Merge pull request #792 from ratt-ru/stimela2

Stimela2 cab

stimela/cargo/base/stimela2/Dockerfile

@@ -0,0 +1,32 @@
+FROM kernsuite/base:9
+MAINTAINER <[email protected]>
+RUN docker-apt-install cmake \
+    wget \
+    subversion \
+    build-essential \
+    cmake \
+    gfortran \
+    g++ \
+    libncurses5-dev \
+    libreadline-dev \
+    flex \
+    bison \
+    libblas-dev \
+    liblapacke-dev \
+    libcfitsio-dev \
+    libgsl-dev \
+    wcslib-dev \
+    libhdf5-serial-dev \
+    libfftw3-dev \
+    python-numpy \
+    libboost-python-dev \
+    libboost-all-dev \
+    libpython2.7-dev \
+    liblog4cplus-dev \
+    libhdf5-dev \
+    casacore-dev \
+    wsclean
+
+RUN pip install cult-curgo stimela quartical breizorro 
+RUN ulimit -p 11000
+RUN stimela

stimela/cargo/cab/stimela2/parameters.json

@@ -0,0 +1,51 @@
+{
+    "task": "stimela2",
+    "base": "stimela/stimela2",
+    "tag": "1.7.10",
+    "description": "a workflow management framework for creating portable and reproducible data processing pipelines",
+    "prefix": "--",
+    "binary": "stimela run",
+    "version":"2.0.0",
+    "junk":[],
+    "msdir": true,
+    "parameters": [
+        {
+            "info": "Recipe file",
+            "name": "recipe",
+            "io": "input",
+            "default": null,
+            "dtype": "file",
+            "required": false
+        },
+        {
+            "info": "Support files",
+            "name": "support-files",
+            "io": "output",
+            "default": null,
+            "dtype": "list:file",
+            "required": false
+        },
+        {
+            "info": "Name of recipe to run",
+            "name": "recipe-name",
+            "dtype": "str",
+            "required": false
+        },
+        {
+            "info": "Step(s) to run from recipe",
+            "default": null,
+            "required": false,
+            "delimiter": ",",
+            "name": "step",
+            "dtype": "list:str"
+        },
+        {
+            "info": "Parameter(s) to override defaults. e.g. ['ms=foo.ms', 'image_size=2048']",
+            "default": null,
+            "required": false,
+            "delimiter": " ",
+            "name": "params",
+            "dtype": "list:str"
+        }
+    ]
+}

stimela/cargo/cab/stimela2/src/run.py

@@ -0,0 +1,59 @@
+import os
+import sys
+import shlex
+import shutil
+import subprocess
+import yaml
+import glob
+
+
+CONFIG = os.environ["CONFIG"]
+INPUT = os.environ["INPUT"]
+OUTPUT = os.environ["OUTPUT"]
+MSDIR = os.environ["MSDIR"]
+
+with open(CONFIG, "r") as _std:
+    cab = yaml.safe_load(_std)
+
+junk = cab["junk"]
+args = []
+
+for param in cab['parameters']:
+    name = param['name']
+    value = param['value']
+
+    if value is None:
+        continue
+
+    if name in ['recipe']:
+        recipe = value
+        continue
+
+    if name in ['recipe-name']:
+        recipe_name = value
+        continue
+
+    if name in ['support-files']:
+        continue
+
+    if name in ['step']:
+        delimiter = ',' #param['delimiter']
+        args += ['{0}{1} {2}'.format(cab['prefix'], name, delimiter.join(value))]
+
+    if name in  ['params']:
+        delimiter = ' ' #param['delimiter']
+        args += ['{0}'.format(delimiter.join(value))]
+
+_runc = " ".join([cab["binary"]] + [recipe, recipe_name] + args)
+
+try:
+    subprocess.check_call(shlex.split(_runc))
+finally:
+    for item in junk:
+        for dest in [OUTPUT, MSDIR]: # these are the only writable volumes in the container
+            items = glob.glob("{dest}/{item}".format(**locals()))
+            for f in items:
+                if os.path.isfile(f):
+                    os.remove(f)
+                elif os.path.isdir(f):
+                    shutil.rmtree(f)