Hi, The bowtie issue was resolved. I resolved it by adding a table entry in the xml file "tool_data_table_conf.xml". Hummmm :) .... Now, I am having the same issue with the SamTools displaying a reference genome.... :)... My reference fasta file is located at (/usr/local/galaxy_data/hg19/samtools/) I ran the following command to build the samtools index file
samtools faidx hg19.fasta This generated the hg19.fasta.fai
Here is the content of the above path after running the samtools indexing command: -rwxr-xr-x 1 galaxy galaxy hg19.fasta -rw-rw-r-- 1 galaxy galaxy hg19.fasta.fai For my sam_fa_indices.loc file here is the info I am using to reference the index file: ############ Index<TAB>hg19<TAB>/usr/local/galaxy_data/hg19/samtools/hg19.fasta ########### I restarted my server but I do not see anything when I go to GUI->NGS:SamTools->Sam-To-Bam->Choose the source for the reference list:<HISTORY> I do not see anything so far. Is there something I am missing or is there anything else I need to change at this point. Regards, -----Original Message----- From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Hakeem Almabrazi Sent: Thursday, January 31, 2013 10:50 AM To: Carlos Borroto Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] FW: install reference genome Bwa and Bowtie! 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 ___________________________________________________________ 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/