[DOCKTESTERS] [PAWG-TECH] Draft agenda for PCAWG-TECH teleconference

[Miguel Vazquez]

Ok Keiran, I leave it up to you guys then. I'll try again when the issue is
resolved somehow.

Thanks for you help

Miguel

On Wed, Oct 12, 2016 at 12:16 PM, Keiran Raine <kr2 at sanger.ac.uk> wrote:

> Hi,
>
> This is assuming that it is possible to write to the location the BAM are
> in.
>
> I think Denis would be best placed to make the minor modification as I
> don't know the process they are using for build and deploy of the images (I
> made modifications and then handed over for CWL).
>
> Regards,
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> kr2 at sanger.ac.uk
> Tel:+44 (0)1223 834244 Ext: 4983
> Office: H104
>
> On 12 Oct 2016, at 10:37, Miguel Vazquez <miguel.vazquez at cnio.es> wrote:
>
> [The rest of the list where out of the loop for this part of the
> conversation, I'm putting them back in. In short, the Sanger pipeline
> produces the BAS file but not co-located with the BAM]
>
> Hi Keiran,
>
> Would it be possible then to change this and try again? what needs to
> happen? I guess you'll need to change the code and a new docker image be
> produced. Would this be our best alternative?
>
>
> Miguel
>
>
>
> On Tue, Oct 11, 2016 at 4:07 PM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>
>> In the original version we didn't do this step, if we have write access
>> it can be made to do that
>>
>> Keiran Raine
>> Principal Bioinformatician
>> Cancer Genome Project
>> Wellcome Trust Sanger Institute
>>
>> kr2 at sanger.ac.uk
>> Tel:+44 (0)1223 834244 Ext: 4983
>> Office: H104
>>
>> On 11 Oct 2016, at 13:49, Miguel Vazquez <miguel.vazquez at cnio.es> wrote:
>>
>> Hi Keiran,
>>
>> If the BAS and BAM files need to be collocated, why is it not created
>> next to the BAM file?
>>
>> Would it not be better if it read
>>
>> private Job basFileBaseJob(int tumourCount, String sampleBam, String
>> process, int index) {
>> Job thisJob = prepTimedJob(tumourCount, "basFileGenerate", process,
>> index);
>> File f = new File(sampleBam);
>> thisJob.getCommand()
>> .addArgument(getWorkflowBaseDir()+ "/bin/wrapper.sh")
>> .addArgument(installBase)
>> .addArgument("bam_stats")
>> .addArgument("-i " + sampleBam)
>> .addArgument("-o " + sampleBam + ".bas")
>> ;
>> return thisJob;
>> }
>>
>> Best
>>
>> Miguel
>>
>> On Tue, Oct 11, 2016 at 2:44 PM, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>>
>>> Relevant section of code:
>>>
>>> https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/bl
>>> ob/develop/src/main/java/io/seqware/pancancer/CgpSomaticCore
>>> .java#L769-L780
>>>
>>> Keiran Raine
>>> Principal Bioinformatician
>>> Cancer Genome Project
>>> Wellcome Trust Sanger Institute
>>>
>>> kr2 at sanger.ac.uk
>>> Tel:+44 (0)1223 834244 Ext: 4983
>>> Office: H104
>>>
>>> On 11 Oct 2016, at 13:40, Keiran Raine <kr2 at sanger.ac.uk> wrote:
>>>
>>> Hi,
>>>
>>> There is a step generating the BAS files:
>>>
>>> [2016/10/10 07:28:37] |  Running command: bash
>>> /datastore/oozie-6599f0b9-8af7-44ca-a608-03c5bbc159c6/genera
>>> ted-scripts/s58_basFileGenerate_control_11-runner.sh
>>> [2016/10/10 07:28:37] |  Running command: bash
>>> /datastore/oozie-6599f0b9-8af7-44ca-a608-03c5bbc159c6/genera
>>> ted-scripts/s58_basFileGenerate_tumours_12-runner.sh
>>>
>>> But if the BAM files and BAS aren't co-located then you have a problem.
>>> You could symlink the BAM files into the work space and have all tools work
>>> from that path instead, deleting the symlinks at the end.
>>>
>>> This is one of the changes we had to implement differently as the BAS
>>> file data was being held in the GNOS xml data structures during the initial
>>> processing.  Moving to this means that any BAM input is sufficient.
>>>
>>> Hope this is easier to solve now,
>>>
>>> Keiran Raine
>>> Principal Bioinformatician
>>> Cancer Genome Project
>>> Wellcome Trust Sanger Institute
>>>
>>> kr2 at sanger.ac.uk
>>> Tel:+44 (0)1223 834244 Ext: 4983
>>> Office: H104
>>>
>>> On 11 Oct 2016, at 13:31, Miguel Vazquez <miguel.vazquez at cnio.es> wrote:
>>>
>>> Keiran,
>>>
>>> Its downloading the files still but in fact it does not seem to download
>>> any BAS file. Could you please educate me a bit on what are these and how I
>>> can create them?
>>>
>>> Best
>>>
>>> Miguel
>>>
>>> On Tue, Oct 11, 2016 at 2:22 PM, Miguel Vazquez <miguel.vazquez at cnio.es>
>>> wrote:
>>>
>>>>
>>>> 4. It looks like the *_pindel_input_* steps run for only 22-23 seconds
>>>>> which could indicate a problem with either the headers or the absence of
>>>>> the BAS file from the expected location.
>>>>>
>>>>>
>>>> I think that you just revealed the problem. There is in fact no BAS
>>>> files only BAM and BAI. There where BAS files for the test data HCC1143
>>>> which is the one that in fact work. It seems like BAS files are not
>>>> gathered by gnos, could that be? or that my script fails to copy them. I'll
>>>> try to gather a different sample with my client and check.
>>>>
>>>> Not knowing a thing about these files explains why I didn't notice.
>>>> I'll get back to you when I know more.
>>>>
>>>> Best
>>>>
>>>> Miguel
>>>>
>>>
>>>
>>>
>>>
>>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a company
>>> registered in England with number 2742969, whose registered office is 215
>>> Euston Road, London, NW1 2BE.
>>>
>>
>>
>>
>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a company
>> registered in England with number 2742969, whose registered office is 215
>> Euston Road, London, NW1 2BE.
>>
>
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a company
> registered in England with number 2742969, whose registered office is 215
> Euston Road, London, NW1 2BE.
>
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