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

redirecting to unnamed history
by Michael Mason 19 Aug '14

19 Aug '14

Hi I am running a work flow on data in a history with 54 input fastq files. About every other time I run Galaxy generates another history (unnamed) and sends a third to half the jobs to it. I am not clicking "send results to a new history" so I am not sure why this is happening. Any ideas? Is there something I should be looking for in galaxy's log file. Thanks for any help, Mike Info from hg head. changeset: 13753:d3b1f484c4b6 branch: stable tag: tip parent: 13751:deba1986ea22 parent: 13752:0af879ff3097 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Jul 15 11:33:46 2014 -0400 summary: Merged in dannon/galaxy-central-prmaker/stable (pull request #439) changeset: 13709:5273e0bf9ae5 parent: 13707:15d426f19dcc parent: 13708:8b6e1ffaa053 user: Dannon Baker <dannonbaker(a)me.com> date: Mon Jun 02 13:16:51 2014 -0400 summary: merge next-stable ________________________________ --CONFIDENTIALITY NOTICE--: The information contained in this email is intended for the exclusive use of the addressee and may contain confidential information. If you are not the intended recipient, you are hereby notified that any form of dissemination of this communication is strictly prohibited. www.benaroyaresearch.org

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Problem selecting datasets with a specified datatype
by George Weingart 19 Aug '14

19 Aug '14

Hi, I am trying to set up in our Galaxy a program that takes two inputs that have different datatypes. The problem is that Galaxy selects only datasets of the first datatype and displays all datasets for the second with all types, not only with the specified datatype (We want it to display for the second dataset only those with datatype=”lefse_res”). Both datasets are input and are both required to run the step. My code looks as follows: <inputs> <param format="tabular" name="inp_data1" type="data" label="Input 1" /> <param format="lefse_res" name="inp_data2" type="data" label="Input 2"/> </inputs> Should I be doing it in another way? Thanks! George Weingart

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bug: API broken under remote_user
by Eric Rasche 19 Aug '14

19 Aug '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 https://trello.com/c/AGKePuHZ/1630-expose-use-remote-user-via-configuration… I don't know if this is the correct card (it's been a long day and I may be misreading it) but the API is completely broken under REMOTE_USER authentication. running ./scripts/api/display.py {key} http://localhost:8300 returns 403 forbidden. running ./scripts/api/display.py {key} https://fqdn/galaxy/ returns 401 Authorization Required -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux) iQIcBAEBAgAGBQJTmPeFAAoJEMqDXdrsMcpVtmkP/1r36cFmedYJXnMFl2CG0e7P VtSoMHYbtesc/IKnGwKEH1xtf2RNF7p8n0/0mC3QNAoI0n3A8XDoZRXaWzgmsZ4z heGipPgotCyhFt/ud2W8eb0IlZ3AhtyWwvhG1hXcwQV4eXXHfuQCepPEbfyUUR2N F+VCLMGMv3dnsv0ForC7iYesV4qqOsX48Wry6InVD41UpXOE0Bor5uB/HcohYjKS sVhOmNSjLpME35Rka4vUW4oNIzeeBsQIQyrpCuZ2KTKImEkSoSEbTho9fhNUi0ll EHlTu+qt4iaXZpqNOKU05p3TqdjxAmc2w/McmMzifwPZdmrxTZjaitFn+g1qXxYs 0ZVJtL/OZviFHuK+8qbbsCPIYYm/dVr5EPy821/F01dAGNw9k+lbk5kZdgC8zcBz xFc5yk+QZGuc3KeDYLOidtn4c471Ez4LhgTd9wapYkSwva7aM5T1betpPZKufZbw +SSC/KFi6J2rjVDOkHLCry185Bwha2hrn1tc2hd1+A/5zOuyqQ/u0isvRu+O7dxO uGF33WjXCYqwVGNzXN+pZMVPStIXKlLmoA2CoWbUM9rHSQWHVRQKIiZ05v2tZYn7 /cpYLOwudWbQtDX+AscPd18bJ4OqSmy+aXo9nSkmJMbCWtN9TxKljx3MNzfg8DxV r+SaijGDeWJ3xgiv2L6U =svZc -----END PGP SIGNATURE-----

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Plans for Docker image generation in galaxy
by Marius van den Beek 19 Aug '14

19 Aug '14

Hi everyone, it’s my first post to the list, so forgive me if I miss something obvious, I tried to get all the information I could so if there was already a discussion I’d be glad if you can point me towards this. I’m posting to start a discussion about how galaxy is going to handle interactions with Docker. I know there are already some tools and resources out there that make use of Docker. As I understood, we can already specify Docker as a job destination in the tool xml, along with an image to use (See https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt for a detailed example). This is cool, and allows for the controlling of resources, but I think we could take the integration to the next step if we allowed the generation of Docker images in galaxy. I was thinking if there is a trusted baseimage (ie without root access), we could let users install all the packages they need, commit after the install, and let them use this new docker image. This could be beneficial for generating new tools with a sandboxed version of the Galaxy Tool Factory ( http://www.ncbi.nlm.nih.gov/pubmed/23024011) I am currently working on this ( https://bitbucket.org/mvdbeek/dockertoolfactory) and I would like to have your opinion on how to manage these user-generated Docker images. Some questions that I came across: Do we store the committed images in the user’s history (they could potentially become very big!)? How to display available images to the user? Something like a per-user image registry? How to identify available images (dataset_id as the tag?) How to transfer user-generated images to the toolshed? Is it a good idea at all to store user-generated images in the toolshed? What do we do if the security of the baseimage is compromised? Obviously we can blacklist execution of images, but what if somebody installed a dangerous image from the toolshed, and is not aware of this? Ultimately I think this could be a way to have advanced users run their own scripts inside galaxy, to generate their own tools and tool-dependencies inside galaxy, and why not, even have “user-space tools”. It would bridge the gap between galaxy users and galaxy tool-developers, so I’m curious what you’re thinking about this. Cheers, Marius

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Upload file not working with new install
by Iry Witham 18 Aug '14

18 Aug '14

Hi Team, I have installed a fresh version of Galaxy and am having an issue with the 'Upload File' tool. When I attempt to use it it just sits and spins. No data gets uploaded. I have looked through the universe.wsgi.ini file and cannot find anything there that stands out. Can you point me to a possible solution? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Test run frequency on TestToolShed
by Peter Cock 18 Aug '14

18 Aug '14

Hi all, Are the main and test tool-sheds currently meant to be running the tool functional tests every 48 hours? I created and updated these repositories last week, but they have yet to be tested: https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Thanks, Peter P.S. it would be nice to be able to sort the "Repositories I own" lists etc by date (particularly for my typical workflow of posting an update to the TestToolShed, waiting for a green light from the tests, and then pushing this to the main ToolShed).

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My last day as a core Galaxy Development Team member
by Greg Von Kuster 17 Aug '14

17 Aug '14

Hello Galaxians, I have moved into a new position here at Penn State University, so for the first time in 8 years I am not a member of the core Galaxy development team. This has been a very difficult transition for me - Galaxy has been, and continues to be, extremely important to me. I've really appreciated working with the Galaxy team and the large Galaxy community over these 8 years and I hope I can continue to work with Galaxy in some capacity. I've been fortunate to have found many friends in the bioinformatics community, and I hope those relationsips will continue as well. I feel that Galaxy is far from reaching its peak and that its future remains very bright. I look forward to seeing how far it will go. Warm regards to each of you, Greg Von Kuster

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Re: [galaxy-dev] Galaxy dont work on my Bio-Linux‏
by qiaoyan 16 Aug '14

16 Aug '14

Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can help you. Sincerely Yan Qiao

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Re: [galaxy-dev] Galaxy dont work on my Bio-Linux
by qiaoyan 16 Aug '14

16 Aug '14

Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can help you. Sincerely Yan Qiao

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Re: [galaxy-dev] Galaxy dont work on my Bio-Linux
by qiaoyan 16 Aug '14

16 Aug '14

Hi petr, I have the same problem with you. But the problem has been solved in recent days. You can open a new terminal and run the following command: cd /usr/lib/galaxy-server sh run.sh --reload This will start up the server. Then open galaxy icon and it will run normally! I hope it can help you. Sincerely Yan Qiao

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