[DOCKTESTERS] Issues with Consensus Docker

Thu May 11 10:43:29 EDT 2017

Thanks Solomon for your explanations. I've produced the tbi files with
tabix and I've now prepared a script that downloads the resources following
your instructions. I'll let you know how it goes.

On Thu, May 11, 2017 at 4:30 PM, Solomon Shorser <solomon.shorser at oicr.on.ca
> wrote:

> Hi Miguel,
>
> The .tbi files need to be there, but they do not need to be *explicitly*
> included in the input JSON file.
>
> CWL has the option to specify "secondary" files that go with a main file.
> In the CWL, an input VCF is defined like this example:
>
>     dkfz_embl_input_file:
>       type: File
>       inputBinding:
>         position: 3
>         prefix: "-d"
> *      secondaryFiles:*
> *        - .tbi*
>
> Specifying ".tbi" as secondary files indicates to CWL that it should look
> for any .tbi file that matches the same name as the actual file bound to
> this input should also be included (see: http://www.commonwl.org/v1.0/
> CommandLineTool.html#Expressions section 5.2 CommandOutputParameter ,
> "secondaryFiles").
>
> As for the error related to creating the .tbi files: the format is similar
> to gzip but they should actually be created with a tool named "tabix" (I
> think you can install with apt on linux). Creating the tabix file can
> probably be done with a command that looks like this: "tabix -p vcf
> myDataFile.vcf.gz".
>
>
>
> dbs_dir is supposed to be a Directory that contains the necessary
> references files. The original documentation from Jonathan Dursi shows
> there is a command to create this directory:
>
> mkdir dbs
> docker run -it -v "${PWD}/dbs":/dbs consensus_call download reference /dbs
> docker run -it -v "${PWD}/dbs":/dbs consensus_call download annotations /dbs
> docker run -it -v "${PWD}/dbs":/dbs consensus_call download cosmic /dbs
>
> (see: https://github.com/SolomonShorser-OICR/consensus_
> call_docker#downloading-auxiliary-files)
>
> This is *not* done within the dockstore tool as downloading this
> directory could take a long time (it is about 6 GB on my system) so I would
> recommend running the commands above before running the dockstore tool,
> then pointing the "dbs_dir" parameter to this directory.
>
> I've attached a sample of the input JSON file I used.
>
> Can you send me the link to the documentation you were reading? I think
> the dockstore usage needs to be made more clear, so please let me know
> where you were reading so I can update the right file.
>
>
> Thanks,
> Solomon Shorser.
>
>
> On 2017-05-11 10:07 AM, Miguel Vazquez wrote:
>
> Hi all,
>
> I've started trying to test the Consensus Docker and I've ran into a few
> difficulties. Some pertain the application itself and some I are questions
> I have related to CWL or Docker.
>
> 1- Missing input dbs_dir: The documentation suggests that this is a
> directory with resources that need to be set up beforehand using the same
> docker container with different parameters. I'm not sure how to handle
> this. To keep going I've just pointed to some arbitrary directory
>
> 2- Missing tbi files on input VCFs: The CWL explicitly asks for the input
> VCF. In the documentation it seems like the inputs are in fact compressed
> with gzip. Up to here is fine, though I wonder if there would not be a more
> explicit way to indicate this in. The problem comes when I run it that I
> get an error complaining about a missing tbi file:
>
>   Missing input file [Errno 2] No such file or directory:
> '/mnt/1TB/work/DockerTest-Miguel/data/DO52621//broad.oxoG.annotated.vcf.gz
> *.tbi*'
>
> It is not a problem to produce it using tabix but what is confusing to me
> is that there is no mention of any tbi file in the Dockstore.json file. How
> does this work?
>
> 3- After producing the tbi files I get this error, which I think is
> related to (1)
>
>   Invalid filename: '' contains illegal characters
>
>
> Best regards
>
> Miguel
>
> ----Dockstore.json-----
>
>
> {
>   "broad_input_file": {
>     "path": "/tmp/fill_me_in.txt",
>     "class": "File"
>   },
>   "dkfz_embl_input_file": {
>     "path": "/tmp/fill_me_in.txt",
>     "class": "File"
>   },
>   "variant_type": "fill me in",
>   "consensus_vcf_index": {
>     "path": "/tmp/fill_me_in.txt",
>     "class": "File"
>   },
>
>
>
> *  "dbs_dir": {     "path": "/tmp/fill_directory_in",     "class":
> "Directory"   },*
>   "muse_input_file": {
>     "path": "/tmp/fill_me_in.txt",
>     "class": "File"
>   },
>   "consensus_zipped_vcf": {
>     "path": "/tmp/fill_me_in.txt",
>     "class": "File"
>   },
>   "sanger_input_file": {
>     "path": "/tmp/fill_me_in.txt",
>     "class": "File"
>   }
> }
>
>
>
>
> _______________________________________________
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>
>
> *Solomon Shorser*
> Software Developer
>
> *Ontario Institute for Cancer Research*
> MaRS Centre
> 661 University Avenue
> Suite 510
> Toronto, Ontario
> Canada M5G 0A3
>
> Email: solomon.shorser at oicr.on.ca
> Telephone: (647) 258-4319
> Toll-free: 1-866-678-6427
> Twitter: @OICR_news
>
> www.oicr.on.ca
>
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