[galaxy-user] GATK Not running

2012-12-11 Thread Farooq,Umar (res)
Hi, I am trying to incorporate GATK in my pipeline but not been able to make it work. I aligned my data with Hg 19 and then ran sam tool filter and then picard duplicate removal. I uploaded dbSNP and the reference FASTA file for Hg 19 in galaxy to run this pipeline. But for some reason GATK too

Re: [galaxy-user] GATK Not running

2012-12-11 Thread Farooq,Umar (res)
ssentially cannot use GATK in galaxy. From: Joshua Orvis [jor...@gmail.com] Sent: Tuesday, December 11, 2012 5:34 PM To: Philipe Moncuquet Cc: Farooq,Umar (res); galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] GATK Not running I'm having som

Re: [galaxy-user] GATK Not running

2012-12-13 Thread Farooq,Umar (res)
: total time 0.06 From: Daniel Blankenberg [d...@bx.psu.edu] Sent: Wednesday, December 12, 2012 4:29 PM To: Farooq,Umar (res) Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] GATK Not running Hi Umar, Can you click the eye icon to view the contents