Re: [galaxy-dev] FW: install reference genome Bwa and Bowtie!
Hi, The bowtie issue was resolved. I resolved it by adding a table entry in the xml file "tool_data_table_conf.xml". Hu :) 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: Indexhg19/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: 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-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@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: hg19hg19hg19/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 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: # 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/ ___ 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/
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: hg19hg19hg19/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 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: # 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/
Re: [galaxy-dev] FW: install reference genome Bwa and Bowtie!
Thank you Carlos again. I was just looking at that and in fact I got it to work by following the sample file. I was misled by the tutorial http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup in regard to create this file. *** Setting Up loc File Get the index files to an accessible location Create the file bwa_index.loc in the Galaxy tool-data directory You can add the following header line if you want: #buildname filepath with a single tab separating the two Then start adding the entries for each build The file's path should include the first part of the index files' names (the base) So if they are named like reference_in.fasta.amb and are stored in /path/to/base/indices, the entry should be: reference_in /path/to/base/indices/reference_in.fasta a tab separating the two ** Now it is working but I am still not clear about the header line # . Which one of the identifier names should match the actual reference_in name? Or it does not matter? Thanks -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 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: # 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/
Re: [galaxy-dev] FW: install reference genome Bwa and Bowtie!
On Thu, Jan 31, 2013 at 9:09 AM, Hakeem Almabrazi 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: # 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/
[galaxy-dev] FW: install reference genome Bwa and Bowtie!
-Original Message- From: Hakeem Almabrazi Sent: Thursday, January 31, 2013 7:54 AM To: 'Carlos Borroto' Subject: RE: [galaxy-dev] install reference genome Bwa and Bowtie! Thank you Carlos for your help, 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 ### The same issue is happening with bowtie. Is there anything I need to do somewhere else in the system (DB, configuration files etc) i.e in ~ tool-data/shared/ucsc/builds.txt file. Regards, Hakeem -Original Message- From: Carlos Borroto [mailto:carlos.borr...@gmail.com] Sent: Wednesday, January 30, 2013 10:22 PM To: Hakeem Almabrazi Subject: Re: [galaxy-dev] install reference genome Bwa and Bowtie! On Wed, Jan 30, 2013 at 7:19 PM, Hakeem Almabrazi wrote: > 4. I created the loc files (bowtie_indices.loc and > bowtie_indices_color.loc and bwa_index.loc) and populate them with the > recommended contents) and place them in ~/tool_data/ folder. Most of the time I run into this issue this is the step where I'm messing up. Double check you are using TABs (not spaces) to separate values in these files. Also check you have only one TAB between values, some of the examples have more than one for pretty formatting but that will cause the configuration not to work. Hope it helps, 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/
