Merge pull request #85 from oesteban/enh/one-session-one-run

[Enh] One-session-one-run

Dockerfile

@@ -12,13 +12,8 @@ RUN source activate crnenv && \
     python -c "from mriqc.data import get_brainweb_1mm_normal; get_brainweb_1mm_normal()"
 
 WORKDIR /root/
-ADD build/files/run_mriqc /usr/bin/run_mriqc
-ADD build/files/run_tests /usr/bin/run_tests
-ADD build/files/run_dfcheck /usr/bin/run_dfcheck
-
-RUN chmod +x /usr/bin/run_mriqc && \
-	chmod +x /usr/bin/run_tests && \
-	chmod +x /usr/bin/run_dfcheck
+ADD build/files/run_* /usr/bin/
+RUN chmod +x /usr/bin/run_*
 
 ENTRYPOINT ["/usr/bin/run_mriqc"]
 CMD ["--help"]

agave/docker-app/app.json

@@ -5,6 +5,7 @@
   "label": "The MRIQC workflow in docker",
   "defaultNodeCount": 1,
   "defaultRequestedTime": "48:00:00",
+  "defaultQueue": "debug",
   "shortDescription": "Run CRN's workflows in Agave's Dockerized cloud.",
   "longDescription": "Generic template for running an arbitrary application in Agave's hosted Docker cloud. Apps should be a gzipped archive.",
   "executionSystem": "docker.tacc.utexas.edu",

build/Dockerfile

@@ -15,7 +15,6 @@ RUN git clone $GIT_URL && \
     python setup.py install && \
     python -c "from mriqc.data import get_brainweb_1mm_normal; get_brainweb_1mm_normal()"
 
-WORKDIR /root/
 ADD files/run_* /usr/bin/
 RUN chmod +x /usr/bin/run_*
 

build/circle_tests.sh

@@ -3,26 +3,30 @@
 set -x
 set -e
 
-declare -a MRIQC_TESTS=(
-	"-i data/ds003_downsampled -o outputs/ms-func/out -w outputs/ms-func/work --skip-anatomical" #
-	"-i data/ds003_downsampled -o outputs/ms-anat/out -w outputs/ms-anat/work --skip-functional --use-plugin plugin.yml --save-memory" #
-# -i data/ds003_sub-01/ -o outputs/ss-all/out -w outputs/ss-all/work
-)
+# declare -a MRIQC_TESTS=(
+# 	"-i data/ds003_downsampled -o outputs/ms-func/out -w outputs/ms-func/work --skip-anatomical" #
+# 	"-i data/ds003_downsampled -o outputs/ms-anat/out -w outputs/ms-anat/work --skip-functional --use-plugin plugin.yml --save-memory" #
+# # -i data/ds003_sub-01/ -o outputs/ss-all/out -w outputs/ss-all/work
+# )
 
-if [[ $CIRCLE_NODE_INDEX -eq 0 ]]; then
-	docker run -i -v /etc/localtime:/etc/localtime:ro --entrypoint="/usr/bin/run_tests" oesteban/mriqc
-fi
 
-i=0
-for test_params in "${MRIQC_TESTS[@]}"; do
-	if [ $(($i % $CIRCLE_NODE_TOTAL)) -eq $CIRCLE_NODE_INDEX ]; then
-	    docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch oesteban/mriqc ${test_params}
-	fi
-	((i=i+1))
-done
+# i=0
+# for test_params in "${MRIQC_TESTS[@]}"; do
+# 	if [ $(($i % $CIRCLE_NODE_TOTAL)) -eq $CIRCLE_NODE_INDEX ]; then
+# 	    docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch oesteban/mriqc ${test_params}
+# 	fi
+# 	((i=i+1))
+# done
 
 if [[ $CIRCLE_NODE_INDEX -eq 0 ]]; then
-	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_dfcheck" oesteban/mriqc -i /scratch/outputs/ms-func/out/fMRIQC.csv -r /root/src/mriqc/mriqc/data/tests/ds003_downsampled_fMRI.csv
-elif [[ $CIRCLE_NODE_INDEX -eq 1 ]]; then
-	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_dfcheck" oesteban/mriqc -i /scratch/outputs/ms-anat/out/aMRIQC.csv -r /root/src/mriqc/mriqc/data/tests/ds003_downsampled_sMRI.csv
+	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch oesteban/mriqc -B /scratch/data/ds003_downsampled -d func -o outputs/ms-func/out -w outputs/ms-func/work
+	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_mriqc_plot" oesteban/mriqc -d func -o outputs/ms-func/out -w outputs/ms-func/work
+	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch oesteban/mriqc -B /scratch/data/ds003_downsampled -S $(seq -f '%02g' 01 05) -d anat -o outputs/ms-anat/out -w outputs/ms-anat/work
+	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_mriqc_plot" oesteban/mriqc -d anat -o outputs/ms-anat/out -w outputs/ms-anat/work
+fi
+
+if [[ $CIRCLE_NODE_INDEX -eq 1 ]]; then
+	docker run -i -v /etc/localtime:/etc/localtime:ro --entrypoint="/usr/bin/run_tests" oesteban/mriqc
+	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch oesteban/mriqc -B /scratch/data/ds003_downsampled -S $(seq -f '%02g' 06 13) -d anat -o outputs/ms-anat/out -w outputs/ms-anat/work
+	docker run -i -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /scratch --entrypoint="/usr/bin/run_mriqc_plot" oesteban/mriqc -d anat -o outputs/ms-anat/out -w outputs/ms-anat/work
 fi

build/files/run_mriqc_plot

@@ -0,0 +1,4 @@
+#!/bin/bash
+source activate crnenv
+
+mriqc_plot $@

mriqc/__init__.py

@@ -31,7 +31,7 @@
 
 """
 
-__versionbase__ = '0.6.0'
+__versionbase__ = '0.8.1'
 __versionrev__ = 'a1'
 __version__ = __versionbase__ + __versionrev__
 __author__ = 'Oscar Esteban'