Re: [galaxy-dev] install reference genome Bwa and Bowtie!

2013-02-01 Thread Jennifer Jackson
32 AM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! Hi Hakeem, The set up for samtools looks correct. If the problems that you had with BWA/Bowtie were due to an error in our wiki, please send in the suggested changes to me. We w

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

2013-02-01 Thread Hakeem Almabrazi
m Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! Hi Hakeem, The set up for samtools looks correct. If the problems that you had with BWA/Bowtie were due to an error in our wiki, please send in the suggested changes to me. We want this

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

2013-02-01 Thread Jennifer Jackson
there anything else I need to change at this point. Regards, -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, January 31, 2013 6:45 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] install reference genome Bwa and Bowti

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

2013-02-01 Thread Hakeem Almabrazi
ifer Jackson [mailto:j...@bx.psu.edu] Sent: Thursday, January 31, 2013 6:45 PM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! Hello Hakeem, It is difficult to troubleshoot without knowing all the exact details of your config

Re: [galaxy-dev] install reference genome Bwa and Bowtie!

2013-01-31 Thread Jennifer Jackson
Hello Hakeem, It is difficult to troubleshoot without knowing all the exact details of your configuration, but it sounds as if you are on the right path and the last few bits should be easy to reconcile with our documentation. In particular, check that the builds.txt file contains the genomes

[galaxy-dev] install reference genome Bwa and Bowtie!

2013-01-30 Thread Hakeem Almabrazi
Hi, I just installed Galaxy in local Centos Vm. I did my best to get everything working ( I think). I followed the instructions in this Wiki (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install reference genomes for the tools Bwa and Bowtie. Here is what I did in details: 1.