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Problems downloading files via bioblend
by Brad Zeitner 22 Aug '14

22 Aug '14

I have a python script that I use to download the qc data generated in one of the steps in a workflow. It used to work on a previous install of galaxy - but we've gone through and updated our Galaxy install so that it's now running on a new file system - and when I try and use the bioblend api to download the dataset the request for the file gets redirected to the login page. The call to download it is - dm = gi.datasets.download_dataset(qcf.get("id"), outfile, False ) Where qcf is the history step This calls the following url:/datasets/4fa2da3cf0e735a4/display?to_ext=html If I visit the url in a browser that's not in a session, it behaves the same way - but works correctly when I am logged in. How can I access this using the api key? When I add the parameters key=${myKey} it still fails. Thanks, -Brad Zeitner ________________________________ --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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Re: [galaxy-dev] Internal Server Error when trying to install a tool from the Tool shed
by John Chilton 22 Aug '14

22 Aug '14

Hello Audrey, Please keep responses on list - it ensures people smarter than me can respond :). Can you tell me what is sitting in front of Galaxy - Apache, Nginx, uwsgi, etc... and send the configurations if possible? I believe the out-of-the-box uwsgi configuration has some problems with really long URL query strings which using the tool shed does produce. -John On Mon, Aug 18, 2014 at 11:56 AM, audrey michel <audreymannion(a)gmail.com> wrote: > Hi John, > > We tried the following on another server where there is no proxy, and we are > able to install tools from this new instance: > > > hg clone https://bitbucket.org/galaxy/galaxy-dist/ > > > $ hg clone https://bitbucket.org/galaxy/galaxy-dist/ > destination directory: galaxy-dist > requesting all changes > adding changesets > adding manifests > adding file changes > added 14316 changesets with 48369 changes to 8546 files (+1 heads) > updating to branch default > 3597 files updated, 0 files merged, 0 files removed, 0 files unresolved > > We then modified just the admin_users, tool_dependency_dir, port and > localhost. This was sufficient to allow us to use the toolshed to install > tools on this particular instance of galaxy. > > So it would appear to be a proxy issue with our other instance of galaxy > which is behind a proxy. Could you advise us on where we need to add > http_proxy as we don't know which file(s) to add this to? We already set the > filter-with = proxy-prefix in the universe_wsgi.ini fiel. > > Thanks in advance, > Audrey > > > > > > > > > On Mon, Aug 18, 2014 at 11:31 AM, audrey michel <audreymannion(a)gmail.com> > wrote: >> >> Hi John, >> >> Thanks for the suggestions. We are going to try a new install on one of >> our other servers and see if the problem occurs there or not. >> >> Will update you when we do this. >> >> Thanks. >> Audrey >> >> >> On Fri, Aug 15, 2014 at 8:20 PM, John Chilton <jmchilton(a)gmail.com> wrote: >>> >>> Okay - I am replying in thread but I not to your original message >>> because there might be private stuff in the log you sent me. It looks >>> like you were trying to install fastqdump from the main tool shed. So >>> I setup a fresh Galaxy instance this morning and the only two things I >>> changed in the universe_wsgi.ini file were admin_users and >>> tool_dependency_dir (required to install tool dependencies) and this >>> install worked for me. Your error message had "Bad Status Line" in it >>> - so it sounds like you were getting non-sense back from the tool >>> shed. >>> >>> This could be because there is some proxy interfering with this >>> request, it could be that it was just an intermittent problem with the >>> tool shed, or ... some configuration problem potentially? I am not >>> sure. >>> >>> It looks like you had cloned galaxy-dist directly - I think it is >>> better to stay on a particular branch - I would do this: >>> >>> hg pull >>> hg update latest_2014.08.11 >>> >>> To make sure you have the latest and greatest Galaxy and then retry? >>> >>> If you still have problems and it is the same strack trace - please >>> let me know. Next up would be to eliminate the proxy theory - not sure >>> how to do that though :(. >>> >>> -John >>> >>> On Wed, Aug 13, 2014 at 4:36 PM, John Chilton <jmchilton(a)gmail.com> >>> wrote: >>> > I am not sure what the problem is - more details would really help. >>> > For instance - What version of Galaxy are you using? What repository >>> > are you trying to install? Do other repositories work? Does the Galaxy >>> > log have a more complete stack trace? >>> > >>> > Any additional details would be most helpful. >>> > >>> > Thanks, >>> > -John >>> > >>> > On Tue, Aug 12, 2014 at 9:11 AM, audrey michel >>> > <audreymannion(a)gmail.com> wrote: >>> >> Hi, >>> >> >>> >> We get the following error when we try to install any tool from the >>> >> Tool >>> >> shed when using the Admin panel: >>> >> >>> >> >>> >> Internal Server Error >>> >> >>> >> Galaxy was unable to successfully complete your request >>> >> >>> >> An error occurred. >>> >> >>> >> This may be an intermittent problem due to load or other unpredictable >>> >> factors, reloading the page may address the problem. >>> >> >>> >> The error has been logged to our team. >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> We would be grateful if you could advise on this issue. >>> >> >>> >> Kind Regards, >>> >> Audrey Michel >>> >> Baranov Lab >>> >> School of Biochemistry & Cell Biology >>> >> University College Cork >>> >> Ireland >>> >> >>> >> >>> >> >>> >> ___________________________________________________________ >>> >> 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: >>> >> http://lists.bx.psu.edu/ >>> >> >>> >> To search Galaxy mailing lists use the unified search at: >>> >> http://galaxyproject.org/search/mailinglists/ >> >> >

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bioblend run_workflow (no_wait?)
by Evan Bollig 21 Aug '14

21 Aug '14

I'm using bioblend to launch a workflow, but i find that the gi.workflows.run_workflow() command does not provide an option for no_wait. Can anyone provide justification for why this needs to be synchronous? -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Problem uploading files to RNA-Rocket
by David Salcines 21 Aug '14

21 Aug '14

Hi, I was trying to upload some FASTQ files via FTP using the FileZilla client but although the program connects to the server it doesn't log in. I checked the user and the password several times and I tried to use another account but I still got the same error. I also tried to upload the files via URL (using Mega) but when the upload is finished the files appear to be empty. Thanks David

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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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