Merge pull request #84 from oesteban/agave

Agave app description generator

agave/app/wrapper.sh

@@ -0,0 +1,21 @@
+#!/usr/bin/env bash
+# @Author: oesteban
+# @Date:   2015-10-21 11:58:53
+# @Last Modified by:   oesteban
+# @Last Modified time: 2015-11-13 10:00:55
+
+OUTPUT_FOLDER=$SCRATCH/${AGAVE_JOB_NAME}-${AGAVE_JOB_ID}
+# Create output folder in scratch
+mkdir -p ${OUTPUT_FOLDER}
+
+echo "Running mriqc on ${bidsFile}" >> ${OUTPUT_FOLDER}/${AGAVE_JOB_NAME}.out
+
+# Activate anaconda env
+source activate crn-2.7
+
+# Call mriqcp
+FSLOUTPUTTYPE='NIFTI_GZ' mriqc -i ${bidsFile} -o ${OUTPUT_FOLDER}/out -w ${OUTPUT_FOLDER}/tmp  2>> ${OUTPUT_FOLDER}/${AGAVE_JOB_NAME}.err 1>> ${OUTPUT_FOLDER}/${AGAVE_JOB_NAME}.out
+
+# Collect outputs
+archivepath=$(echo ${OUTPUT_FOLDER}/out | cut -d: -f2 | xargs)
+ln -s $archivepath .

agave/docker-app/app.json

@@ -0,0 +1,43 @@
+{
+  "name": "mriqc-docker",
+  "version": "0.1.0",
+  "helpURI": "http://mriqc.readthedocs.org",
+  "label": "The MRIQC workflow in docker",
+  "defaultNodeCount": 1,
+  "defaultRequestedTime": "48:00:00",
+  "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",
+  "executionType": "CLI",
+  "parallelism": "SERIAL",
+  "deploymentPath": "apps/mriqc-docker",
+  "deploymentSystem": "openfmri-storage",
+  "templatePath": "wrapper.sh",
+  "testPath": "test/test.sh",
+  "tags": [
+    "docker", "qc", "preprocessing"
+  ],
+  "modules": [],
+  "inputs": [
+    {
+      "id": "bidsFolder",
+      "details": {
+        "label": "folder",
+        "description": "input folder, should be BIDS compliant",
+        "argument": null,
+        "showArgument": false
+      },
+      "value": {
+        "visible": true,
+        "required": true,
+        "type": "string",
+        "default": "agave://openfmri-storage/ds003_downsampled.tar"
+      },
+      "semantics": {
+        "ontology": []
+      }
+    }
+  ],
+  "parameters": [],
+  "checkpointable": false
+}

agave/docker-app/test/test.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+set -x
+export AGAVE_JOB_ID="test123345"
+export AGAVE_JOB_NAME="testuser-runner"
+export AGAVE_JOB_CALLBACK_FAILURE=""
+

agave/docker-app/wrapper.sh

@@ -0,0 +1,23 @@
+#set -x
+
+echo "Running mriqc-docker on ${bidsFolder}" >> ${AGAVE_JOB_NAME}.out
+
+# Run the container in docker, mounting the current job directory as /scratch in the container
+# Note that here the docker container image must exist for the container to run. If it was
+# not built using a passed in Dockerfile, then it will be downloaded here prior to
+# invocation. Also note that all output is written to the mounted directory. This allows
+# Agave to stage out the data after running.
+
+docker run -i --rm -v `pwd`:/scratch -w /scratch oesteban/mriqc -i ${bidsFolder} -o outputs -w workdir 2>> ${AGAVE_JOB_NAME}.err 1>> ${AGAVE_JOB_NAME}.out
+
+if [ ! $? ]; then
+	echo "Docker process exited with an error status." >&2
+	${AGAVE_JOB_CALLBACK_FAILURE}
+	exit
+fi
+
+# Good practice would suggest that you clean up your image after running. For throughput
+# you may want to leave it in place. iPlant's docker servers will clean up after themselves
+# using a purge policy based on size, demand, and utilization.
+
+#sudo docker rmi $DOCKER_IMAGE

mriqc/__init__.py

@@ -31,7 +31,9 @@
 
 """
 
-__version__ = '0.5.0a3'
+__versionbase__ = '0.6.0'
+__versionrev__ = 'a1'
+__version__ = __versionbase__ + __versionrev__
 __author__ = 'Oscar Esteban'
 __email__ = 'code@oscaresteban.es'
 __maintainer__ = 'Oscar Esteban'
@@ -42,10 +44,10 @@
 __status__ = 'Prototype'
 __description__ = 'NR-IQMs (no-reference Image Quality Metrics) for MRI'
 __longdesc__ = """
-MRIQC provides a series of image processing workflows to extract and compute a series of 
-NR (no-reference), IQMs (image quality metrics) to be used in QAPs (quality assessment 
+MRIQC provides a series of image processing workflows to extract and compute a series of
+NR (no-reference), IQMs (image quality metrics) to be used in QAPs (quality assessment
 protocols) for MRI (magnetic resonance imaging).
-This open-source neuroimaging data processing tool is being developed as a part of the 
+This open-source neuroimaging data processing tool is being developed as a part of the
 MRI image analysis and reproducibility platform offered by the CRN. This pipeline derives
 from, and is heavily influenced by, the PCP Quality Assessment Protocol.
 This tool extracts a series of IQMs from structural and functional MRI data. It is also

mriqc/interfaces/qc.py

@@ -2,7 +2,6 @@
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-# pylint: disable=no-member
 #
 # @Author: oesteban
 # @Date:   2016-01-05 11:29:40
@@ -324,4 +323,3 @@ def _run_interface(self, runtime):
             'perc_fd': num_fd * 100 / (len(fddata) + 1)
         }
         return runtime
-

mriqc/utils/agave_appgen.py

@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# @Author: oesteban
+# @Date:   2016-03-16 11:28:27
+# @Last Modified by:   oesteban
+# @Last Modified time: 2016-03-16 15:12:13
+
+"""
+Agave app generator
+
+"""
+import json
+from argparse import ArgumentParser, RawTextHelpFormatter
+import mriqc
+
+agaveapp = {
+    'name': mriqc.__name__,
+    'version': mriqc.__versionbase__,
+    'helpURI': 'http://mriqc.readthedocs.org',
+    'label': 'mriqc',
+    'shortDescription': mriqc.__description__,
+    'longDescription': mriqc.__longdesc__,
+    'executionSystem': 'slurm-ls5.tacc.utexas.edu',
+    'executionType': 'HPC',
+    'parallelism': 'PARALLEL',
+    'defaultQueue': 'normal',
+    'defaultNodeCount': 1,
+    'deploymentPath': 'apps/mriqc',
+    'deploymentSystem': 'openfmri-storage',
+    'templatePath': 'wrapper.sh',
+    'testPath': 'test/test.sh',
+    'tags': ['qc', 'sMRI', 'fMRI'],
+    'modules': [],
+    'inputs': [{
+        'id': 'bidsFolder',
+        'details': {
+            'label': 'folder',
+            'description': 'input root folder of a BIDS-compliant tree',
+            'argument': None,
+            'showArgument': False
+        },
+        'value': {
+            'visible': True,
+            'required': True,
+            'type': 'string',
+            'default': 'agave://openfmri-storage/data/ds003_downsampled'
+        },
+        'semantics': {
+            'ontology': []
+        }
+    }],
+    'parameters': [],
+    'checkpointable': False
+}
+
+def main():
+    """Entry point"""
+
+    parser = ArgumentParser(description='ABIDE2BIDS downloader',
+                            formatter_class=RawTextHelpFormatter)
+    g_inputs = parser.add_argument_group('Inputs')
+    g_inputs.add_argument('--help-uri', action='store')
+    g_inputs.add_argument('--input-name', action='store')
+    g_inputs.add_argument('-E', '--exec-system', action='store')
+
+
+    g_outputs = parser.add_argument_group('Outputs')
+    g_outputs.add_argument('-o', '--output', action='store',
+                           default='app.json')
+
+    opts = parser.parse_args()
+
+    if opts.input_name is not None:
+        agaveapp['inputs'][0]['id'] = opts.input_name
+    if opts.exec_system:
+        agaveapp['executionSystem'] = opts.exec_system
+
+    with open(opts.output, 'w') as appfile:
+        json.dump(agaveapp, appfile, indent=4)
+
+
+
+if __name__ == '__main__':
+    main()