Re: [galaxy-dev] some problem with the fastq interlacer

2012-12-12 Thread David Roquis
Hi, I recently had a problem with fastq interlacer lately, I had to patch it on my galaxy instance to make it work again. Here is the patch (from the developper). Sincerely David Date: Tue, 11 Dec 2012 17:33:05 +0800 From: caizexi...@yahoo.com.cn To: galaxy-dev@lists.bx.psu.edu CC:

[galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

2012-12-12 Thread Sachit Adhikari
How do I add hg16 into the build-in index? ___ 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/

Re: [galaxy-dev] Server Error / Edit attribut of a dataset generated by a tool

2012-12-12 Thread Daniel Blankenberg
Hi Sarah, This looks to be due to a non-unicode character in the dataset's info field. Are you using a Galaxy revision = 7563:fca4e12478d6? Thanks for using Galaxy, Dan On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote: Hello, One of my users gets the following message when he wishes to

Re: [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?

2012-12-12 Thread Jennifer Jackson
Hello Sachit, Instructions for setting up local indexes are in our wiki here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Bowtie2 is not specifically listed, but the instructions for Bowtie and Bowtie2 are nearly identical. The same indexes are used for Bowtie2 and Tophat2. When

Re: [galaxy-dev] Tool dependency installation fail, any documentation?

2012-12-12 Thread Greg Von Kuster
This page of the tool shed wiki has most of the details. The tool dependency tag definitions are evolving rapidly as more tools are being included in the Galaxy tool migration process. I'm trying to keep information updated, but at times the wiki page will lag due to resource deficiencies.

[galaxy-dev] tools imported from toolshed stay in waiting to run status

2012-12-12 Thread Philipe Moncuquet
Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on waiting to run. Other tools work fine, and this generic

[galaxy-dev] Doesn't have enable_beta_job_managers options in configuration file

2012-12-12 Thread Sachit Adhikari
My Galaxy Doesn't have enable_beta_job_managers option in universe_conf.ini file. ___ 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