November 2014 - galaxy-dev - lists.galaxyproject.org

MarkupSafe egg missing? e.args[1].key != e.args[0].key
by Peter Cock 18 Nov '14

18 Nov '14

Hello all, There looks to be an egg problem with the latest galaxy-central, here are excepts from a failed Galaxy install on my TravisCI test setup, https://travis-ci.org/peterjc/pico_galaxy/builds/41233860 Here's another project build with the same error: https://travis-ci.org/peterjc/galaxy_blast/builds/41235899 $ ./run.sh --stop-daemon || true Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample ... Initializing static/welcome.html from welcome.html.sample Some eggs are out of date, attempting to fetch... Fetched http://eggs.galaxyproject.org/Mako/Mako-0.4.1-py2.7.egg Fetched http://eggs.galaxyproject.org/importlib/importlib-1.0.3-py2.7.egg Fetched http://eggs.galaxyproject.org/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-l… Fetched http://eggs.galaxyproject.org/ordereddict/ordereddict-1.1-py2.7.egg Fetched http://eggs.galaxyproject.org/Fabric/Fabric-1.7.0-py2.7.egg Fetched http://eggs.galaxyproject.org/Babel/Babel-1.3-py2.7.egg Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-0.3.18-py2.7.egg Fetched http://eggs.galaxyproject.org/Parsley/Parsley-1.1-py2.7.egg Fetched http://eggs.galaxyproject.org/Cheetah/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4… Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 46, in <module> c.resolve() # Only fetch eggs required by the config File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 192, in resolve if e.args[1].key != e.args[0].key: IndexError: tuple index out of range Fetch failed. No PID file exists in paster.pid $ python scripts/fetch_eggs.py Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Traceback (most recent call last): File "scripts/fetch_eggs.py", line 46, in <module> c.resolve() # Only fetch eggs required by the config File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/home/travis/build/peterjc/pico_galaxy/galaxy-central-master/lib/galaxy/eggs/__init__.py", line 192, in resolve if e.args[1].key != e.args[0].key: IndexError: tuple index out of range The command "python scripts/fetch_eggs.py" failed and exited with 1 Looking at http://eggs.galaxyproject.org/MarkupSafe/ for Python 2.7 and Linux x86_64 there is a ucs4 egg: MarkupSafe-0.12-py2.7-linux-x86_64-ucs4.egg 09-Jun-2011 03:09 30724 So, why is this failing? Not I am not explicitly installing MakupSafe (so I do not expect there to be a conflicting version installed). Also it would seem there is a bug in the resolve method assuming that e.arg will always have (at least) two entries? Thanks, Peter

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Help with new PscanChIP test tool shed repository.
by Federico Zambelli 17 Nov '14

17 Nov '14

Dear all, I've uploaded to the test tool shed a pscan_chip_test repository and I'm looking for help in testing it since it's my first time setting up a Galaxy repository. Pscan-ChIP is a motif enrichment analysis tool. The stand-alone web interface is available here: www.beaconlab.it/pscan_chip_dev Any suggestion, bug report or feed back will be greatly appreciated. Best, Federico -- ============================================ Federico Zambelli, Ph.D. ELIXIR-Italy Technical Coordinator Bioinformatics, Evolution and Comparative Genomics Lab Dept. of Biosciences University of Milano - Italy Institute of Biomembranes and Bioenergetics National Research Council (CNR) Bari - Italy Our comforting conviction that the world makes sense rests on a secure foundation: our almost unlimited ability to ignore our ignorance. ============================================

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Is release_2014.10.06 "official"?
by Lance Parsons 17 Nov '14

17 Nov '14

I see that the tags release_2014.10.06 and latest_2014.10.06 were created some time ago, but there was never any announcement. Are these considered officially released? Should I upgrade my instance to this version? Most importantly, are there any release notes so I can see what, if anything, I need to do to prepare for this update? Thanks. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Re: [galaxy-dev] customize the Upload File tool form (version 1.1.4)
by Christophe Antoniewski 16 Nov '14

16 Nov '14

Hi, This is a quick follow up about the instructions given by Aysam and Martin, which may help others (including me ;-). Indeed I upgraded our galaxy-dist to the last commit and the /client directory showed up. To get the instructions working I had to install as root some grunt related packages, otherwise it failed: including $ sudo apt-get install software-properties-common $ sudo apt-get install python-software-properties $ sudo apt-get update $ sudo npm -g install grunt $ sudo npm install -g grunt-cli Then I had the "grunt watch" working and could make the changes - *opening another shell session* (I say this because it is not evident for those who are not familiar with grunt). Yet the changes still do not show up in the browser. My guess is that the galaxy configuration model has changed too, with the creation of a config directory. I suppose that the use of the /client directory is specified in the new galaxy.ini file which replaces universe_wsgi.ini in / . More generally, I did not see instructions on how to move from the old .ini file*sss* at / to the new configuration model using the /config directory without crashing the production instance. Is it available somewhere in the wiki or in a discussion ? Chris Christophe Antoniewski Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine <http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-e…> 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 1 44 27 34 39 Fax +33 1 44 27 34 45 Mobile +33 6 68 60 51 50 christophe.antoniewski(a)upmc.fr http://drosophile.org 2014-11-12 16:11 GMT+01:00 Aysam Guerler <aysam.guerler(a)gmail.com>: > Hi Christophe, > > In order to apply the changes scripts have to be packed properly. Please > follow these steps: > > 1. Go to the client/ directory and type 'npm install' > 2. Now type 'grunt watch'. This will start a listener which captures code > changes and repacks scripts automatically > 3. Finally, make your changes to the code files in > client/galaxy/scripts/mvc/upload and reload your browser > > Let me know if that works for you or if you have any other questions. > > Thanks, > Sam > > >

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Error in creating admin user during tool shed bootstrap
by Bruno Grande 14 Nov '14

14 Nov '14

I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post <http://gregvonkuster.org/galaxy-tool-shed-june-2-2014-release/>. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (*e.g.* the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno

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Jobs stuck in "new" state - Data Library datasets to blame?
by Lance Parsons 14 Nov '14

14 Nov '14

Recently, I updated our Galaxy instance to use two processes (one for web, the other as a job handler). This has been working well, except in a few cases. I've noticed that a number of jobs get stuck in the "new" status. In a number of cases, I've resolved the issue by downloading and uploading one of the input files and rerunning the job using the newly uploaded file. In at least one of these cases, the offending input file was one that was copied from a Data Library. Can anyone point me to something to look for in the database, etc. that would cause a job to think a dataset was not ready for use as a job input? I'd very much like to fix these datasets since having to re-upload data libraries would be very tedious. Thanks in advance. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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SMALT Docker integration run unsteadily
by Weiyan Shen 14 Nov '14

14 Nov '14

Dear all , I am following the guide on https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt‍ to test the smalt docker integration tutorial. The SMALT within docker on my local Galaxy sometimes works well as follow: 502 7789 0.0 0.0 271680 6236 ? Sl 21:42 0:00 /usr/bin/docker run -e GALAXY_SLOTS=1 -v /data/Docker/galaxy-dist:/data/Docker/galaxy-dist:ro -v /data/Docker/galaxy-dist/tools/docker:/data/Docker/galaxy-dist/tools/docker:ro -v /data/Docker/galaxy-dist/database/job_working_directory/000/82:/data/Docker/galaxy-dist/database/job_working_directory/000/82:rw -v /data/Docker/galaxy-dist/database/files:/data/Docker/galaxy-dist/database/files:rw -v /data/Docker/galaxy-dist/database/files:/data/Docker/galaxy-dist/database/files:rw -w /data/Docker/galaxy-dist/database/job_working_directory/000/82 --net none smalt-galaxy:shenweiyan /data/Docker/galaxy-dist/database/job_working_directory/000/82/container.sh But sometimes it failed with the error: setup mount namespace bind mounts Creating new bind-mount target, mkdir /var/lib/docker/devicemapper/mnt/405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b/rootfs/data/Docker/galaxy-dist/database/files:: read-only file system2014/11/14 21:28:13 Error response from daemon: Cannot start container 405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b: setup mount namespace bind mounts Creating new bind-mount target, mkdir /var/lib/docker/devicemapper/mnt/405781730f76d0f3d08eb86e8e14448c47914e727508224f9c70a1ae72cf302b/rootfs/data/Docker/galaxy-dist/database/files:: read-only file system‍‍‍It seems that docker running with sudoer unsteadily.Any idear how do I fix it? Kind regards, weiyan‍

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Plugin for debug / replay and display parameters
by Rémy Dernat 14 Nov '14

14 Nov '14

Hi, We created a plugin to display all history parameters in a single page and generate a shell script from an history. It adds two inputs to the main menu: "parameters" (for all users) and "debug" (for admins). An admin can easily switch from an history to another without having to impersonate a user. On the other hand, a standard user can view all its histories / parameters on a single page. The main goal is to help for debugging: - the developer who created a wrapper can see what happens - the admin can go to every histories and see why the user told him that "it is not working" The idea of the shell script is to get the script and replay it. However, we still need the galaxy environment. This part is still in development (adding GALAXY_SLOTS...). A nice evolution would be to get the input files into a big compressed archive with this script, although it needs to distinguish inputs file like "upload", "paste" from the others inputs because of the size of the archive generated by such a script. We started to code this plugin before the galaxy team add informations about tools in an history (View details) and "impersonate a user", but we still think that the plugin is usefull. You can make your own opinion by testing it: git clone https://github.com/remyd1/galaxy_debug_params Install it with: cd galaxy_debug_params bash galaxy_plugin_installer.sh -d /path/to/galaxy-dist Best regards, Remy Dernat and Aurelien Bernard.

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LAST CALL! Re: GMOD user talks at PAG
by Scott Cain 13 Nov '14

13 Nov '14

Hi All, Last call: does anybody else want to give a GMOD-related talk at PAG this January? We already have some good talk proposals, but we could use a few more. Scott On Mon, Nov 10, 2014 at 3:04 PM, Scott Cain <scott(a)scottcain.net> wrote: > Hello, > > I'm looking for some people to give talks about how you've used GMOD tools > at your site at the Plant and Animal Genomes meeting in San Diego this > January. If you're already going to PAG, or are looking for an excuse to > go to San Diego in January, I encourage you to send me a brief note with a > title for your talk. If you haven't registered for PAG but will give a > talk, you can register at early bird pricing (a savings of $100 dollars I > think). > > Unfortunately, I'm running a little late with this announcement, so if > you'd like to give a talk, please get back to me by November 13 (Thursday). > > Thanks and I hope to see you in San Diego in a few months, > Scott > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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Dataset collection generation from a tool
by Aaron Petkau 13 Nov '14

13 Nov '14

Hello, Does anyone know if it's possible to generate as output from a tool a dataset collection when it's input is only a single file? I'm imagining a tool which takes as input a file containing a list of URLs for files outside of Galaxy and generates as output a dataset collection that can then be linked up to later tools. Thanks, Aaron

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