- galaxy-dev - lists.galaxyproject.org

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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openms python3 & print
by Matthias Bernt 10 Aug '17

10 Aug '17

Hi, I got an error from OpenMS which seems to be related to python3: Fatal error: Exit code 1 (Error running OpenMS tool.) File "/gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py", line 22 print "Running shell command %s" % command ^ SyntaxError: Missing parentheses in call to 'print' Command line was python /gpfs1/data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms/openms_wrapper.py --executable 'DecoyDatabase' --config /gpfs1/data/galaxy_server/galaxy/jobs_dir/000/240/tmpYOuUf9 I would volunteer to improve this. But where can I find the sources? Would it be better to - use the compatibility import (easiest) - switch to print() - use logging Best, 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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openms again
by Matthias Bernt 10 Aug '17

10 Aug '17

Hi, just fixed the print() issue locally and ran into the next problems which were easy to fix: - ConfigParser -> configparser - iteritems -> items (The modified sources are attached if they are of interest) Now I have an error that seems to be deeper: Failed to find specific OpenMS option [shuffle] in node [<Element 'NODE' at 0x2b96a3b1c048>] Any ideas? 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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install tools to https galaxy instance with insecure ssl?
by Evan Bollig PhD 04 Aug '17

04 Aug '17

Hey Björn, I'm using your galaxy-stable docker image to boot Galaxy on port 443 by default (i.e., with USE_HTTPS=True). Since the certificate is self-signed, transactions with the URL (https://127.0.0.1) warn of insecure SSL. Is it possible to force shed-install to use --insecure and accept the SSL cert for CLI tool installation? [centos@estasdf ~]$ docker exec -it 2b8 install-tools newtools.yml Enable installation from the Test Tool Shed. System is up and running. Starting with the installation. Traceback (most recent call last): File "/usr/local/bin/shed-install", line 11, in <module> sys.exit(script_main()) File "/usr/local/lib/python2.7/dist-packages/ephemeris/shed_install.py", line 764, in script_main itm.install_tools() File "/usr/local/lib/python2.7/dist-packages/ephemeris/shed_install.py", line 636, in install_tools itl = installed_tool_revisions(self.gi) # installed tools list File "/usr/local/lib/python2.7/dist-packages/ephemeris/shed_install.py", line 240, in installed_tool_revisions itl = tsc.get_repositories() File "/usr/local/lib/python2.7/dist-packages/bioblend/galaxy/toolshed/__init__.py", line 36, in get_repositories return self._get() File "/usr/local/lib/python2.7/dist-packages/bioblend/galaxy/client.py", line 136, in _get status_code=r.status_code) bioblend.ConnectionError: HTTPSConnectionPool(host='localhost', port=443): Max retries exceeded with url: /api/tool_shed_repositories?key=admin?key=admin (Caused by SSLError(SSLError(1, '_ssl.c:510: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed'),)), 0 attempts left: Cheers, -E -- Evan F. Bollig, PhD Scientific Computing Consultant, Application Developer | Scientific Computing Solutions (SCS) Minnesota Supercomputing Institute | msi.umn.edu University of Minnesota | umn.edu boll0107(a)umn.edu | 612-624-1447 | Walter Lib Rm 556

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controlling dataset formats in output collections
by Wolfgang Maier 04 Aug '17

04 Aug '17

Dear all, as the title says I'm wondering whether there is any way to control the format of the elements of a collection generated by a tool. I know how to specify the type of the collection itself (list, paired or nested), but this is about the elements themselves. For example, I would like to be able to set the elements' format to fastqsanger or fastqsanger.gz directly in the outputs section of the toolwrapper. Thanks for any pointers, Wolfgang

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August News: GCC2018: in Portland (w/ BOSC); GCC2017 & ISMB/BOSC presentations; and more
by Dave Clements 01 Aug '17

01 Aug '17

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Venn diagram example data
by Steven Shen 27 Jul '17

27 Jul '17

Dear Galaxy list, I am interested in Galaxy Charts visualization.But venn diagram confuses me when I upload my tabular data, it seems venn diagram need one column observations at least, actually I don't clear what should be contained in the one column observations. So is there any venn diagram example data or usage for this charts plugin ? Sad to say I am not good at JavaScript :) Thank you very much. Regards, Steven

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galaxy-tours : putting the box next to the preview display
by Hans-Rudolf Hotz 27 Jul '17

27 Jul '17

Dear All I am working on a simple galaxy tour. The galaxy tour builder (https://github.com/TailorDev/galaxy-tourbuilder) is great and helps a lot, but unfortunately, not in this particular case: - element: "#current-history-panel > ul.list-items > div:nth-child(1) > div.details > div.actions.clear > div.left > a.download-btn.icon-btn" title: "Download your dataset" intro: "You can download every dataset by using the floppy disc symbol." position: "left" will put the box next to the floppy disc symbol. What do I have to write as 'element' in order to get the box pointing to the actual preview data (i.e. the white box)? Thank you very much for your help Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Accessing only to "not deleted" history datasets from a visualization plugin
by LPER 26 Jul '17

26 Jul '17

Hi everyone, I am currently working on a visualization plugin and I would like to have access from this plugin to multiple history datasets. I managed so far to view all the history dataset in the console with the following commands : var query = '/api/histories/'+'${trans.security.encode_id(trans.history.id)}/contents?details=all'; $.ajax({url: query, dataType : 'json', async: false, success: function(data){console.log(data);}}); Data is an array containing history dataset objects. However, it contains all the history datasets, even those that were deleted and deleted permanently from the disk. I can filter data according to the boolean purged attribute of each dataset to get only the datasets visible to the user, but I was wondering if there was a quicker and more efficient way to do this by getting only the "not deleted" history datasets with the query? Thanks in advance for your answer(s), Cheers and have a nice day! Lisa Sent with [ProtonMail](https://protonmail.com) Secure Email.

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genome upload
by Marion Cerri 25 Jul '17

25 Jul '17

To whom it concerns, I am Marion Cerri, post doc in the Parniske’s lab, in Munich. I am working with ChIP-seq data in the moment. I would like to use the Lotus japonicus (version 3.0) for mapping reads, but the genome is not available on galaxy. Would it be possible to upload it ? Do I have to provide the file to you, and if so in fasta format ? Thanks in advance Best Regards Marion Cerri

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