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%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%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%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 <l...@sanger.ac.uk <mailto:l...@sanger.ac.uk>>


Then I tried to follow this guide:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup to get the
reference files and
http://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_mapping and
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.xml



I 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/1.2.3>"
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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