[DOCKTESTERS] Thanks!

Mon Apr 3 11:54:48 EDT 2017

Excellent George. Thank you!

Miguel

On Apr 3, 2017 5:42 PM, "George Mihaiescu" <George.Mihaiescu at oicr.on.ca>
wrote:

> Hi,
>
> The DKFZ workflow finished in one day and there were no differences
> observed by the compare_result script.
>
> I attached the updated report for all four workflow runs.
>
> Thank you,
> George
>
> From: Miguel Vazquez <mikisvaz at gmail.com>
> Date: Wednesday, March 29, 2017 at 5:09 AM
> To: George Mihaiescu <George.Mihaiescu at oicr.on.ca>
> Cc: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk>, Junjun Zhang
> <Junjun.Zhang at oicr.on.ca>, "docktesters at lists.icgc.org" <
> docktesters at lists.icgc.org>
> Subject: Re: [DOCKTESTERS] Thanks!
>
> George,
>
> If you where using my scripts you should have a file:
> tests/DKFZ/DO218695/Dockstore.json . Do you mind sharing it with us? I
> find a bit hard to debug these sorts of errors because its not clear to me
> if the problem is in the underlying tools or the dockstore layer. I think
> reason has it that the problem must be in the interface, that dockstore
> cannot setup the environment for the tool, since the tools work and the
> inputs are probably suitable for them, so my guess is that some inputs are
> not there or they are not placed in the right location, or something like
> that.
>
> Anyway, lets start by looking at the Dockstore.json
>
> Best
>
> Miguel
>
> On Mon, Mar 27, 2017 at 4:36 PM, George Mihaiescu <
> George.Mihaiescu at oicr.on.ca> wrote:
>
>> Hi,
>>
>> Last week thanks to Denis who provided the DKFZ dependencies, I was able
>> to start that workflow.
>>
>> It ran for about 10 hours at 100% CPU, but then it failed with the
>> following errors:
>>
>> root at dockstore4-dkfz:~/PCAWG-Docker-Test#
>> + cntSuccessful=4
>> ++ expr 4 - 4
>> + cntErrornous=0
>> + [[ 0 -gt 0 ]]
>> + [[ 0 == 0 ]]
>> + echo 'No errors found for /mnt/datastore/testdata/run_id
>> /roddyExecutionStore/exec_170322_175138477_roddy_snvCalling/
>> jobStateLogfile.txt'
>> No errors found for /mnt/datastore/testdata/run_id
>> /roddyExecutionStore/exec_170322_175138477_roddy_snvCalling/
>> jobStateLogfile.txt
>> + for logfile in '${jobstateFiles[@]}'
>> ++ cat /mnt/datastore/testdata/run_id/roddyExecutionStore/exec_1703
>> 22_175637640_roddy_indelCalling/jobStateLogfile.txt
>> ++ grep -v null:
>> ++ grep :STARTED:
>> ++ wc -l
>> + cntStarted=2
>> ++ cat /mnt/datastore/testdata/run_id/roddyExecutionStore/exec_1703
>> 22_175637640_roddy_indelCalling/jobStateLogfile.txt
>> ++ grep -v null:
>> ++ grep :0:
>> ++ wc -l
>> + cntSuccessful=2
>> ++ expr 2 - 2
>> + cntErrornous=0
>> + [[ 0 -gt 0 ]]
>> + [[ 0 == 0 ]]
>> + echo 'No errors found for /mnt/datastore/testdata/run_id
>> /roddyExecutionStore/exec_170322_175637640_roddy_indelCallin
>> g/jobStateLogfile.txt'
>> + [[ true == true ]]
>> No errors found for /mnt/datastore/testdata/run_id
>> /roddyExecutionStore/exec_170322_175637640_roddy_indelCallin
>> g/jobStateLogfile.txt
>> There was at least one error in a job status logfile. Will exit now!
>> + echo 'There was at least one error in a job status logfile. Will exit
>> now!'
>> + exit 5
>> mv: cannot stat `/mnt/datastore/resultdata/*': No such file or directory
>> Result directory listing is:
>> + gosu root chmod -R a+wrx /var/spool/cwl
>> Error while running job: Error collecting output for parameter
>> 'germline_indel_vcf_gz': Did not find output file with glob pattern:
>> '['*.germline.indel.vcf.gz']'
>> [job temp5679700718223668526.cwl] completed permanentFail
>> Final process status is permanentFail
>> Workflow error, try again with --debug for more information:
>>   Process status is ['permanentFail']
>> org.apache.commons.exec.ExecuteException: Process exited with an error:
>> 1 (Exit value: 1)
>>         at org.apache.commons.exec.DefaultExecutor.executeInternal(Defa
>> ultExecutor.java:404)
>>         at org.apache.commons.exec.DefaultExecutor.access$200(DefaultEx
>> ecutor.java:48)
>>         at org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecuto
>> r.java:200)
>>         at java.lang.Thread.run(Thread.java:745)
>> java.lang.RuntimeException: problems running command: cwltool
>> --enable-dev --non-strict --outdir /root/PCAWG-Docker-Test/tests/
>> DKFZ/DO218695/./datastore/launcher-e1ebdf3e-6f35-43f7-8ba2-1fb559d0d948/outputs/
>> --tmpdir-prefix /root/PCAWG-Docker-Test/tests/
>> DKFZ/DO218695/./datastore/launcher-e1ebdf3e-6f35-43f7-8ba2-1fb559d0d948/working/
>> /tmp/1490197113216-0/temp5679700718223668526.cwl
>> /root/PCAWG-Docker-Test/tests/DKFZ/DO218695/./datastore/laun
>> cher-e1ebdf3e-6f35-43f7-8ba2-1fb559d0d948/workflow_params.json
>>
>>
>> Any idea what went wrong?
>>
>> Thank you,
>> George
>>
>> From: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk>
>> Date: Monday, March 20, 2017 at 3:13 PM
>> To: George Mihaiescu <George.Mihaiescu at oicr.on.ca>
>> Cc: Miguel Vazquez <mikisvaz at gmail.com>, Junjun Zhang <
>> Junjun.Zhang at oicr.on.ca>, "docktesters at lists.icgc.org" <
>> docktesters at lists.icgc.org>
>> Subject: Re: [DOCKTESTERS] Thanks!
>>
>> Hi George,
>>
>> Do you have the DKFZ workflow dependencies tarball in place (and named
>> correctly)?
>> That's the file it's clearly not finding:
>>
>> 17:06:08.641 [main] ERROR io.dockstore.common.FileProvisioning - Could
>> not copy /root/PCAWG-Docker-Test/resources//dkfz-workflow-dependencies_150318_0951.tar.gz
>> to /root/PCAWG-Docker-Test/tests/DKFZ/DO218695/./datastore/laun
>> cher-81c42580-21ad-4480-9ee9-a0d2a7a14bf2/inputs/ee5564fe-
>> ba17-4383-afd8-e785394e365f/dkfz-workflow-dependencies_150318_0951.tar.gz
>> java.nio.file.NoSuchFileException: /root/PCAWG-Docker-Test/tests/
>> DKFZ/DO218695/./datastore/launcher-81c42580-21ad-4480-9ee9-
>> a0d2a7a14bf2/inputs/ee5564fe-ba17-4383-afd8-e785394e365f/
>> dkfz-workflow-dependencies_150318_0951.tar.gz
>>
>>
>> You can find the link to this reference tarball on the DKFZ pipeline
>> github page (https://github.com/ICGC-TCGA-PanCancer/dkfz_dockered_workfl
>> ows)
>>
>> Hope this helps,
>> Jonas
>>
>>
>> On 20 Mar 2017, at 17:19, George Mihaiescu <George.Mihaiescu at oicr.on.ca>
>> wrote:
>>
>> Hi,
>>
>> How do I run the DKFZ workflow?
>> I first ran the DELLY which ended with the following output:
>> Uploading: #somatic_sv_vcf from /root/PCAWG-Docker-Test/tests/
>> Delly/DO218695/./datastore/launcher-0ce3d535-bd87-4234-a5c0-
>> a3df48d7c5a5/outputs/run_id.embl-delly_1-3-0-preFilter.20150318.somatic.sv.vcf.gz
>> to : /root/PCAWG-Docker-Test/tests/Delly/DO218695//output//DO2186
>> 95.delly.somatic.sv.vcf.gz
>> [##################################################] 100%
>> Uploading: #cov_plots from /root/PCAWG-Docker-Test/tests/
>> Delly/DO218695/./datastore/launcher-0ce3d535-bd87-4234-a5c0-
>> a3df48d7c5a5/outputs/run_id.embl-delly_1-3-0-preFilter.20150318.sv.cov.plots.tar.gz
>> to : /root/PCAWG-Docker-Test/tests/Delly/DO218695//output//DO2186
>> 95.delly.sv.cov.plots.tar.gz
>>
>> After that, I tried to run the DKFZ but it errors as below:
>>
>> root at dockstore4-dkfz:~/PCAWG-Docker-Test# bin/run_test.sh DKFZ DO218695
>> Running:
>> cd /root/PCAWG-Docker-Test/tests/DKFZ/DO218695/ && dockstore tool launch
>> --script --entry quay.io/pancancer/pcawg-dkfz-workflow:2.0.1_cwl1.0
>> quay.io/jwerner_dkfz/DKFZBiasFilter:1.2.2   --json Dockstore.json
>> WARNING: You're currently running as root; probably by accident.
>> Press control-C to abort or Enter to continue as root.
>> Set DOCKSTORE_ROOT to disable this warning.
>>
>> Creating directories for run of Dockstore launcher at:
>> ./datastore//launcher-81c42580-21ad-4480-9ee9-a0d2a7a14bf2
>> Provisioning your input files to your local machine
>> Downloading: #delly-bedpe from /root/PCAWG-Docker-Test/tests/
>> Delly/DO218695/output//DO218695.delly.somatic.sv.bedpe.txt into
>> directory: /root/PCAWG-Docker-Test/tests/DKFZ/DO218695/./datastore/laun
>> cher-81c42580-21ad-4480-9ee9-a0d2a7a14bf2/inputs/9c1f2887-
>> bce0-41dd-a4d2-52f000d79e65
>> Downloading: #normal-bam from /root/PCAWG-Docker-Test/data/DO218695/normal.bam
>> into directory: /root/PCAWG-Docker-Test/tests/
>> DKFZ/DO218695/./datastore/launcher-81c42580-21ad-4480-9ee9-
>> a0d2a7a14bf2/inputs/0a43e408-0cdf-4d99-99a3-e9860161a246
>> Downloading: #reference-gz from /root/PCAWG-Docker-Test/resour
>> ces//dkfz-workflow-dependencies_150318_0951.tar.gz into directory:
>> /root/PCAWG-Docker-Test/tests/DKFZ/DO218695/./datastore/laun
>> cher-81c42580-21ad-4480-9ee9-a0d2a7a14bf2/inputs/ee5564fe-
>> ba17-4383-afd8-e785394e365f
>> 17:06:08.641 [main] ERROR io.dockstore.common.FileProvisioning - Could
>> not copy /root/PCAWG-Docker-Test/resources//dkfz-workflow-dependencies_150318_0951.tar.gz
>> to /root/PCAWG-Docker-Test/tests/DKFZ/DO218695/./datastore/laun
>> cher-81c42580-21ad-4480-9ee9-a0d2a7a14bf2/inputs/ee5564fe-
>> ba17-4383-afd8-e785394e365f/dkfz-workflow-dependencies_150318_0951.tar.gz
>> java.nio.file.NoSuchFileException: /root/PCAWG-Docker-Test/tests/
>> DKFZ/DO218695/./datastore/launcher-81c42580-21ad-4480-9ee9-
>> a0d2a7a14bf2/inputs/ee5564fe-ba17-4383-afd8-e785394e365f/
>> dkfz-workflow-dependencies_150318_0951.tar.gz ->
>> /root/PCAWG-Docker-Test/resources/dkfz-workflow-dependencies
>> _150318_0951.tar.gz
>>         at sun.nio.fs.UnixException.translateToIOException(UnixExceptio
>> n.java:86)
>>         at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.
>> java:102)
>>         at sun.nio.fs.UnixFileSystemProvider.createLink(UnixFileSystemP
>> rovider.java:476)
>>         at java.nio.file.Files.createLink(Files.java:1086)
>>         at io.dockstore.common.FileProvisioning.provisionInputFile(File
>> Provisioning.java:273)
>>         at io.github.collaboratory.LauncherCWL.copyIndividualFile(Launc
>> herCWL.java:726)
>>         at io.github.collaboratory.LauncherCWL.doProcessFile(LauncherCW
>> L.java:688)
>>         at io.github.collaboratory.LauncherCWL.pullFilesHelper(Launcher
>> CWL.java:659)
>>         at io.github.collaboratory.LauncherCWL.pullFiles(LauncherCWL.
>> java:586)
>>         at io.github.collaboratory.LauncherCWL.run(LauncherCWL.java:185)
>>         at io.dockstore.client.cli.nested.AbstractEntryClient.handleCWL
>> Launch(AbstractEntryClient.java:1028)
>>         at io.dockstore.client.cli.nested.AbstractEntryClient.launchCwl
>> (AbstractEntryClient.java:968)
>>         at io.dockstore.client.cli.nested.AbstractEntryClient.launchCwl
>> (AbstractEntryClient.java:951)
>>         at io.dockstore.client.cli.nested.AbstractEntryClient.launch(
>> AbstractEntryClient.java:935)
>>         at io.dockstore.client.cli.nested.AbstractEntryClient.processEn
>> tryCommands(AbstractEntryClient.java:247)
>>         at io.dockstore.client.cli.Client.run(Client.java:704)
>>         at io.dockstore.client.cli.Client.main(Client.java:796)
>> java.lang.RuntimeException: Could not copy /root/PCAWG-Docker-Test/resour
>> ces//dkfz-workflow-dependencies_150318_0951.tar.gz to
>> /root/PCAWG-Docker-Test/tests/DKFZ/DO218695/./datastore/laun
>> cher-81c42580-21ad-4480-9ee9-a0d2a7a14bf2/inputs/ee5564fe-
>> ba17-4383-afd8-e785394e365f/dkfz-workflow-dependencies_150318_0951.tar.gz
>>
>>
>> P.S. I have three other Sanger tests running that were started at
>> different intervals (and on VMs with different CPU/memory/disk), but none
>> of them has completed yet.
>>
>> Thank you,
>> George
>>
>>
>> From: Miguel Vazquez <mikisvaz at gmail.com>
>> Date: Monday, March 13, 2017 at 8:52 AM
>> To: George Mihaiescu <George.Mihaiescu at oicr.on.ca>
>> Cc: Junjun Zhang <Junjun.Zhang at oicr.on.ca>, Jonas Demeulemeester <
>> Jonas.Demeulemeester at crick.ac.uk>, "docktesters at lists.icgc.org" <
>> docktesters at lists.icgc.org>
>> Subject: Re: [DOCKTESTERS] Thanks!
>>
>> Hi George,
>>
>> Answers inline
>>
>> On Mon, Mar 13, 2017 at 2:43 PM, George Mihaiescu <
>> George.Mihaiescu at oicr.on.ca> wrote:
>>
>>> Hi Miguel,
>>>
>>> I've started the test by running "bin/run_test.sh Sanger DO50398", so I
>>> guess with just one workflow running it should complete faster than two
>>> weeks.
>>>
>>
>> I think it still should take a long time. My scripts will run one
>> workflow after another.
>>
>>
>>>
>>> Because I'm running in Collaboratory I've changed the
>>> "get_icgc_donor.sh" script to use a docker container that has the icgc
>>> client inside and pull data from Collaboratory. There is no "bam.bas" file
>>> downloaded, just a ".bam" and a ".bam.bai" files, not sure if this is an
>>> issue.
>>>
>>>
>> I wondered the same thing first time I did this, but this file is
>> produced by the pipeline. There was some problem with this that was dealt
>> with by the developers and updated in the docker. So I think you won't have
>> a problem
>>
>>
>>> By looking at the "bin/compare_result_type.sh" it looks like it's using
>>> the gnos client to pull down the existing VCF files for comparison reasons,
>>> but I think we store those files in Collaboratory as well, so I'll work
>>> with Junjun to adapt the script for this.
>>>
>>>
>> Let me know if you need any help
>>
>>
>>> I think I initially tried to run the DKFZ workflow, but it complained
>>> about having to run Delly first, so I abandoned this for now.
>>>
>>
>> Yes, if you look at the run_batch.sh you will see that when using DKFZ it
>> will always run Delly first. Delly prepares some files the the  DKFZ file
>> needs, namely related to copy number I believe.
>>
>>
>>>
>>> I'll set up a new VM and run the "run_batch.sh" on the DO52140 donor.
>>>
>>
>> Remember that you will need to add the relevant has-keys for the
>> different files in the etc/donor_files.csv. Its a bit tedious right now.
>> You need to go to the ICGC DCC and find these codes manually for the files
>> you need. Ask me if you need help. Once you have all you can run all the
>> workflows for that donor and evaluate results.
>>
>> https://github.com/mikisvaz/PCAWG-Docker-Test/blob/master/et
>> c/donor_files.csv
>>
>>
>> Regards
>>
>> Miguel
>>
>>
>>>
>>> George
>>>
>>> From: Miguel Vazquez <mikisvaz at gmail.com>
>>> Date: Monday, March 13, 2017 at 6:53 AM
>>> To: George Mihaiescu <George.Mihaiescu at oicr.on.ca>
>>> Cc: Junjun Zhang <Junjun.Zhang at oicr.on.ca>, Jonas Demeulemeester <
>>> Jonas.Demeulemeester at crick.ac.uk>, "docktesters at lists.icgc.org" <
>>> docktesters at lists.icgc.org>
>>> Subject: Re: [DOCKTESTERS] Thanks!
>>>
>>> Hi George,
>>>
>>> The Sanger workflow is very lengthy, it takes about two weeks in my
>>> tests.
>>>
>>> About correctness, my scripts also cover that part, if you are not using
>>> them they might still help you to clarify how we do it. The idea is to take
>>> each of the output files produced: SNV_MNV, Indel, SV, and CNV, for both
>>> germline and somatic and compare it with the result uploaded to GNOS (not
>>> all pipelines produce all files). This is the relevant part in the
>>> run_batch.sh script:
>>>
>>> https://github.com/mikisvaz/PCAWG-Docker-Test/blob/master/bi
>>> n/run_batch.sh#L42-L46
>>>
>>> The bin/compare_result_type.sh script will take care of downloading the
>>> correct file from GNOS and running the comparison. The comparison itself is
>>> simple since all files are VCFs, it consists in taking out the variants in
>>> terms of chromosome, position, reference and alternative allele and
>>> measuring the overlaps.
>>>
>>> https://github.com/mikisvaz/PCAWG-Docker-Test/blob/master/bi
>>> n/compare_result_type.sh
>>>
>>> About which donors to test, DO52140 is one Jonas and I have both tested
>>> and could be interesting to get a third opinion. Also, any other donor
>>> could be interesting to see if something new comes up. I'm not sure which
>>> options is best.
>>>
>>> Miguel
>>>
>>>
>>>
>>>
>>> On Mon, Mar 13, 2017 at 5:12 AM, George Mihaiescu <
>>> George.Mihaiescu at oicr.on.ca> wrote:
>>>
>>>> Hi,
>>>>
>>>> I've started Sanger on DO50398 and it's been running for more than 24
>>>> hours, currently at "Workflow step succeeded: s58_bbAllele_merge_59"
>>>>
>>>> I just started a second run on a different VM on same donor, just to
>>>> compare run times.
>>>> The VM used has 8 cores, 48 GB of RAM and 1.1 TB disk and I'll send
>>>> some monitoring graphs when it finishes the workflow, but I have no idea
>>>> how to check its correctness.
>>>>
>>>> Give me a list of donors and what workflows you want me to run and I'll
>>>> try to schedule them tomorrow.
>>>>
>>>> George
>>>>
>>>>
>>>> From: Junjun Zhang <Junjun.Zhang at oicr.on.ca>
>>>> Date: Sunday, March 12, 2017 at 10:45 PM
>>>> To: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk>, George
>>>> Mihaiescu <George.Mihaiescu at oicr.on.ca>
>>>> Cc: Miguel Vazquez <miguel.vazquez at cnio.es>, Denis Yuen <
>>>> Denis.Yuen at oicr.on.ca>, "docktesters at lists.icgc.org" <
>>>> docktesters at lists.icgc.org>
>>>> Subject: Re: [DOCKTESTERS] Thanks!
>>>>
>>>> Thanks Miguel and Jonas for your help here!
>>>>
>>>> Do you have any update on the latest testing? Please feel free updating
>>>> the wiki with any update: https://wiki.oicr.on.c
>>>> a/display/PANCANCER/2017-03-13+PCAWG-TECH+Teleconference
>>>>
>>>> Regards,
>>>> Junjun
>>>>
>>>>
>>>>
>>>> From: Jonas Demeulemeester <Jonas.Demeulemeester at crick.ac.uk>
>>>> Date: Saturday, March 11, 2017 at 7:15 PM
>>>> To: George Mihaiescu <George.Mihaiescu at oicr.on.ca>
>>>> Cc: Miguel Vazquez <miguel.vazquez at cnio.es>, Junjun Zhang <
>>>> junjun.zhang at oicr.on.ca>, Denis Yuen <Denis.Yuen at oicr.on.ca>, "
>>>> docktesters at lists.icgc.org" <docktesters at lists.icgc.org>
>>>> Subject: Re: [DOCKTESTERS] Thanks!
>>>>
>>>> Hi George,
>>>>
>>>> Yup, I've been running the PCAWG dockers mainly using Miguel's set of
>>>> scripts.
>>>> Give them a go and if you run into issues, just let us know!
>>>>
>>>> Cheers,
>>>> Jonas
>>>>
>>>>
>>>> On 11 Mar 2017, at 17:00, George Mihaiescu <George.Mihaiescu at oicr.on.ca>
>>>> wrote:
>>>>
>>>> Sure, I'll give it a try and report later.
>>>>
>>>> Thank you,
>>>>
>>>> *George Mihaiescu*
>>>> Senior Cloud Architect
>>>>
>>>> *Ontario Institute for Cancer Research*
>>>> MaRS Centre
>>>> 661 University Avenue
>>>> Suite 510
>>>> Toronto, Ontario
>>>> Canada M5G 0A3
>>>>
>>>> Email: George.Mihaiescu at oicr.on.ca
>>>> Toll-free: 1-866-678-6427
>>>> Twitter: @OICR_news
>>>>
>>>> www.oicr.on.ca
>>>>
>>>> This message and any attachments may contain confidential and/or
>>>> privileged information for the sole use of the intended recipient. Any
>>>> review or distribution by anyone other than the person for whom it was
>>>> originally intended is strictly prohibited. If you have received this
>>>> message in error, please contact the sender and delete all copies.
>>>> Opinions, conclusions or other information contained in this message may
>>>> not be that of the organization.
>>>>
>>>>
>>>>
>>>> From: Miguel Vazquez <miguel.vazquez at cnio.es>
>>>> Date: Saturday, March 11, 2017 at 10:57 AM
>>>> To: Junjun Zhang <Junjun.Zhang at oicr.on.ca>
>>>> Cc: Denis Yuen <Denis.Yuen at oicr.on.ca>, Jonas Demeulemeester <
>>>> jonas.demeulemeester at crick.ac.uk>, George Mihaiescu <
>>>> George.Mihaiescu at oicr.on.ca>, "docktesters at lists.icgc.org" <
>>>> docktesters at lists.icgc.org>
>>>> Subject: Re: [DOCKTESTERS] Thanks!
>>>>
>>>> Hi Junjun,
>>>>
>>>> I think Jonas has been using my scripts to run some of the tests, maybe
>>>> George could try them as well, it should be very easy for him to try the
>>>> Sanger, Delly+DKFZ, BWA-Mem, and the BiasFilter.
>>>>
>>>> https://github.com/mikisvaz/PCAWG-Docker-Test
>>>>
>>>> He would just need to update the tokens for DACO access and the scripts
>>>> will take care of downloading the BAM files, running the workflows and
>>>> evaluating the result.
>>>>
>>>> The documentation there is reasonably updated, but if this sounds good
>>>> then perhaps he could contact me and I could walk him through the details.
>>>>
>>>> Best regards
>>>>
>>>> Miguel
>>>>
>>>> On Fri, Mar 10, 2017 at 9:51 PM, Junjun Zhang <Junjun.Zhang at oicr.on.ca>
>>>> wrote:
>>>>
>>>>> Dear Docktesters,
>>>>>
>>>>> George Mihaiescu, cloud architect, of the Collaboratory at OICR plans
>>>>> to run some bioinformatics workflows to test Collab environment.
>>>>>
>>>>> Just thought this is a good opportunity to use as extra help for
>>>>> testing out the PCAWG dockerized workflows.
>>>>>
>>>>> Miguel, Denis and others, what workflows / datasets do you think would
>>>>> be good for George to run?
>>>>>
>>>>> Thanks,
>>>>> Junjun
>>>>>
>>>>>
>>>>>
>>>>> From: <docktesters-bounces+junjun.zhang=oicr.on.ca at lists.icgc.org> on
>>>>> behalf of Denis Yuen <Denis.Yuen at oicr.on.ca>
>>>>> Date: Wednesday, March 1, 2017 at 10:26 AM
>>>>> To: "docktesters at lists.icgc.org" <docktesters at lists.icgc.org>
>>>>> Subject: [DOCKTESTERS] Thanks!
>>>>>
>>>>> Hi,
>>>>>
>>>>> Just wanted to say thanks to Miguel and Jonas for keeping the workflow
>>>>> testing data page up-to-date.
>>>>>
>>>>> https://wiki.oicr.on.ca/display/PANCANCER/Workflow+Testing+Data
>>>>>
>>>>>
>>>>> As we work on new versions or debugging, it is invaluable to know what
>>>>> versions of the workflows have worked outside OICR, thanks!
>>>>>
>>>>>
>>>>>
>>>>> *Denis Yuen*
>>>>> Senior Software Developer
>>>>>
>>>>>
>>>>> *Ontario**Institute**for**Cancer**Research*
>>>>> MaRSCentre
>>>>> 661 University Avenue
>>>>> Suite510
>>>>> Toronto, Ontario,Canada M5G0A3
>>>>>
>>>>> Toll-free: 1-866-678-6427
>>>>> Twitter: @OICR_news
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>> The Francis Crick Institute Limited is a registered charity in England
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