[galaxy-dev] microarray NGS

2011-11-09 Thread Ivan Merelli
Hi Galaxy Users, I'm interested in integrating microarray and NGS data. My problem concerns the uploading of an affybatch object in Galaxy (I have a local instance of galaxy, but exacly the same problem is present in http://main.g2.bx.psu.edu) After processing the upload, the only message in

Re: [galaxy-dev] microarray NGS

2011-11-18 Thread Ivan Merelli
for your uploaded dataset, click on the pencil (Edit attributes) and then click the button that says Auto-detect. Best, Eric From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Ivan Merelli [ivan.mere...@itb.cnr.it

Re: [galaxy-dev] microarray NGS

2011-11-19 Thread Ivan Merelli
, but I've only had time so far to partially debug it. Best, Eric From: Ivan Merelli [ivan.mere...@itb.cnr.it] Sent: Friday, November 18, 2011 10:33 AM To: Paniagua, Eric Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] microarray NGS Dear Eric

[galaxy-dev] bam to ucsc

2011-11-19 Thread Ivan Merelli
Hi, I'm experiencing an error while trying to upload bam files from my local instance of galaxy to ucsc. In particular the bam tracks appear in the ucsc genome browser, but instead of data I got this error: End of file reading 1 bytes (got 0) I searched the mailing list, but the only hint I

Re: [galaxy-dev] microarray NGS

2011-11-22 Thread Ivan Merelli
is strictly internal. I do intend to try contributing anything that will be generally useful back to galaxy-central though. Best, Eric From: Ivan Merelli [ivan.mere...@itb.cnr.it] Sent: Saturday, November 19, 2011 10:40 AM To: Paniagua, Eric Cc: ross.laza

[galaxy-dev] rgenetics galaxy

2011-11-25 Thread Ivan Merelli
Hi, I'm trying to use rgenetics in galaxy, but I have some problem in installting rpy-1.0.3 with R-2.13.1. I found this guide, which is about the same problem of mine: http://gmod.827538.n3.nabble.com/Rpy-1-0-3-and-R-2-13-1-td3359590.html but didn't work for me (although the part about the

[galaxy-dev] tool restrict access

2012-01-02 Thread Ivan Merelli
Hi, how can I restrict the access of a Galaxy tool to a specific user in an login free instance of Galaxy? I see a suggestion in this post http://gmod.827538.n3.nabble.com/Galaxy-Tool-permission-Access-td3348890.html but it's really workround, I was seeking for a cleaner solution... Thanks,

[galaxy-dev] Fwd: tool restrict access

2012-01-04 Thread Ivan Merelli
: Ivan Merelli ivan.mere...@itb.cnr.it A: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Hi, how can I restrict the access of a Galaxy tool to a specific user in an login free instance of Galaxy? I see a suggestion in this post http://gmod.827538.n3.nabble.com/Galaxy-Tool-permission-Access

Re: [galaxy-dev] Fwd: tool restrict access

2012-01-09 Thread Ivan Merelli
Hi Jeremy, thank you for your answer. I followed your hint modifyng (for example) the ucsc_tablebrowser.xml as follows (not sure about the display tag to have a simple error message, but this is another problem): tool name=UCSC Main id=ucsc_table_direct1 tool_type=data_source

Re: [galaxy-dev] Fwd: tool restrict access

2012-01-13 Thread Ivan Merelli
Hi Jeremy, sorry for bother you again. I do some tests and the problem seems not in the semi-colons (the cheetah manual is not very clear in this sense, I put them but it did not solve the problem), but in the display tag which is simply incorrect in that position, a call to a python script is

[galaxy-dev] job quotas

2012-01-19 Thread Ivan Merelli
Hi, is it possible to restrict the number of concurrent jobs for a single user in a local instance of galaxy? I see that in the public site this feature is implemented, but I don't find documentation about how to implement this locally. I think it's not possible through pbs because all users