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

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>

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" 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