fixes for old-style service descriptors

Author: tdudgeon

Dockerfile-rdkit

@@ -10,4 +10,4 @@ RUN apt-get -y update && apt-get -y install zip unzip
 COPY src/python /opt/python
 RUN pip install -e /opt/python
 # And the pipeline-utilities
-RUN pip install matplotlib im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*
+RUN pip install molvs standardiser matplotlib im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*

src/python/pipelines/docking/obabel_prepare_pdb.dsd.json

@@ -44,9 +44,6 @@
   },
   "inputRoutes": [ {"route": "FILE"} ],
   "outputRoutes": [ {"route": "FILE"} ],
-  "imageName": "abradle/obabel",
-  "command": "cp -r /pipelines /tmp/pipelines && pip install -e /tmp/pipelines && python -m pipelines.docking.obabel_prepare_pdb -i ${PIN}pdb.pdb.gz -o ${POUT}mol2 -mol2${protonate ? ' -prot ' + protonate : ''} --meta",
-  "volumes": {
-      "pipelines": "/pipelines"
-    }
+  "imageName": "informaticsmatters/rdkit_pipelines",
+  "command": "python -m pipelines.docking.obabel_prepare_pdb -i ${PIN}pdb.pdb.gz -o ${POUT}mol2 -mol2${protonate ? ' -prot ' + protonate : ''} --meta"
 }

src/python/pipelines/rdkit/sanifier_enumerator.dsd.json

@@ -109,9 +109,6 @@
   "thinDescriptors": [{"input": "input"}],
   "inputRoutes": [ {"route": "FILE"} ],
   "outputRoutes": [ {"route": "FILE"} ],
-  "imageName": "abradle/standardiser",
-  "command": "cp -r /pipelines /tmp/pipelines && pip install -e /tmp/pipelines && python -m pipelines.rdkit.sanifier -i ${PIN}input.data.gz -if json -o ${POUT}output -of json -mf $molFormat ${tautomers ? ' -et' : ''}${stereoisomers ? ' -es' : ''} --meta",
-  "volumes": {
-      "pipelines": "/pipelines"
-    }
+  "imageName": "informaticsmatters/rdkit_pipelines",
+  "command": "python -m pipelines.rdkit.sanifier -i ${PIN}input.data.gz -if json -o ${POUT}output -of json -mf $molFormat ${tautomers ? ' -et' : ''}${stereoisomers ? ' -es' : ''} --meta"
 }

src/python/pipelines/rdkit/sanifier_standardiser_flatkinson.dsd.json

@@ -54,9 +54,6 @@
   "thinDescriptors": [{"input": "input", "preserve": false}],
   "inputRoutes": [ {"route": "FILE"} ],
   "outputRoutes": [ {"route": "FILE"} ],
-  "imageName": "abradle/standardiser",
-  "command": "cp -r /pipelines /tmp/pipelines && pip install -e /tmp/pipelines && python -m pipelines.rdkit.sanifier -i ${PIN}input.data.gz -if json -o ${POUT}output -of json -st -stm flatkinson --meta",
-  "volumes": {
-      "pipelines": "/pipelines"
-    }
+  "imageName": "informaticsmatters/rdkit_pipelines",
+  "command": "python -m pipelines.rdkit.sanifier -i ${PIN}input.data.gz -if json -o ${POUT}output -of json -st -stm flatkinson --meta"
 }

src/python/pipelines/rdkit/sanifier_standardiser_molvs.dsd.json

@@ -54,9 +54,6 @@
   "thinDescriptors": [{"input": "input", "preserve": false}],
   "inputRoutes": [ {"route": "FILE"} ],
   "outputRoutes": [ {"route": "FILE"} ],
-  "imageName": "abradle/standardiser",
-  "command": "cp -r /pipelines /tmp/pipelines && pip install -e /tmp/pipelines && python -m pipelines.rdkit.sanifier -i ${PIN}input.data.gz -if json -o ${POUT}output -of json -st -stm molvs --meta",
-  "volumes": {
-      "pipelines": "/pipelines"
-    }
+  "imageName": "informaticsmatters/rdkit_pipelines",
+  "command": "python -m pipelines.rdkit.sanifier -i ${PIN}input.data.gz -if json -o ${POUT}output -of json -st -stm molvs --meta"
 }