galaxy-dev July 2017

galaxy-dev@lists.galaxyproject.org

33 participants
34 discussions

Re: [galaxy-dev] Shiny in Galaxy
by Yvan Le Bras 14 Mar '18

14 Mar '18

Dear Mohamed, Karim, galaxy-dev list, A rapid e-mail to inform you that we plan to work on this task in the upcoming weeks with Thimothée and Valentin, copied. We have had some exchanges with Eric (Rasche) and Björn (Grüning) and it seems that using the Galaxy "interactive environment" functionality is a good way to proceed. Don't hesitate to give us more informations to collaborate on it... Wishing you a good week end. Cheers, Yvan -------- Message d'origine -------- De : "Md. Rezaul Karim" <rezaul.karim(a)insight-centre.org> Date : 26/05/2017 15:45 (GMT+01:00) À : Mohamed Kassam <k.mamoud(a)gmail.com> Cc : Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org> Objet : Re: [galaxy-dev] Shiny in Galaxy +1 On May 26, 2017 2:44 PM, "Mohamed Kassam" <k.mamoud(a)gmail.com> wrote: Dear all, I have a shiny application working in my RStudio, but I would like to integrate it to Galaxy that the users can call my application via Galaxy . Thanks in Advance, Mohamed ___________________________________________________________ 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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Groovy tool for galaxy
by Anshul Tak 23 Aug '17

23 Aug '17

Hi, I have a question regarding galaxy. Can I execute groovy scipts using galaxy? I installed groovy in galaxy docker image and all the dependencies. However, when I try to execute a tool which require groovy engine it says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh: line 9: groovy: command not found" So I understood the error that galaxy is not able to find groovy but ideally it should take the groovy engine as it is installed. Can you give me some pointers to solve this issue? -- With Regards, Anshul Tak

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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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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

3 3

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

1 1

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.

1 0

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

2 1

Uncaught Error When Installing Tools From Toolshed
by William, Van Der Pol 24 Jul '17

24 Jul '17

Hello All, I have recently cloned and installed a clean version of Galaxy. I installed a tool from the toolshed and Galaxy says it is properly installed, however when I try to open the tool in the main page all I see is an "Uncaught Error" message. Does anyone have any ideas on what is causing this or at least how I can get a more telling error message? Thanks -Liam

3 2

Creating a tool dependency packages
by Delisle Lucille 24 Jul '17

24 Jul '17

Dear Galaxy list, I do not know if it is the right place to ask my question. I would like to create a tool dependency package for numexpr (a python library). I tried to do it taking examples from different tool dependency packages from iuc for example. I added my repository to the testtoolshed but when I tried to install it. The directory lib/python of my tool is empty. My repository is : package_python_2_7_numexpr_2_6_2<https://testtoolshed.g2.bx.psu.edu/repository/browse_repository?id=23c1f7fe…> The big difference I see between the one from iuc and mine is the url: For example, for pybigwig, the URL is : https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz For my library numexpr I could not find such a url so I put the one I thought would be the good one: https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad… Thank you very much for your help, Lucille Delisle, PhD PostDoc Duboule Lab Laboratory of Developmental Genomics EPFL SV ISREC UPDUB SV 2843 Station 19 CH-1015 Lausanne Tel : +41 21 693 97 08

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Galaxy @ ISMB/ECCB/BOSC 2017: Talks, posters, dinner, BoF, and tutorial
by Dave Clements 20 Jul '17

20 Jul '17

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galaxy-dev July 2017