[galaxy-dev] user creation using API

2013-01-07 Thread Hagai Cohen
Hi, I would like to auto create users on my local Galaxy instance. I saw that in the create user on the API, I should enable use_remote_user (which as I understand means that I have to use Apache or nginx). Is there another way besides using Apache to create users automatically? Thanks, Hagai

[galaxy-dev] variables not defined

2013-01-07 Thread MONJEAUD
Hello all, I am using my own Galaxy instance and I had a problem with page and visualization tabs. For example, when I want to edit attributes of a page, I've got this error traceback : |NameError: global name 'VALID_SLUG_RE' is not defined| and when I want to remove or share a page or a

Re: [galaxy-dev] In which Encryption form does Galaxy store password?

2013-01-07 Thread Ido Tamir
Its hashed (sha1) and you can not reverse the hash. Storing passwords in a reversible manner is bad practice. http://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/util/hash_util.html You could maybe authenticate your users from the other program with the same method against the

Re: [galaxy-dev] backtrace when attempting to view a shared workflow

2013-01-07 Thread Langhorst, Brad
I've recently updated to the december 20th revision of galaxy and still have a problem with a few workflows. You can find the backtraces below. based on these I'm starting to look in /mnt/ngswork/galaxy/galaxy-dist/lib/galaxy/workflow/modules.py - but any hints would be appreciated. thanks

[galaxy-dev] fastq_combiner

2013-01-07 Thread Jennifer Hillman-Jackson
Hello, The tool you are looking for is: galaxy-dist / tools / fastq / fastq_combiner.py galaxy-dist / tools / fastq / fastq_combiner.xml Hopefully this helps. Next time, please be sure to send questions directly to the galaxy-...@bx.psu.edu email address. Your question went to

Re: [galaxy-dev] (no subject)

2013-01-07 Thread Jennifer Hillman-Jackson
Security warning: DO NOT CLICK on the link in this thread. Rehan Saleem - it is likely that your original sending hotmail email account has been compromised. We have removed it from the galaxy-...@bx.psu.edu mailing list to prevent further unmoderated posts until the problem is cleared.

Re: [galaxy-dev] Stumped by GridOperation

2013-01-07 Thread James Taylor
Ted, have you considered if you can do what you need with the 'allowed' method of GridOperation? It let's you define a callable condition that determines if that operation is allowed on a given item. It does not have access to trans but it would be reasonable to add that. -- James Taylor,

[galaxy-dev] How to get output images to appear in Galaxy

2013-01-07 Thread Jennifer Hillman-Jackson
Repost to Galaxy Dev On 1/7/13 5:14 AM, Makis Ladoukakis wrote: Dear Galaxy users, I have a tool which among other files it produces certain images in .png format. Does anyone know if there is a way to make them appear inside the display data interface? Thank you in advance, Efthymios

Re: [galaxy-dev] user creation using API

2013-01-07 Thread John Chilton
I am pretty confident there is no way to do this via the API currently, though I imagine it wouldn't be terribly complicated to add and the community would appreciate the contribution. If API-based access isn't a strong requirement and you have direct access to the Galaxy server here is a

Re: [galaxy-dev] backtrace when attempting to view a shared workflow

2013-01-07 Thread Daniel Blankenberg
Hi Brad, Thanks for reporting this issue. I've committed what I hope is a fix for your issue in changeset 8527:eb4dac39eed5 in galaxy-central. Once you are able to apply these changes, would you mind letting us know if this resolves your broken workflows? Thanks for using Galaxy, Dan On

Re: [galaxy-dev] Uploading large files to history through API (some random thoughts)

2013-01-07 Thread Kyle Ellrott
The pull request for this patch is still on the queue. Is anything happening with this? Kyle On Tue, Nov 27, 2012 at 8:56 AM, John Chilton chil...@msi.umn.edu wrote: I went down something of a rabbit hole last night, I thought that uploading files through the API using multipart/form-data

Re: [galaxy-dev] Transfer Manager

2013-01-07 Thread Kyle Ellrott
I'm trying to figure out if I can do this all through the API (so I can skip setting up FTP servers and sharing database servers). I can scan one system, and initiate downloads on the destination system (using upload1). So as far as moving files from one machine to another, it should be fine. I

Re: [galaxy-dev] Stumped by GridOperation

2013-01-07 Thread Ted Goldstein
Hi Greg and James, This has become a plumbing project. What starts off as fixing a leaky faucet ends being a $200 bill replacing the entire sink ;-). But I don't see anyway around it. Yes, there is a lot of power in the allowed method since it uses a function or a lambda. There are two

[galaxy-dev] Galaxy submitting jobs to remote cluster

2013-01-07 Thread Thomas Uram
Hello: I am trying to configure Galaxy to submit jobs to a remote cluster (specifically, an XSEDE resource to which I don't have administrative access). I'm familiar with LWR and have read another response about configuring the Galaxy host as a PBS submit host. What is the best approach to

Re: [galaxy-dev] File import recovery

2013-01-07 Thread Kyle Ellrott
Editing the DB and manually fixing all the errors in the UI doesn't seem like a long term solution. Is there a way to do this through the API? If not, where should I start working to add it in? Kyle On Wed, Jan 2, 2013 at 7:41 AM, Nate Coraor n...@bx.psu.edu wrote: On Dec 31, 2012, at 8:18

Re: [galaxy-dev] backtrace when attempting to view a shared workflow

2013-01-07 Thread Langhorst, Brad
Hi Dan: After much wrestling with hg graft and gnashing of teeth I failed to cherry pick that changeset and just added the code manually in lib/galaxy/tools/__init__.py However, I'm not observing any change as a result. I cannot clone, view, export or edit this workflow (or the other problem

[galaxy-dev] Tool tests

2013-01-07 Thread Cameron Jack
Hi, I hope I'm writing to the right area (if not, please point me in the right direction and I'll go on my way). I have a set of tools that our team have built and been using for functional genomics analysis, which I would like to integrate into Galaxy. My first concern is with the tests.

Re: [galaxy-dev] variables not defined

2013-01-07 Thread Jeremy Goecks
These bugs have been fixed in our development repository (galaxy-central) and will be available in the next distribution, which should occur in the coming week. Thanks, J. On Jan 7, 2013, at 6:23 AM, MONJEAUD wrote: Hello all, I am using my own Galaxy instance and I had a problem with

[galaxy-dev] anybody seen 403s after a recent upgrade?

2013-01-07 Thread Langhorst, Brad
galaxy.web.framework WARNING 2013-01-07 22:06:30,044 User logged in as '(null)' externally, but has a cookie as 'langho...@neb.commailto:langho...@neb.com' invalidating session - - [07/Jan/2013:22:06:30 -0400] GET /api/histories/4c8cd68e0b9ed4a7 HTTP/1.1 403 -