)googlemail.com wrote: Hi David, Daniel Blankenberg wrote one (CC'd): https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blas… http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_bla… I've never used it in production and don't have enough understandingof it and the Data Manager framework to understand what if anythingneeds working on. Locally we have mirrors of the NCBI blast databases (updated with cron),local databases for organisms of interest - these are all listed in the *.locfiles by hand. Separately, our users can and do make their own databases withinGalaxy using makeblastdb. Regards, Peter On Thu, Aug 10, 2017 at 10:32 PM, David Kovalic <kovalic(a)analome.com> wrote: Hi, Does anyone know if a data manager exists in the tool shed for creating and integrating NCBI BLAST+ indices within galaxy? I can't seem to find it in the tools shed or searching the internet Surly such a tool must exist. Any info would be greatly appreciated. Thanks, David David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail: kovalic(a)analome.com ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/

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Samtools problem in Docker
by Deepak Tanwar 15 Aug '17

15 Aug '17

Hello everyone, I am facing problem in uploading bam files on Galaxy. I am using Docker image of Galaxy. I have installed samtools version 0.1.19 and added it to the path /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools Error: Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH. Thank you, Deepak

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Tool Shed tools - Uncaught Error
by Yip, Miu ki 13 Aug '17

13 Aug '17

Hi all, We’re having a bit of trouble with a local version of Galaxy where all the tools that were installed via tool shed is showing an uncaught error on the user interface. The tools have clearly been installed and can be seen in the admin panel on the interface as well as the psql database via the command line. It seems like the in house tools are all working fine and the tool shed tools were working fine until recently. Can anyone suggest what steps to take next to fix this error or to find the cause? We are using docker galaxy and it doesn’t seem like anything is appearing on the error logs. Thanks!

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Bowtie2 index building
by Deepak Tanwar 11 Aug '17

11 Aug '17

Hello, I am trying to build Bowtie2 index for hg19. I a using Docker image of Galaxy. Computer I am using have 12 cores and 64 GB of RAM. Error I am getting is: Fatal error: Exit code 1 () Building a SMALL index Could not allocate space for a joined string of 2897310462 elements. Switching to a packed string representation. Building a SMALL index Could not find approrpiate bmax/dcv settings for building this index. Already tried a packed string representation. Please try indexing this reference on a computer with more memory. Error: Encountered internal Bowtie 2 exception (#1) Command: bowtie2-build --wrapper basic-0 /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19 fa.fa hg19 fa Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt. Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt. Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt. Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt. Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt. Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt. Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt. Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt. Error building index. Please help! Thank you, Deepak

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Data manager for ncbi_blast_plus in the main tool shed?
by David Kovalic 11 Aug '17

11 Aug '17

Hi, Does anyone know if a data manager exists in the tool shed for creating and integrating NCBI BLAST+ indices within galaxy? I can't seem to find it in the tools shed or searching the internet Surly such a tool must exist. Any info would be greatly appreciated. Thanks, David David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail: kovalic(a)analome.com

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Installing Galaxy, Conda and Python
by Lachlan Musicman 11 Aug '17

11 Aug '17

Hola, We are attempting to install Galaxy, from git, version 17.05 We largely have it installed, but seem to be falling over at the installation of dependencies. In particular, conda via Galaxy can't find Gnuplot 4.6, and the conda libraries don't show a gnuplot < 5.x The error: 10.126.160.84 - - [11/Aug/2017:13:49:08 +1100] "GET /galaxy/admin/manage_tool_dependencies HTTP/1.1" 200 - "http://<server>/galaxy/admin" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_12_6) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/60.0.3112.90 Safari/537.36" [pid: 24515|app: 0|req: 3/4] 10.126.160.84 () {66 vars in 1432 bytes} [Fri Aug 11 13:49:08 2017] GET /galaxy/admin/manage_tool_dependencies => generated 13534 bytes in 220 msecs (HTTP/1.1 200) 2 headers in 73 bytes (1 switches on core 0) galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,042 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot(a)4.6 gnuplot=4.6 Fatal Python error: Py_Initialize: Unable to get the locale encoding ImportError: No module named 'encodings' Current thread 0x00007fd60463c740 (most recent call first): galaxy.tools.deps.resolvers.conda DEBUG 2017-08-11 13:49:12,070 Removing failed conda install of [CondaTarget[gnuplot,version=4.6]] galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,072 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot(a)4.6 gnuplot=4.6 Fatal Python error: Py_Initialize: Unable to get the locale encoding ImportError: No module named 'encodings' Current thread 0x00007fb0d2eb6740 (most recent call first): galaxy.tools.deps.resolvers.conda DEBUG 2017-08-11 13:49:12,102 Removing failed conda install of gnuplot, version '4.6' galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,106 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot@_uv_ gnuplot Fatal Python error: Py_Initialize: Unable to get the locale encoding ImportError: No module named 'encodings' Current thread 0x00007fc80d5df740 (most recent call first): galaxy.tools.deps.resolvers.conda DEBUG 2017-08-11 13:49:12,139 Removing failed conda install of [CondaTarget[gnuplot,unversioned]] galaxy.tools.deps.conda_util DEBUG 2017-08-11 13:49:12,142 Executing command: /galaxy/production_database/dependencies/_conda/bin/conda create -y --name __gnuplot@_uv_ gnuplot Fatal Python error: Py_Initialize: Unable to get the locale encoding ImportError: No module named 'encodings' https://anaconda.org/bioconda/gnuplot/files shows that there is a 4.6.0-1 in there, but for whatever reason it's not being found by the search function? When I try the recommended [root@<server> bin]# ./anaconda search -t conda gnuplot Using Anaconda API: https://api.anaconda.org Run 'anaconda show <USER/PACKAGE>' to get more details: Packages: Name | Version | Package Types | Platforms ------------------------- | ------ | --------------- | --------------- BioBuilds/gnuplot | 5.0.5 | conda | linux-ppc64le, linux-64, osx-64 : Portable command-line driven graphing utility OpenAlea/gnuplot | 5.0.4 | conda | linux-64, osx-64 alexbw/lua-gnuplot | 1.0.1 | conda | linux-64, osx-64 : Torch interface to Gnuplot bioconda/gnuplot | 5.0.4 | conda | linux-64, osx-64 : Gnuplot, plotting from command line bioconda/gnuplot-py | 1.8 | conda | linux-64, osx-64 conda-forge/gnuplot | 5.0.6 | conda | linux-64, osx-64 : Gnuplot, plotting from command line gbaty/gnuplot | 5.0.1 | conda | linux-64 : Gnuplot is a portable command-line driven graphing utility for many platforms. johannr/py-gnuplot | 1.8 | conda | linux-64, osx-64 : A Python interface to the gnuplot plotting program. Found 8 packages There's no 4.6 there, hence the fail I guess. Does anyone have a work around for this? cheers L. ------ "The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic civics is the insistence that we cannot ignore the truth, nor should we panic about it. It is a shared consciousness that our institutions have failed and our ecosystem is collapsing, yet we are still here — and we are creative agents who can shape our destinies. Apocalyptic civics is the conviction that the only way out is through, and the only way through is together. " *Greg Bloom* @greggish https://twitter.com/greggish/status/873177525903609857

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Galaxy Project @ Johns Hopkins is hiring
by Dave Clements 10 Aug '17

10 Aug '17

Hello all, The Galaxy Project at Johns Hopkins is hiring software engineers and postdocs: The Taylor Lab <http://taylorlab.org/> at Johns Hopkins University <https://jhu.edu/> in Baltimore, Maryland is hiring software engineers and post-docs <https://galaxyproject.org/galaxy-is-hiring/> to work on the Galaxy Project <https://galaxyproject.org/>. This is a rare opportunity to perform research and develop software at the leading edge of life sciences, genomics, data-intensive computing, and big data analytics. Johns Hopkins offers a challenging and rewarding work environment and is ranked as a global top 20 university by Times Higher Education <https://www.timeshighereducation.com/world-university-rankings/johns-hopkin…> . Interested? See the full postings <https://galaxyproject.org/galaxy-is-hiring/>. *Watch this space for more upcoming openings...* [image: Galaxy Project hiring in the Taylor Lab] <https://galaxyproject.org/galaxy-is-hiring/> [image: Johns Hopkins University] <http://www.johnshopkins.edu/> Please forward this to anyone who might be interested. And I can say from experience that it's an excellent team to be a part of. Thanks, Dave C -- https://galaxyproject.org/ https://getgalaxy.org/ https://usegalaxy.org/ https://gcc2017.sciencesconf.org/

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numpy problem
by Matthias Bernt 10 Aug '17

10 Aug '17

Dear dev-list, again some problems with software in galaxy: I can not get numpy to install. Here is the excerpt from the logs: Successfully downloaded from url: https://depot.galaxyproject.org/software/numpy/numpy_1.9p1_src_all.tar.gz tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,264 + export PYTHONPATH=$PYTHONPATH:/gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python && export ATLAS=$ATLAS_ROOT_PATH && python setup.py install --install-lib /gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/lib/python --install-scripts /gpfs1/data/galaxy_server/galaxy/database/dependencies/numpy/1.9/iuc/package_numpy_1_9/83d12e13dbbd/bin tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,384 Writing custom site.cfg for ATLAS in Galaxy tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,385 Traceback (most recent call last): tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 264, in <module> tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,385 setup_package() tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,385 File "setup.py", line 210, in setup_package tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,385 raise RuntimeError("Writing custom site.cfg failed! %s" % ex) tool_shed.galaxy_install.tool_dependencies.recipe.install_environment:numpy DEBUG 2017-07-18 17:08:29,385 RuntimeError: Writing custom site.cfg failed! 'ATLAS_LIB_DIR' I need this tool for running: "Group data by a column and perform aggregate operation on other columns." which gives me currently a numpy error: Traceback (most recent call last): File "/gpfs1/data/galaxy_server/galaxy/tools/stats/grouping.py", line 15, in <module> import numpy ImportError: No module named numpy Thanks a lot. Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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galaxy-dev August 2017