Hi, Camille.

If you can find some time to upload some of your bam files, could you
please test the revised bam merge tool on http://test.g2.bx.psu.edu/
and let me know how you go. This won't be on the main site until the
next scheduled update in a few weeks.

If you need this locally, the changes are in galaxy-central from where
anyone can grab them - the key file you need to update is
tools/samtools/sam_merge.xml and you'll also need MergeSamFiles.jar
from a recent Picard release to be available in your
tool-data/shared/jars directory.

Hope this helps - thanks for pointing out the bug.

On Thu, Aug 4, 2011 at 12:02 PM, Ross <ross.laza...@gmail.com> wrote:
> Hi, Camille,
>
> I can see this really needs a 'proper' fix - preferably taking
> advantage of the automated header merge.
> Preserving the metadata from each bam automatically is safer and less
> error-prone but you could use the existing "Replace sam/bam header"
> tool to do the surgery once you have a correct header in SAM format in
> your history?
>
> I'm currently testing changes which replace the current samtools merge
> code with a call to Picard MergeSamFiles.
> I'll add a switch to control whether all input headers are merged in
> case there are situations where it's not wanted.
>
> I'll let you know when you can try it out on our test instance and
> which revision of the galaxy-central repository contains the changes
> so you can get it working on your local installation.
>
> On Wed, Aug 3, 2011 at 11:49 PM, Camille Stephan
> <camille.step...@irbbarcelona.org> wrote:
>> Hi Ross,
>> thanks for your answer. I found a dirty fix for merging pairs of bam files,
>> had to change a couple of things in my local installation though.
>>
>> - Add group reads to each BAM file separately using Picard's Add or Replace
>> Groups (with ID=s1 and ID=s2 for each file)
>> - Create the "rg.txt" file containing something like this:
>>
>> @RG     ID:s1        SM:s1        LB:s1        PL:Illumina
>> @RG     ID:s2        SM:s2        LB:s2        PL:Illumina
>>
>> Modify sam_merge.py to call:
>>
>> "samtools merge -rh path/to/rg.txt %s %s..."
>>
>> It works. The problem is all (pairs of) files will end up with the same IDs
>> and labels, unless the rg.txt file is changed every time.
>> Would it be very difficult to add to the Galaxy wrapper the option of
>> creating rg.txt on the fly and adding the -h option to the samtools call?
>>
>> I'm not familiar with creating wrappers for Galaxy, any suggestion as to
>> where to start?
>>
>> Thanks again,
>> Camille
>>
>>
>>
>> On Wed, Aug 3, 2011 at 2:34 PM, Ross <ross.laza...@gmail.com> wrote:
>>>
>>> Camille, thanks for reporting this - I think you have found a bug.
>>> We definitely need to be able to preserve metadata when we merge bams.
>>> Thanks for your suggestion of using mergeSamFiles - yes, I think it
>>> might be a good fix for this problem - but it will take a little while
>>> and won't reach the Main site for a few weeks once it's done. It is
>>> possible to write your own wrapper locally if you need it fast.
>>> Sorry for the inconvenience and thanks again.
>>>
>>> On Wed, Aug 3, 2011 at 6:15 PM, Camille Stephan
>>> <camille.step...@irbbarcelona.org> wrote:
>>> > Hello guys,
>>> > I'm trying to run a pipeline of the best practices for snp and indel
>>> > discovery as described by the people at Broad and I'm running into
>>> > troubles
>>> > with the GATK tools in a local installation of Galaxy.
>>> > The main problem I have is that merging bam files with the samtools
>>> > merge
>>> > tool doesn't keep read group for each sample, causing "Count Covariates"
>>> > to
>>> > crash. The pipeline works fine with a single bam file, but I need to
>>> > realign
>>> > at least two files at a time.
>>> > Is there a way to set the read group of a merged bam inside Galaxy? Are
>>> > there plans to include the "merge" tool from Picard in Galaxy? Is there
>>> > an
>>> > easy way for me to do this locally? (Although I would like to run this
>>> > in
>>> > the cloud later on when the workflow is ready).
>>> >
>>> > Thanks!
>>> > Camille
>>> >
>>> > --
>>> > ***
>>> > Camille Stephan-Otto Attolini, PhD
>>> > Senior Research Officer, Bioinformatics and Biostatistics unit
>>> > IRB Barcelona
>>> > Tel (+34) 93 402 0553
>>> >
>>> >
>>> > ___________________________________________________________
>>> > The Galaxy User list should be used for the discussion of
>>> > Galaxy analysis and other features on the public server
>>> > at usegalaxy.org.  Please keep all replies on the list by
>>> > using "reply all" in your mail client.  For discussion of
>>> > local Galaxy instances and the Galaxy source code, please
>>> > use the Galaxy Development list:
>>> >
>>> >  http://lists.bx.psu.edu/listinfo/galaxy-dev
>>> >
>>> > To manage your subscriptions to this and other Galaxy lists,
>>> > please use the interface at:
>>> >
>>> >  http://lists.bx.psu.edu/
>>> >
>>>
>>>
>>>
>>> --
>>> Ross Lazarus MBBS MPH;
>>> Associate Professor, Harvard Medical School;
>>> Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
>>> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>>
>>
>>
>> --
>> ***
>> Camille Stephan-Otto Attolini, PhD
>> Senior Research Officer, Bioinformatics and Biostatistics unit
>> IRB Barcelona
>> Tel (+34) 93 402 0553
>>
>>
>
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

___________________________________________________________
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