Re: [galaxy-user] visualization through Trackster on local Galaxy installation

2014-01-31 Thread Yupu Liang
Using full path in the ini file fix the problem! Thanks, Yupu On Jan 30, 2014, at 10:21, Jennifer Jackson j...@bx.psu.edu wrote: Hi Yupu, I'm sorry, I mixed up the processing for custom builds with the processing for installed builds in my initial reply. A .2bit .len file are appropriate

[galaxy-user] problem with scientific notation sorting and filtering in galaxy

2014-01-31 Thread Douglas Cavener
I have found that numbers in scientific notation (e.g 9.8E-9) are incorrectly sorted or filtered by Galaxy. Looks like the negative exponent is ignored and so if you sorting something like P values (see example below) then you find these ordered above P=1 instead at the other end of the list

[galaxy-user] special character $ gets converted to X in tool

2014-01-31 Thread Ketan Maheshwari
Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this

Re: [galaxy-user] special character $ gets converted to X in tool

2014-01-31 Thread Peter Cock
On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets

[galaxy-user] February 2014 Galaxy Update Newsletter

2014-01-31 Thread Dave Clements
Hello all, The 25th Edition of Galaxy Update is outhttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02. Highlights from the February 2014 Galaxy Updatehttps://wiki.galaxyproject.org/GalaxyUpdates/2014_02 include: - 42 new

[galaxy-user] GATK - Base recalibrator

2014-01-31 Thread Bolduc, Francois
Hi all, I'm trying to call variants using GATK best practices workflow. So after performing Realigner Target Creator step, one should jump on Base Recalibrator step. Unfortunatly, I don't see this program under GATK tab. Is there a way to perform this step in Galaxy? There are the Count

Re: [galaxy-user] GATK - Base recalibrator

2014-01-31 Thread Geraldine Van der Auwera
Hi Frank, Yes, that's equivalent; BaseRecalibrator is a single tool that combines those two steps in more recent versions. The version of GATK in Galaxy (1.6 afaik) is a pretty old one. I would strongly recommend using the most recent version of GATK (2.8) as it will give you better results.

Re: [galaxy-user] problem with scientific notation sorting and filtering in galaxy

2014-01-31 Thread Dave Clements
Hi Douglas, I encourage you and anyone else that has encountered this error to up-vote this issue in the Galaxy Trello board: https://trello.com/c/QZlmb0Yf That will help us prioritize work. Thanks for reporting this. Dave C On Thu, Jan 30, 2014 at 10:24 AM, Douglas Cavener d...@psu.edu

Re: [galaxy-user] special character $ gets converted to X in tool

2014-01-31 Thread Ketan Maheshwari
Thanks! Just wanted to report that \$ does not work; \ adds one more X. On Fri, Jan 31, 2014 at 11:29 AM, Peter Cock p.j.a.c...@googlemail.comwrote: On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari ketancmaheshw...@gmail.com wrote: Hi, In a test tool that I am working on, I need to