Hi Carlos, What about the bowtie? I am still having the same issue with it. Loc file: ~/tool-data/bowtie_indices.loc Contents: hg19 hg19 hg19 /usr/local/galaxy_data/hg19/bowtie/base/hg19 (WITH TABS) listing all the files in (/usr/local/galaxy_data/hg19/bowtie/base/hg19) -rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.1.ebwt -rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.2.ebwt -rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.3.ebwt -rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.4.ebwt -rw-rw-r-- 1 galaxy galaxy 37 /usr/local/galaxy_data/hg19/bowtie/base/hg19.rev.1.ebw -rw-rw-r-- 1 galaxy galaxy /usr/local/galaxy_data/hg19/bowtie/base/hg19.rev.2.ebw Is there anything not right here? I really appreciate your help... ... -----Original Message----- From: Carlos Borroto [mailto:carlos.borroto@gmail.com] Sent: Thursday, January 31, 2013 8:50 AM To: Hakeem Almabrazi Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: FW: [galaxy-dev] install reference genome Bwa and Bowtie! On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi <halmabrazi@idtdna.com> wrote:
I was sure that was not the case (all in tabs). Here is my bwa_indices.loc file look like ##################### #bwaReference /usr/local/galaxy_data/hg19/bwa/ hg19_reference_genome /usr/local/galaxy_data/hg19/bwa/hg19_reference_genome.fasta #######################
This doesn't seem right, please take a look to the sample .loc file: http://toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/file/ffa8aaa14f7c/t... You need something like: #<unique_build_id> <dbkey> <display_name> <file_path> hg19 hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa Best, Carlos