dockstore: sudo: unknown uid 1012: who are you?

Moving on from issue #469 et al, I’m hitting a wall now with docker uid: … from what I can tell, it does not have to do with DOCKSTORE_ROOT env var at all, but I assume docker’s --privileged flag might help in here?

Seems like cwltool is passing my hosts’s UID to the container and of course cannot find it in the running docker container.

@denis-yuen Thanks a ton for following this up with me, any hints with this one? How are you mapping UID’s between host and container now? Or are you just running it all as root?:

Executing: cwltool --enable-dev --non-strict --enable-net --outdir /home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/outputs/ --tmpdir-prefix /home/rvalls/dev/CGP-Somatic-Docker/./datasto
re/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/working/ /home/rvalls/dev/CGP-Somatic-Docker/Dockstore.cwl /home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/workflow_params.json
org.apache.commons.exec.ExecuteException: Process exited with an error: 1 (Exit value: 1)
        at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
        at org.apache.commons.exec.DefaultExecutor.access$200(DefaultExecutor.java:48)
        at org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:200)
        at java.lang.Thread.run(Thread.java:745)
stderr : /home/rvalls/.miniconda/bin/cwltool 1.0.20160712154127
[job Dockstore.cwl] /tmp/tmp0xcfN1$ docker \
    run \
    -i \
    --volume=/home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/inputs/1870eb79-6cce-49a0-9d83-5e8de445c872/HCC1143.bam.bai:/var/lib/cwl/stgebf8302e-eea7-4be2-ade7-492b3c1048a9/HCC1143.ba$
.bai:ro \
    --volume=/home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/inputs/b7582d9b-caf6-4c09-9659-7c60478c703d/HCC1143_BL.bam.bai:/var/lib/cwl/stg8a35bc14-b785-441a-aaf5-fedc5f622d3d/HCC1143_
BL.bam.bai:ro \
    --volume=/home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/inputs/b7582d9b-caf6-4c09-9659-7c60478c703d/HCC1143_BL.bam:/var/lib/cwl/stg8a35bc14-b785-441a-aaf5-fedc5f622d3d/HCC1143_BL.b
am:ro \
    --volume=/home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/inputs/f54a1fa2-51f1-4389-9f82-4165f8a66bb3/GRCh37d5_CGP_refBundle.tar.gz:/var/lib/cwl/stg7d26b651-ed4d-4da3-a452-8eb2b0c233
55/GRCh37d5_CGP_refBundle.tar.gz:ro \
    --volume=/home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/inputs/1870eb79-6cce-49a0-9d83-5e8de445c872/HCC1143.bam:/var/lib/cwl/stgebf8302e-eea7-4be2-ade7-492b3c1048a9/HCC1143.bam:ro
\
    --volume=/home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/inputs/5dcd7597-a86e-4482-99c6-5440da5e7a2b/GRCh37d5_battenberg.tar.gz:/var/lib/cwl/stgf33af064-c789-467d-adcc-3ea11965b515/
GRCh37d5_battenberg.tar.gz:ro \
    --volume=/tmp/tmp0xcfN1:/var/spool/cwl:rw \
    --volume=/home/rvalls/dev/CGP-Somatic-Docker/datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/workingen7nUi:/tmp:rw \
    --workdir=/var/spool/cwl \                                                                                                                                                                                                             --read-only=true \
    --user=1012 \                                                                                                                                                                                                                          --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/var/spool/cwl \
    quay.io/pancancer/pcawg-sanger-cgp-workflow:2.0.2 \                                                                                                                                                                                    python \                                                                                                                                                                                                                               /home/seqware/CGP-Somatic-Docker/scripts/run_seqware_workflow.py \
    --tumor \
    /var/lib/cwl/stgebf8302e-eea7-4be2-ade7-492b3c1048a9/HCC1143.bam \
    --normal \
    /var/lib/cwl/stg8a35bc14-b785-441a-aaf5-fedc5f622d3d/HCC1143_BL.bam \
    --refFrom \
    /var/lib/cwl/stg7d26b651-ed4d-4da3-a452-8eb2b0c23355/GRCh37d5_CGP_refBundle.tar.gz \
    --bbFrom \                                                                                                                                                                                                                             /var/lib/cwl/stgf33af064-c789-467d-adcc-3ea11965b515/GRCh37d5_battenberg.tar.gz                                                                                                                                                    [ERROR] command: sudo mkdir -p /var/spool/cwl/.seqware && sudo chown -R seqware /var/spool/cwl/ exited with code: 1                                                                                                                    sudo: unknown uid 1012: who are you?

Traceback (most recent call last):
  File "/home/seqware/CGP-Somatic-Docker/scripts/run_seqware_workflow.py", line 277, in <module>                                                                                                                                       RUNNING...
 sudo mkdir -p /var/spool/cwl/.seqware && sudo chown -R seqware /var/spool/cwl/

    main()
  File "/home/seqware/CGP-Somatic-Docker/scripts/run_seqware_workflow.py", line 233, in main
    execute("sudo mkdir -p /var/spool/cwl/.seqware && sudo chown -R seqware /var/spool/cwl/")
  File "/home/seqware/CGP-Somatic-Docker/scripts/run_seqware_workflow.py", line 197, in execute
    raise RuntimeError
RuntimeError
Error deleting container: Error response from daemon: Cannot destroy container e75965a88bc303bd04c7cff0e45f73b690ce4739afeda2224b1aa3f124db8b1f: Unable to remove filesystem for e75965a88bc303bd04c7cff0e45f73b690ce4739afeda2224b1aa3f124db8b1f: remove /cm/shared/docker_volumes/containers/e75965a88bc303bd04c7cff0e45f73b690ce4739afeda2224b1aa3f124db8b1f: directory not empty                                                                                          Error while running job: Error collecting output for parameter 'somatic_cnv_tar_gz': Did not find output file with glob pattern: '['*.somatic.cnv.tar.gz']'
[job Dockstore.cwl] completed permanentFail
Final process status is permanentFail
Workflow error, try again with --debug for more information:
  Process status is ['permanentFail']

stdout :
java.lang.RuntimeException: problems running command: cwltool --enable-dev --non-strict --enable-net --outdir /home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/outputs/ --tmpdir-prefix /home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/working/ /home/rvalls/dev/CGP-Somatic-Docker/Dockstore.cwl /home/rvalls/dev/CGP-Somatic-Docker/./datastore/launcher-4f257681-2907-4b2e-bd65-c9eaae282f84/workflow_params.json