README.md

phase1md5challenge

This source tree contains a Vagrant configuration which creates a Centos 7 virtual machine with cwl-runner and all of its needed prerequesites installed. This allows the user to bring up the virtual machine and invoke a few commands to run the md5sum workflow.

Contains files for GA4GH Tool Execution Challenge.

Requirements

• Vagrant
• Virtual Box

• =4gb ram

• Linux/Mac with a terminal, Windows should also work but the instructions are not provided.

NOTE: Although not required installation of Git is used to download this source tree to the local machine.

Running the workflow from Linux/Mac computer

Below are steps to run the md5sum workflow in a Vagrant virtual machine. The instructions below assume a Linux or Mac OS, but it should in theory work on a Windows box

Step 1) Download configuration files

git clone https://github.com/coleslaw481/phase1md5challenge.git
cd phase1md5challenge

NOTE: If Git command line tool is NOT available simply download this source tree via https://github.com/coleslaw481/phase1md5challenge, unzip the downloaded file, cd into the unzipped directory, and continue with step 2.

Step 2) Spin up the virtual machine with Vagrant

Please note this command takes a few minutes since it is setting up a virtual machine.

vagrant up

Step 3) Connect to the virtual machine and download needed files

vagrant ssh

wget https://raw.githubusercontent.com/briandoconnor/dockstore-tool-md5sum/master/Dockstore.cwl
wget https://raw.githubusercontent.com/briandoconnor/dockstore-tool-md5sum/master/md5sum.input
wget https://raw.githubusercontent.com/briandoconnor/dockstore-tool-md5sum/master/test.json

Step 4) Run the workflow

time cwl-runner --non-strict Dockstore.cwl test.json

The answer will be stored in md5sum.txt file

Example output from running above command:

Resolved 'Dockstore.cwl' to 'file:///home/vagrant/Dockstore.cwl'
['docker', 'pull', 'quay.io/briandoconnor/dockstore-tool-md5sum:1.0.2']
1.0.2: Pulling from briandoconnor/dockstore-tool-md5sum
8aec416115fd: Pull complete 
695f074e24e3: Pull complete 
946d6c48c2a7: Pull complete 
bc7277e579f0: Pull complete 
2508cbcde94b: Pull complete 
a3ed95caeb02: Pull complete 
b1f19f922e23: Pull complete 
3fa75a7b6e87: Pull complete 
Digest: sha256:23bf499256200ecb7f841304325348fa4b8b0d822b36ab6363c4c6ed857d120f
Status: Downloaded newer image for quay.io/briandoconnor/dockstore-tool-md5sum:1.0.2
[job Dockstore.cwl] /tmp/tmp9juTjX$ docker \
    run \
    -i \
    --volume=/home/vagrant/md5sum.input:/var/lib/cwl/stg3b40cc3a-1294-44f8-8022-222ceb328527/md5sum.input:ro \
    --volume=/tmp/tmp9juTjX:/var/spool/cwl:rw \
    --volume=/tmp/tmpgPSGtz:/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/stg3b40cc3a-1294-44f8-8022-222ceb328527/md5sum.input
[job Dockstore.cwl] completed success
{
    "output_file": {
        "format": "http://edamontology.org/data_3671", 
        "checksum": "sha1$1250816c19c6f5524c5366b56c7a1eed6f3c3ab3", 
        "basename": "md5sum.txt", 
        "location": "file:///home/vagrant/md5sum.txt", 
        "path": "/home/vagrant/md5sum.txt", 
        "class": "File", 
        "size": 33
    }
}
Final process status is success

real	0m26.730s
user	0m1.292s
sys	0m0.261s

COPYRIGHT AND LICENSE

See LICENSE.txt