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 <juch...@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 <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> 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>
>>>>
>>>>
>>>> _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<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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