[galaxy-dev] Local Toolshed misbehaviours?

2012-03-16 Thread Daniel Sobral
Hello, I've installed a local toolshed server in http://myserver/toolshed/ (served by Apache) I am able to run it and create a repository with a tool. In my local galaxy server (http://myserver/galaxy/) I am able to see the repositories in that toolshed server, but when I try to install the

[galaxy-dev] Depositing Data in a user's account

2012-03-16 Thread Alex Kalderimis
Hi all, at InterMine we are looking to improve various aspects of our UI, and also our interaction with Galaxy. To that end, it would be great to find out what ways there are of depositing data in a user's account. The ideal would be to make requests from javascript that either open in another

Re: [galaxy-dev] Stalled upload jobs under Admin, Manage jobs

2012-03-16 Thread Peter Cock
On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraor n...@bx.psu.edu wrote: On Feb 10, 2012, at 6:47 AM, Peter Cock wrote: Hello all, I've noticed we have about a dozen stalled upload jobs on our server from several users. e.g. Job ID        User    Last Update     Tool    State   Command Line    

Re: [galaxy-dev] Local Toolshed misbehaviours?

2012-03-16 Thread Greg Von Kuster
Hi Daniel, What does your tool shed paster log say when you get the 404 error trying to install? You can see the paster log by running the following from your Galaxy installation directory when your tool shed is running. tail -f community_webapp.log Greg Von Kuster On Mar 16, 2012, at 4:34

Re: [galaxy-dev] Local Toolshed misbehaviours?

2012-03-16 Thread Daniel Sobral
Hi Greg, The paster log from the toolshed server does not tells me much: - - [16/Mar/2012:12:27:31 +0100] GET /toolshed/repository/preview_tools_in_changeset?repository_id=2bccd98f7ba1e82achangeset_revision=a42c4c034c26webapp=galaxy HTTP/1.1 200 -

Re: [galaxy-dev] Local Toolshed misbehaviours?

2012-03-16 Thread Greg Von Kuster
Daniel, how about your paster log from your Galaxy instance - what does it tell you? Your logs should tell you what is causing the 404 error. Clicking the install button when browsing the tool shed from Galaxy will produce something like the following in your tool shed paster log:

Re: [galaxy-dev] Error Setting BAM Metadata

2012-03-16 Thread Nate Coraor
On Feb 3, 2012, at 3:14 PM, Liisa Koski wrote: Yes it isand my galaxy is up to date. Hi Liisa, Sorry for not getting back to you. Did you ever figure out what was up with this? Since you're pasting a URL, I'm wondering if the URL fetch is failing. --nate Thanks, Liisa

Re: [galaxy-dev] Importing data from password protected UCSC Genome Browser

2012-03-16 Thread Nate Coraor
On Feb 7, 2012, at 5:52 AM, Federico De Masi wrote: Dear colleagues, I have been struggling with this issue for quite a while now, and I don't seem to find a solution (neither in situ nor in webo). here it is: Because of the confidentiality of our data, I have setup both a Galaxy

[galaxy-dev] Compare two datasets fails due to encoding error

2012-03-16 Thread Mikel Egaña Aranguren
Hi; I have developed a Perl tool that generates a tabular file with 3 columns. I need to compare it with another tabular file (Gene Ontology Annotation file) and I use Join, substract, group, Compare two datasets. When I try to do so, I get the error pasted bellow. I assume my perl code is

Re: [galaxy-dev] problem after last upgrade

2012-03-16 Thread Michal Stuglik
Hi Greg, Database downgrade and then upgrade succeeded! galaxy instance is working now! many thanks! michal On 03/15/2012 08:57 PM, Greg Von Kuster wrote: Hi Michel, No idea why, but for some reason your database migration script number 92 failed. You should try the following from your

[galaxy-dev] CAGE data - trimming SAM files (functionality suggestion)

2012-03-16 Thread Lukasz Jan Kielpinski
Hello, I work sometimes with galaxy analysing of short reads but actually I very much lack the function of keeping only first nucleotide of the read in SAM file. This is not so straightforward to do, I need to modifiy sequence, quality scores and CIGAR. It would be very useful for looking e.g on

Re: [galaxy-dev] sharplabtool in Galaxy Tool Shed

2012-03-16 Thread Greg Von Kuster
Hello Xuebing, Your updates that will be available for an installed repository are restricted to the version that is installed where the version is defined by the change set revision number. This enables different versions of tools in the repository to always be accessible and installable.