[DOCKTESTERS] DKFZ bias filter docker

[Ivo Buchhalter]

Hi Denis,

I just talked to Manuel. He told me that there is/was some architectural 
problem with the Docker I made. He and Johannes already fixed most of 
it. If it works out for you we will provide you with a CWL by the end of 
next week. I suppose it is better not to work on it in parallel and I am 
sure you have enough on your plate.

I hope that works for you!

Best,
Ivo


On 10/19/2016 09:33 PM, Denis Yuen wrote:
> Hi,
>
> Thanks, this definitely helps to make it more clear.
> I think this will give us enough information for us to start working on a CWL descriptor or to assist one being written.
>
> ________________________________________
> From: Ivo Buchhalter [i.buchhalter at dkfz-heidelberg.de]
> Sent: October 19, 2016 2:19 AM
> To: Denis Yuen; Ivo Buchhalter; docktesters at lists.icgc.org
> Cc: Werner, Johannes; prinz; Schlesner, Matthias
> Subject: Re: [DOCKTESTERS] DKFZ bias filter docker
>
> Hi Denis,
>
> Sorry for the missing information. I updated the README in the
> repository. I hope things are more clear now.
>> 1) How does this relate to the existing dkfz workflow? ( https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows ) Is this a step that follows that workflow or is this a portion of that workflow that has been split out?
> The filter is part of the DKFZ workflow. Since the other workflows don't
> use similar filters the DKFZ stand alone filter was run on the complete
> data set after merging the calls (only somatic SNV calls).
>> 2) Could we get a readme that describes how to use this?
> I updated the README. I hope it's more clear now.
>> 3) Do you have some non-confidential small test data that we can use to run/test this quickly before running a real donor through this?
> I will check if we can provide this later but the filter generally runs
> only a couple of minutes (on a normal somatic "PASS" vcf with <= 10 000
> variants).
>
> Best,
> Ivo
>
>
>> Thanks!
>>
>> ________________________________________
>> From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Ivo Buchhalter [i.buchhalter at dkfz-heidelberg.de]
>> Sent: October 18, 2016 3:06 AM
>> To: docktesters at lists.icgc.org
>> Cc: Werner, Johannes; prinz; Schlesner, Matthias
>> Subject: [DOCKTESTERS] DKFZ bias filter docker
>>
>> Dear dockertesters,
>>
>> I was told to contact you regarding the DKFZ bias filter docker. The
>> docker is basically ready and it also passed internal testing. The
>> scripts and Dockerfile can be found here:
>> https://github.com/eilslabs/DKFZBiasFilter
>> Johannes and Manuel (CCed) have been working on bringing it into
>> Dockstore (they ran into a NFS problem). Johannes is currently on
>> vacation (until October 23rd).
>> Please let me know if it is sufficient to have the docker available on
>> Dockstore some time next week. Alternatively it might be possible that
>> you work with the scripts and Dockerfile on GitHub. If none of this
>> works I (or probably Manuel) can also try to get it running on Dockstore
>> some time later this week.
>>
>> Best,
>> Ivo
>>
>> PS: Sorry to the DKFZ people the email before bounced back because the
>> link of the email address on the Wiki had a typo.
>> _______________________________________________
>> docktesters mailing list
>> docktesters at lists.icgc.org
>> https://lists.icgc.org/mailman/listinfo/docktesters
> On 10/18/2016 05:38 PM, Denis Yuen wrote:
>> Hi,
>>
>> Thanks for the heads-up, we can probably help out with writing the CWL descriptor for this, but I do have a few questions.
>>
>> 1) How does this relate to the existing dkfz workflow? ( https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workflows ) Is this a step that follows that workflow or is this a portion of that workflow that has been split out?
>> 2) Could we get a readme that describes how to use this?
>> 3) Do you have some non-confidential small test data that we can use to run/test this quickly before running a real donor through this?
>>
>> Thanks!
>>
>> ________________________________________
>> From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Ivo Buchhalter [i.buchhalter at dkfz-heidelberg.de]
>> Sent: October 18, 2016 3:06 AM
>> To: docktesters at lists.icgc.org
>> Cc: Werner, Johannes; prinz; Schlesner, Matthias
>> Subject: [DOCKTESTERS] DKFZ bias filter docker
>>
>> Dear dockertesters,
>>
>> I was told to contact you regarding the DKFZ bias filter docker. The
>> docker is basically ready and it also passed internal testing. The
>> scripts and Dockerfile can be found here:
>> https://github.com/eilslabs/DKFZBiasFilter
>> Johannes and Manuel (CCed) have been working on bringing it into
>> Dockstore (they ran into a NFS problem). Johannes is currently on
>> vacation (until October 23rd).
>> Please let me know if it is sufficient to have the docker available on
>> Dockstore some time next week. Alternatively it might be possible that
>> you work with the scripts and Dockerfile on GitHub. If none of this
>> works I (or probably Manuel) can also try to get it running on Dockstore
>> some time later this week.
>>
>> Best,
>> Ivo
>>
>> PS: Sorry to the DKFZ people the email before bounced back because the
>> link of the email address on the Wiki had a typo.
>> _______________________________________________
>> docktesters mailing list
>> docktesters at lists.icgc.org
>> https://lists.icgc.org/mailman/listinfo/docktesters