Hey,

now I am having a new problem: Convert SAM to BAM
Tool execution generated the following error message: 
[samopen] SAM header is present: 93 sequences.
Parse error at line 106: sequence and quality are inconsistent
/bin/sh: line 1: 27934 Aborted                 samtools view -bS "/home/trr/galaxy-dist/database/files/000/dataset_17.dat" > "/tmp/tmp-sam_to_bam_converter-ut5Tag/unsorted.bam"
The tool produced the following additional output: 
[bam_header_read] EOF marker is absent. The input is probably truncated.
(should I make a new post out of this?)

The step I did before was:
7: Map with BWA for Illumina on data 5 and data 3: mapped reads
~21,000 lines, 94 comments
format: sam, database: hg19
BWA Version: 0.7.5a-r405 BWA run on paired-end data

That one seems to work correctly.
Any help appreciated :)

Best
Moritz


On 22 July 2013 11:20, Moritz Juchler <juchler@stud.uni-heidelberg.de> 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 <juchler@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 <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%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 <lh3@sanger.ac.uk <mailto:lh3@sanger.ac.uk>> 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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