[galaxy-dev] uploads stuck in history

2012-02-22 Thread Jorrit Boekel
Dear list, I have stumbled on some strange behaviour when uploading files to galaxy via the upload.py tool. At times, the upload seems to be stalled in history and is never actually performed, followed by a seemingly infinite history update (see log below). My system is Ubuntu 11.10 and runs

[galaxy-dev] Timeout and Galaxy - Cluster could not complete job

2012-02-22 Thread Aurélien Bernard
Hello everybody :) Today, I have a question related to timeout management in Galaxy. More particularly, I'm searching for a way to set (in a configuration file if possible) all timeouts related to DRMAA and timeouts related to communication between Galaxy and SGE. My goal is to increase

Re: [galaxy-dev] Sample Tracking System problem in Galaxy.

2012-02-22 Thread Greg Von Kuster
Hello Luobin, Galaxy Sample Tracking is not supported by the core Galaxy development team, so you're on your own on this one. I'm told the problem is that the format of the library content ID has been changed in the API, so the script needs to be updated to reflect that. Sorry for the

Re: [galaxy-dev] uploads stuck in history

2012-02-22 Thread Hans-Rudolf Hotz
Hi I guess we see similar things: a new history item is created, it turns purple, stays like this apparently forever while no job id is created (ie I don't see the job in any of the report tools). To be honest we ignore them, because: a) it only (as far as I can tell) happens with big data

Re: [galaxy-dev] uploads stuck in history

2012-02-22 Thread Leandro Hermida
Hi all, We get the behavior mentioned some times too, its not reproducible just like you mentioned. Some times it happens with small files, some times with large files and again as you said it doesn't happen all the time. Now I haven't seen this yet on our Galaxy dev server which is the latest

Re: [galaxy-dev] uploads stuck in history

2012-02-22 Thread Jorrit Boekel
Hi, I haven't been patient enough to wait really long, but I can give that a try. As Leandro mentioned, I've also seen it in kilobyte to megabyte sized files. My Galaxy is forked from the latest galaxy-dist. cheers, jorrit On 02/22/2012 04:47 PM, Leandro Hermida wrote: Hi all, We get

Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API

2012-02-22 Thread Anthonius deBoer
Huh? I have many string inputs to some particular workflow steps...Those are parameters etc that need to be entered or chosen from a dropdown..How would we deal with those kinds of entries into a workflow in the API? Or do all of them have to be pre-set?ThanksThonOn Feb 21, 2012, at 04:21 PM,

Re: [galaxy-dev] Error 500 when trying to execute a workflow with the API

2012-02-22 Thread dannonbaker
Ahh, I see what you're asking. I thought you were referring to providing dataset inputs by name, my mistake.Currently running workflows through the API doesn't support defining inputs other than datasets, that is, it expects workflows to be fully pre-defined with nothing 'set at runtime' other

Re: [galaxy-dev] Splitting large jobs over multiple nodes/CPUs?

2012-02-22 Thread Peter Cock
On Thu, Feb 16, 2012 at 9:02 PM, Peter wrote: On Thu, Feb 16, 2012 at 6:42 PM, Chris wrote: On Feb 16, 2012, at 12:24 PM, Peter wrote: I also need to look at merging multiple BLAST XML outputs, but this is looking promising. Yep, that's definitely one where a simple concatenation wouldn't

Re: [galaxy-dev] Splitting large jobs over multiple nodes/CPUs?

2012-02-22 Thread dannonbaker
Awesome, I'll take a look. And, if you're able to pull it together easily enough, clean branches are always nice.-DannonOn Feb 22, 2012, at 10:59 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Basic BLAST XML merging implemented and apparently working:

[galaxy-dev] snpEff: html report is not displaying after update

2012-02-22 Thread Jennifer Jackson
Hello Raj, This tool is from the Tool Shed and is maintained by the tool author. To contact them about functionality or problems, go to the Tool Shed at http://toolshed.g2.bx.psu.edu/, locate the repository (search by 'snpEff'), click on the name, in the the top far right corner locate the

[galaxy-dev] R scripts for DESeq

2012-02-22 Thread Jennifer Jackson
Hi Lisa, I am going to send your question over to the galaxy-...@bx.psu.edu mailing list so that the development community can offer feedback. http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-cloud_instance.2C_or_development_thread Th galaxy-user list is primarily for

[galaxy-dev] limited tool shed browse

2012-02-22 Thread David Hoover
When I click on Admin-'Search and browse tool sheds'-'Galaxy main tool shed', it shows the first page of Valid repositories. However, clicking '2', '3', '4', or 'Show All' has no effect. I can only display the first page of repositories. However, if I search for valid tools using the menu

Re: [galaxy-dev] FastX tools

2012-02-22 Thread Peter Cock
On Tue, Feb 21, 2012 at 5:49 PM, Borrone, James james.w.borr...@okstate.edu wrote: hello, I am trying to use the FastX tools on the Main server to trim and manipulate FASTQ files extracted directly from an sff file (again using the main galaxy web server).  In using Clip and the Reverse

Re: [galaxy-dev] limited tool shed browse

2012-02-22 Thread Greg Von Kuster
Hi David, I cannot reproduce this behavior from my local Galaxy instance, but clicking '2', '3', '4' or 'Show All does take a second or more to display the response. Can you provide more information about the environment you have or what you are doing to reproduce this? Thanks Greg Von

Re: [galaxy-dev] limited tool shed browse

2012-02-22 Thread Greg Von Kuster
What browser / version are you using? On Feb 22, 2012, at 4:18 PM, David Hoover wrote: It's a local install, hg summary gives 6621:26920e20157f. I'm using MySQL as a backend database and have the following options set to non-default: port = 8081 host = 0.0.0.0 tool_config_file =

Re: [galaxy-dev] How to learn about new tools in the official Tool Shed

2012-02-22 Thread Jennifer Jackson
Hi Sarah, Bjoern is correct. A few other choices are: We send out a tweet when new tools are added. This isn't automatic, or necessarily for all tools, but something we plan on continuing. If interested, you could follow us on twitter or track the Twitter wiki:

Re: [galaxy-dev] R scripts for DESeq

2012-02-22 Thread Liusong Yang
Hi Vipin, That is a wonderful news and I am eager to see it in tool shed. I am going to check tool shed frequently these days to get it asap. Thanks Lisa On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com wrote: Hi, We have the recent release version of DESeq at our Galaxy instance,

Re: [galaxy-dev] R scripts for DESeq

2012-02-22 Thread Greg Von Kuster
Lisa, In case you aren't aware, you can set your user preferences for your account in the tool shed to receive an email message when a new repository's first upload occurs. This would keep you from having to check the tool shed. Go to User - Preferences - Manage your email alerts and you'll