various small edits

Dockerfile

@@ -1,23 +1,25 @@
-# Create Docker container that can run afq analysis.
+# Create Docker container that can run afq analysis with the Flywheel SDK.
 
-# Start with the Matlab r2013b runtime container
+# Start with the afq-pipeline container
 FROM scitran/afq-pipeline:v1.0.1
 MAINTAINER Michael Perry <[email protected]>
 
-############################
-# ENV
-
 ENV FLYWHEEL /flywheel/v0
+WORKDIR ${FLYWHEEL}
+COPY run ${FLYWHEEL}/run
 
+###########################
+# Install dependencies
 
-############################
-# FUZZY
-
-RUN apt-get update && apt-get install -y \
+RUN apt-get update && apt-get install -y --force-yes \
     python-pip \
     git \
     python-levenshtein
 
+
+############################
+# FUZZY
+
 RUN pip install --upgrade pip && \
     pip install fuzzywuzzy && \
     pip install fuzzywuzzy[speedup]
@@ -28,12 +30,12 @@ RUN pip install --upgrade pip && \
 
 WORKDIR /opt/flywheel
 # Commit for version of SDK to build
-ENV COMMIT af59edf
+ENV COMMIT bf2e0d6
 ENV LD_LIBRARY_PATH_TMP ${LD_LIBRARY_PATH}
 ENV LD_LIBRARY_PATH ' '
 RUN git clone https://github.com/flywheel-io/sdk workspace/src/flywheel.io/sdk
 RUN ln -s workspace/src/flywheel.io/sdk sdk
-RUN cd sdk && git checkout $COMMIT >> /dev/null && cd ../
+RUN cd sdk && git checkout $COMMIT && cd ../
 RUN sdk/make.sh
 RUN sdk/bridge/make.sh
 ENV PYTHONPATH /opt/flywheel/workspace/src/flywheel.io/sdk/bridge/dist/python/flywheel
@@ -45,18 +47,15 @@ ENV LD_LIBRARY_PATH ${LD_LIBRARY_PATH_TMP}
 
 COPY fw_sdk_functions.py ${FLYWHEEL}/
 COPY fw_sdk_getData.py ${FLYWHEEL}/
-COPY run ${FLYWHEEL}/run
-COPY manifest.json ${FLYWHEEL}/manifest.json
 
 
 ############################
-# ENV preservation
+# ENV preservation for Flywheel Engine
 
 RUN env -u HOSTNAME -u PWD | \
   awk -F = '{ print "export " $1 "=\"" $2 "\"" }' > ${FLYWHEEL}/docker-env.sh
 
-
-############################
 # Configure entrypoint
 RUN chmod +x ${FLYWHEEL}/*
 ENTRYPOINT ["/flywheel/v0/run"]
+COPY manifest.json ${FLYWHEEL}/manifest.json

README.md

@@ -1,6 +1,6 @@
 [![Docker Pulls](https://img.shields.io/docker/pulls/scitran/afq-pipeline-sdk.svg)](https://hub.docker.com/r/scitran/afq-pipeline-sdk/)
 [![Docker Stars](https://img.shields.io/docker/stars/scitran/afq-pipeline-sdk.svg)](https://hub.docker.com/r/scitran/afq-pipeline-sdk/)
 
-## scitran/afq-pipeline-sdk
+## scitran/afq-pipeline
 
-Build context for a [Flywheel Gear](https://github.com/flywheel-io/gears/tree/master/spec) that can run the [AFQ](https://github.com/jyeatman/AFQ) pipeline (fslmerge + dtiInit + AFQ) using the Flywheel SDK to automatically choose input data.
+Build context for a [Flywheel Gear](https://github.com/flywheel-io/gears/tree/master/spec) that can run the [AFQ](https://github.com/jyeatman/AFQ) pipeline (fslmerge + dtiInit + AFQ) using the Flywheel SDK to gather required input data.

manifest.json

@@ -1,6 +1,6 @@
 {
   "name": "afq-pipeline-sdk",
-  "label": "AFQ SDK Pipeline: Automated Fiber Quantification Processing Pipeline",
+  "label": "AFQ Pipeline SDK: Automated Fiber Quantification Processing Pipeline",
   "description": "This SDK Gear will take a user-provided acquisition label and automatically find appropriate inputs for the Gear. The Gear runs a 3-step pipeline designed to run AFQ. The first step is optional, and will merge two diffusion datasets using FSLMERGE. The second step is data preprocessing using DTIINIT. The final step the Automated Fiber Quantification (AFQ), which generates tract profiles of tissue properties for major fiber tracts in the brain.",
   "maintainer": "Michael Perry <[email protected]>",
   "author": "Jason D. Yeatman, et. al, VISTA Lab, FMRIB Software Laboratory",
@@ -11,7 +11,7 @@
   "flywheel": "0",
   "version": "1.0.0",
   "custom": {
-    "docker-image": "scitran/afq-pipeline-sdk:v1.0.0"
+    "docker-image": "scitran/afq-pipeline-sdk:1.0.0"
   },
   "inputs": {
     "api_key": {