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

Thanks! Just wanted to report that \$ does not work; \ adds one more X. On Fri, Jan 31, 2014 at 11:29 AM, Peter Cock wrote: > On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari > wrote: > > Hi, > > > > In a test tool that I am working on, I need to enter text preceded by a $ > > sign to be inte

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

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 wrote: > I ha

Re: [galaxy-user] GATK - Base recalibrator

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. Good

[galaxy-user] GATK - Base recalibrator

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 covari

[galaxy-user] February 2014 Galaxy Update Newsletter

Hello all, The 25th Edition of Galaxy Update is out. Highlights from the February 2014 Galaxy Update include: - 42 new papers

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

On Fri, Jan 31, 2014 at 5:13 PM, Ketan Maheshwari 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 converted to X when it gets >

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

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 or

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

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 whe

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

Using full path in the ini file fix the problem! Thanks, Yupu On Jan 30, 2014, at 10:21, Jennifer Jackson 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 > for what