Hi Moritz
I am not a galaxy tool shed expert, but I recommend you start with
reading these wiki pages:
http://wiki.galaxyproject.org/Tool%20Shed
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy
and then try installing BWA via the tool shed and ask (if any) specific
questions (preferably with a new subject line) on the mailing list.
Regards Hans-Rudolf
On 07/22/2013 11:20 AM, Moritz Juchler wrote:
Hey,
with the "tool file" line I got it working :)
Thanks a lot. Could you answer the question regarding Tool Shed: "If I
would use Tool Shed, could I skip all these manual steps? Is the
installation of BWA with Tool Shed also this complicated or is it more
simle?"
Best
Moritz
On 17 July 2013 09:51, Moritz Juchler <juch...@stud.uni-heidelberg.de
<mailto:juch...@stud.uni-heidelberg.de>> wrote:
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 <h...@fmi.ch
<mailto:h...@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%20Shed
<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
<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
<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>
<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> <mailto:l...@sanger.ac.uk
<mailto:l...@sanger.ac.uk>>>
Then I tried to follow this guide:
http://wiki.galaxyproject.org/__Admin/NGS%20Local%20Setup
<http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup> to
get the
reference files and
http://wiki.galaxyproject.org/__Admin/Config/Tool%__20Dependencies
<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
<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
<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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___________________________________________________________
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