synapse-plugin

Dockstore Synapse file provisioning plugin

Usage

This provision method only supports download for now.

$ cat test.synapse.json                                                                                                                                            
{
  "input_file": {
        "class": "File",
        "path": "syn://syn8299856"
    },
    "output_file": {
        "class": "File",
        "path": "/tmp/md5sum.txt"
    }
}

$ dockstore tool launch --entry  quay.io/briandoconnor/dockstore-tool-md5sum  --json test.synapse.json                                                             
Creating directories for run of Dockstore launcher at: ./datastore//launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4
Provisioning your input files to your local machine
Downloading: #input_file from syn://syn8299856 into directory: /media/large_volume/dockstore_tools/dockstore-tool-md5sum/./datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/inputs/990720a6-d5c8-4ef2-b015-12
c575a8e7f4
Found file syn://syn8299856 in cache, hard-linking
Calling on plugin io.dockstore.provision.SynapsePlugin$SynapseProvision to provision syn://syn8299856
Calling out to cwltool to run your tool
Executing: cwltool --enable-dev --non-strict --outdir /media/large_volume/dockstore_tools/dockstore-tool-md5sum/./datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/outputs/ --tmpdir-prefix /media/large_volu
me/dockstore_tools/dockstore-tool-md5sum/./datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/tmp/ --tmp-outdir-prefix /media/large_volume/dockstore_tools/dockstore-tool-md5sum/./datastore/launcher-14c0bd4c-
821b-49a0-8b14-2ee2085038a4/working/ /tmp/1488401341483-0/temp7036304455702546523.cwl /media/large_volume/dockstore_tools/dockstore-tool-md5sum/./datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/workflow_p
arams.json
/usr/local/bin/cwltool 1.0.20170217172322
Resolved '/tmp/1488401341483-0/temp7036304455702546523.cwl' to 'file:///tmp/1488401341483-0/temp7036304455702546523.cwl'
[job temp7036304455702546523.cwl] /media/large_volume/dockstore_tools/dockstore-tool-md5sum/datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/working/XDSteC$ docker \
    run \
    -i \
    --volume=/media/large_volume/dockstore_tools/dockstore-tool-md5sum/./datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/inputs/990720a6-d5c8-4ef2-b015-12c575a8e7f4/syn8299856:/var/lib/cwl/stgb2cf6387-89a
1-4254-947d-2df8cf6cc6df/syn8299856:ro \
    --volume=/media/large_volume/dockstore_tools/dockstore-tool-md5sum/datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/working/XDSteC:/var/spool/cwl:rw \
    --volume=/media/large_volume/dockstore_tools/dockstore-tool-md5sum/datastore/launcher-14c0bd4c-821b-49a0-8b14-2ee2085038a4/tmp/s1MaIt:/tmp:rw \
    --workdir=/var/spool/cwl \
    --read-only=true \
    --user=1000 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/var/spool/cwl \
    quay.io/briandoconnor/dockstore-tool-md5sum:1.0.2 \
    /bin/my_md5sum \
    /var/lib/cwl/stgb2cf6387-89a1-4254-947d-2df8cf6cc6df/syn8299856
[job temp7036304455702546523.cwl] completed success

Configuration

This plugin gets configuration information from the following structure in ~/.dockstore/config

[dockstore-file-synapse-plugin]                                                                                                                                                                                     
synapse-personal-access-token =                                                                                                                                                                                        

Browse to your profile on https://www.synapse.org and click on "Manage Personal Access Tokens" to generate an access token with "View" and "Download" permissions if you do not already have one. For more information, read this synapse doc.