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.borr...@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 <halmabr...@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/tool-data/bwa_index.loc.sample You need something like: #<unique_build_id> <dbkey> <display_name> <file_path> hg19 hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa Best, Carlos ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
