Hey,
no thats correct I did not use Tool Shed. If I would use it, could I skip all these manual steps? Is the installation of BWA with Tool Shed also this complicated or is it more simle?
How did you not follow my steps :) I wrote down everything clearly, at least thats what I was hoping.
And no I didnt write this line " <tool file="sr_mapping/bwa_wrapper.**xml" />" Thats the first time, I am seeing this tutorial :( I will try this out right now
Best Moritz
On 17 July 2013 09:42, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Moritz
I am struggling to follow what exactly you have done. As far as I can see, you did not use the toolshed (http://wiki.galaxyproject.**org/Tool%20Shedhttp://wiki.galaxyproject.org/Tool%20Shed) to install the BWA alinger tool, but did all manually?
If so, have you added the following line:
<tool file="sr_mapping/bwa_wrapper.**xml" />
to the "tool_conf.xml" file, and restarted Galaxy?
see also: http://wiki.galaxyproject.org/**Admin/Tools/Add%20Tool%**20Tutorialhttp://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial
Hope this helps Hans-Rudolf
On 07/16/2013 08:35 PM, Moritz Juchler wrote:
Hello Ladies and Gentlemen,
I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to choose a bioinformatic pipeline management tool to find SNP's in genomes from hcc patients. My decision was made in favor of galaxy. I have a 64-bit openSuse 11.3 server. I have installed Galaxy locally, since we have a) very large files (>30GB per patient) and b) the data is protection sensitive. I kept close to http://wiki.galaxyproject.org/**Admin/Get%20Galaxyhttp://wiki.galaxyproject.org/Admin/Get%20Galaxy Now I would like to run this bpipe pipeline: http://pastebin.com/sZd5vfdL And the first step is to align my genome to a _hg19 reference genome_
which I have locally under /genedata/human_genome_GRCh37/**.
trr@portalmoritz:~> ls -l /genedata/human_genome_GRCh37/ total 8486312 -rw-r--r-- 1 trr root 3199905909 2013-06-25 16:44 hg19.fa -rw-r--r-- 1 trr root 8591 2013-07-01 16:06 hg19.fa.amb -rw-r--r-- 1 trr root 4040 2013-07-01 16:06 hg19.fa.ann -rw-r--r-- 1 trr root 3137161344 2013-07-01 16:05 hg19.fa.bwt -rw-r--r-- 1 trr root 784290318 2013-07-01 16:06 hg19.fa.pac -rw-r--r-- 1 trr root 1568580688 2013-07-01 16:31 hg19.fa.sa <http://hg19.fa.sa>_bwa is installed and gives me:_
trr@portalmoritz:~> bwa Program: bwa (alignment via Burrows-Wheeler transformation) Version: 0.7.5a-r405 Contact: Heng Li <lh3@sanger.ac.uk <mailto:lh3@sanger.ac.uk>>Then I tried to follow this guide: http://wiki.galaxyproject.org/**Admin/NGS%20Local%20Setuphttp://wiki.galaxyproject.org/Admin/NGS%20Local%20Setupto get the reference files and http://wiki.galaxyproject.org/**Admin/Config/Tool%**20Dependencieshttp://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies .
This is my _$PATH_
trr@portalmoritz:~> echo $PATH /home/trr/bin:/usr/local/bin:/**usr/bin:/bin:/usr/bin/X11:/**usr/X11R6/bin:/usr/games:/**home/trr/bpipe-0.9.8/bin:/** home/trr/bwa-0.7.5a:/home/trr/**samtools-0.1.19
_In the universe_wsgi.ini I changed:_
tool_dependency_dir = /home/trr/galaxy-dist/tool_**dependency_dir debug = False use_interactive = True library_import_dir = /genedata/ allow_library_path_paste = True admin_users = ...This is my _tool_dependency_dir:_
trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa> ls -l total 4 drwxr-xr-x 3 trr users 4096 2013-07-16 14:28 0.7.4 lrwxrwxrwx 1 trr users 6 2013-07-16 14:17 default -> 0.7.4/This is the_version folder of bwa:_
trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4> ls-l total 8 drwxr-xr-x 2 trr users 4096 2013-07-16 14:18 bin -rw-r--r-- 1 trr users 47 2013-07-16 14:22 env.sh
This is the _content of env.sh:_
trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4>cat env.sh PATH="/home/trr/bwa-0.7.5a/:$**PATH" export PATH
And this is the _content of the bin folder:_
trr@portalmoritz:~/galaxy-**dist/tool_dependency_dir/bwa/**0.7.4/bin>ls -l total 3896 -rw-r--r-- 1 trr users 6098 2013-07-16 14:18 bamlite.c -rw-r--r-- 1 trr users 3124 2013-07-16 14:18 bamlite.h -rw-r--r-- 1 trr users 24816 2013-07-16 14:18 bamlite.o -rw-r--r-- 1 trr users 11508 2013-07-16 14:18 bntseq.c -rw-r--r-- 1 trr users 2557 2013-07-16 14:18 bntseq.h -rw-r--r-- 1 trr users 37440 2013-07-16 14:18 bntseq.o -rwxr-xr-x 1 trr users 998217 2013-07-16 14:18 bwa -rw-r--r-- 1 trr users 24225 2013-07-16 14:18 bwa.1 -rw-r--r-- 1 trr users 9416 2013-07-16 14:18 bwa.c -rw-r--r-- 1 trr users 1381 2013-07-16 14:18 bwa.h
....
I got the xmls and .py from https://bitbucket.org/galaxy/**galaxy-dist/src/da9d740fce31/** tools/sr_mappinghttps://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mappingand i didnt change them at all and put them into ~/galaxy-dist/_tools/sr_**mapping_ (since they were missing in this folder)
bwa_color_wrapper.xml bwa_wrapper.py bwa_wrapper.xmlI added _bwa_index_color.loc and bwa_index.loc_ to ~galaxy-dist/_tool-data_ (they were missing as well, there/*were no*/
bwa_index_color.loc.sample or bwa_index.lox.sample files!!!)
I only have this single line in both bwa_index_color.loc and bwa_index.loc
trr@portalmoritz:~/galaxy-**dist/tool-data> cat bwa_index_color.loc #This is a sample file distributed with Galaxy that enables tools # #<unique_build_id> <dbkey> <display_name> <file_path> hg19 hg19 hg19 /genedata/human_genome_GRCh37/**hg19.fa(Spaces are actually tabs!)
After all that, I neither have the "Map with BWA for Illumina <https://main.g2.bx.psu.edu/**tool_runner?tool_id=toolshed.** g2.bx.psu.edu/repos/devteam/**bwa_wrappers/bwa_wrapper/1.2.3https://main.g2.bx.psu.edu/tool_runner?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 **>"
in my local Galaxy version, nor do I find the reference genome. If i missed on any required, please tell me, I will answer you as soon as possible. Sincerly Yours Moritz Juchler
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