Dockerfile

FROM monashbiomedicalimaging/nianalysis
MAINTAINER Tom Close <tom.close@monash.edu>

# Download QA script to run
ENV REFRESHED_AT 2018-03-05-12:19
RUN git clone https://github.com/mbi-image/xnat-nif-qc-analysis.git /repo
ENV PYTHONPATH /repo:$PYTHONPATH

# XNAT container pipeline label
LABEL org.nrg.commands="[{\"index\": null, \"working-directory\": null, \"description\": \"Analyses QC sessions acquired as per the NIF TDRS SOP\", \"command-line\": \"/repo/xnat_pipeline.sh #SESSIONID# #T1# #T2# #DMRI#\", \"inputs\": [{\"replacement-key\": \"#SESSIONID#\", \"required\": true, \"type\": \"string\", \"name\": \"Session ID\", \"description\": \"XNAT ID of the session\"}, {\"command-line-flag\": null, \"name\": \"T1 32Ch Scan Name\", \"default-value\": \"\", \"matcher\": null, \"false-value\": null, \"required\": true, \"true-value\": null, \"replacement-key\": \"#T1#\", \"command-line-separator\": null, \"type\": \"string\", \"description\": \"Name of the T1-weighted saline phantom with 32 Channel Head Coil\"}, {\"command-line-flag\": null, \"name\": \"T2 32Ch Scan Name\", \"default-value\": \"\", \"matcher\": null, \"false-value\": null, \"required\": true, \"true-value\": null, \"replacement-key\": \"#T2#\", \"command-line-separator\": null, \"type\": \"string\", \"description\": \"Name of the T2-weighted saline phantom with 32 Channel Head Coil\"}, {\"command-line-flag\": null, \"name\": \"dMRI 32Ch Scan Name\", \"default-value\": \"\", \"matcher\": null, \"false-value\": null, \"required\": true, \"true-value\": null, \"replacement-key\": \"#DMRI#\", \"command-line-separator\": null, \"type\": \"string\", \"description\": \"Name of the Diffusion MRI saline phantom with 32 Channel Head Coil\"}], \"outputs\": [], \"image\": \"monashbiomedicalimaging/xnat-nif-qc-analysis\", \"label\": null, \"version\": \"1.0\", \"info-url\": null, \"xnat\": [{\"derived-inputs\": [{\"provides-value-for-command-input\": \"Session ID\", \"name\": \"session-id\", \"derived-from-xnat-object-property\": \"label\", \"derived-from-wrapper-input\": \"session\", \"type\": \"string\", \"description\": \"The session's id\"}], \"contexts\": [\"xnat:imageSessionData\"], \"description\": \"Analyses QC sessions acquired as per the NIF TDRS SOP\", \"output-handlers\": [], \"external-inputs\": [{\"required\": true, \"type\": \"Session\", \"name\": \"session\", \"description\": \"Input session\"}], \"name\": \"QC Analysis\"}], \"mounts\": [{\"writable\": true, \"path\": \"/workdir\", \"name\": \"workdir\"}], \"schema-version\": \"1.0\", \"environment-variables\": {}, \"type\": \"docker\", \"ports\": {}, \"name\": \"QC Analysis\"}]"