[galaxy-dev] Local galaxy

2012-12-13 Thread Jennifer Jackson
Repost to mailing list ___ For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev Hi I am doing NGS analysis in our local galaxy, I

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

2012-12-13 Thread Jennifer Jackson
Hello Sachit, There are a few problems with the command line. If you want to install hg19, then hg16 should not be used. Also, the reference_in to the tool should be an uncompressed fasta file. This is described in the tool documentation. You will also need to use as the 'index_basename'

Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-13 Thread Greg Von Kuster
Hi Lance, What process did you use for updating the tool shed repository and how many separate repositories did you use? You should not be updating a local repository, pushing the changes to the tool shed repository, and then attempting to pull the changes back to the same repository. Your

Re: [galaxy-dev] Local galaxy

2012-12-13 Thread Jeremy Goecks
Hi I am doing NGS analysis in our local galaxy, I would like to access the output files for further analysis. I do have an account on the server where galaxy is installed, so I would like to access the output files without actually downloading them( aince they are huge). Can you

Re: [galaxy-dev] Custom Builds Server eroor

2012-12-13 Thread Hans-Rudolf Hotz
Hi Shaun I recently run into troubles creating a visualization for a custom build using a fasta file to provide the sequence lengths. In order to continue, I had to remove the entry from the database, ie: changing the value to {} for name = 'dbkeys' in the 'user_preference' table. I

[galaxy-dev] hg pull aborted

2012-12-13 Thread Sarah Maman
Hello, When updating local instance of our Galaxy, the hg aborted: pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes adding changesets adding manifests adding file changes added 1482 changesets with 3989 changes to 1340 files abort: untracked file in working directory

[galaxy-dev] Fw: Questions about Install GATK on local instance

2012-12-13 Thread ygong
Hi, Could anyone give me some suggestions about that? Thanks very much. Anthonel - Forwarded by Yixiao Gong/cpdr/hjf on 12/13/2012 10:50 AM - From: Yixiao Gong/cpdr/hjf To: galaxy-dev@lists.bx.psu.edu Date: 12/12/2012 02:52 PM Subject:Questions about Install GATK on

Re: [galaxy-dev] Questions about Install GATK on local instance

2012-12-13 Thread Fields, Christopher J
Older versions of GATK can be grabbed from Github: https://github.com/broadgsa/gatk/tags Not sure if they have an official 'older version' download site. chris On Dec 13, 2012, at 9:51 AM, yg...@cpdr.org wrote: Hi, Could anyone give me some suggestions about that? Thanks very much.

Re: [galaxy-dev] Impersonate a User

2012-12-13 Thread greg
The problem is I disabled the logout button in universe.wsgi (I think) (I believe I did that to make it compatible with LDAP?) Thanks, Greg On Tue, Dec 11, 2012 at 5:00 PM, Edward Hills ehills...@gmail.com wrote: Hi Greg, Try clicking the logout button. That should logout of the user you

Re: [galaxy-dev] Questions about Install GATK on local instance

2012-12-13 Thread ygong
Thanks very much, sir. Is there anything else I need to do specially for the setting up? Best, Anthonel From: Fields, Christopher J cjfie...@illinois.edu To: yg...@cpdr.org yg...@cpdr.org Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Date: 12/13/2012 10:59 AM

Re: [galaxy-dev] Questions about Install GATK on local instance

2012-12-13 Thread ygong
Yes, sir. I downloaded the 1.4 version from Chris's link https://github.com/broadgsa/gatk/tags, it looks the same as the one that I saw on the https://github.com/broadgsa/gatk. I couldn't figure out how to intall it because it contains two folders and multiple files except any executable. How

Re: [galaxy-dev] Impersonate a User

2012-12-13 Thread Fields, Christopher J
The user impersonation feature doesn't work with external authentication. There is a bug report on this: https://trello.com/c/zwqNwflD chris On Dec 13, 2012, at 10:01 AM, greg margeem...@gmail.com wrote: The problem is I disabled the logout button in universe.wsgi (I think) (I believe I

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

2012-12-13 Thread Sarah Maman
Hi Daniel, In fact, my version needs to be updated : changeset: 6799:40f1816d6857 tag: tip user:Greg Von Kuster g...@bx.psu.edu date:Wed Mar 07 13:35:34 2012 -0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file. I

[galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread greg
I'm seeing the error below when I try to run Tophat for Illumina. Has anyone seen this before? Could I have installed bowtie incorrectly or am I simply running with the wrong data/parameters? Thanks, Greg (I'm also really confused why the error is mentioned /tmp/* paths. I never assigned

Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-13 Thread Lance Parsons
Since I've had issues with workflow and the toolshed in the past, I have changed my workflow so that my only interaction with the toolshed is either via uploading a tarball via the web interface or installing a tool into my local Galaxy via the web interface (or occasionally just downloading

Re: [galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread greg
I'm confused. So I installed tophat-2.0.6.Linux_x86_64 which seems to contain tophat and tophat2. Can't galaxy use that tophat? Am I supposed to also install tophat 1? Does galaxy somehow failover to use tophat2 otherwise? What am I missing? Thanks, Greg On Thu, Dec 13, 2012 at 2:32 PM,

Re: [galaxy-dev] Downloading datasets without username/password when login is required

2012-12-13 Thread Sytchev, Ilya
So, it turns out that it's currently impossible to download datasets programmatically without using username/password (when require_login is set to True) because Galaxy API does not have functionality to download datasets. Are there any plans to implement this feature? Thanks, Ilya On 12/11/12

Re: [galaxy-dev] Tophat for Illumina Error: Could not find Bowtie 2 index files

2012-12-13 Thread Jeremy Goecks
I'm confused. So I installed tophat-2.0.6.Linux_x86_64 which seems to contain tophat and tophat2. tophat2 redirects to tophat, which is tophat version 2.X.X Can't galaxy use that tophat? You can, but you need to use the Tophat2 wrapper, not the Tophat for Illumina wrapper. And, when you

Re: [galaxy-dev] Updating help text for a tool shed repository

2012-12-13 Thread Greg Von Kuster
Hi Lance, I tried several scenarios today in an attempt to reproduce this but I was not able to. Have you tried uninstalling the repository (check the checkbox to completely uninstall it) and then reinstall it? I'm trying to reproduce this on a mac running mercurial version 2.2.3 and Python

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

2012-12-13 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