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* Initial relative import changes * - Adds a requirements file (for testing) - Fix for Python3 has_key (now "in") - Fix for Python 3 xrange (now range) * - Updated Dockerfile requirements * - Use of Python3 RDKit base image * #30 switched service descriptors to yaml
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FROM informaticsmatters/rdkit-python-debian:Release_2018_09_1 | ||
FROM informaticsmatters/rdkit-python3-debian:Release_2019_03_1 | ||
LABEL maintainer="Tim Dudgeon<[email protected]>" | ||
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USER root | ||
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@@ -10,4 +10,5 @@ RUN apt-get -y update && apt-get -y install zip unzip procps | |
COPY src/python /opt/python | ||
RUN pip install -e /opt/python | ||
# And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit | ||
RUN pip install molvs standardiser matplotlib im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.* | ||
RUN pip install molvs standardiser matplotlib \ | ||
im-pipelines-utils>=2.4.5 im-pipelines-utils-rdkit>=1.5.7 |
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im-pipelines-utils==2.4.* | ||
im-pipelines-utils-rdkit==1.5.* | ||
matplotlib==2.2.* | ||
scipy==1.1.* | ||
numpy==1.14.* | ||
scikit-learn==0.19.* | ||
pandas==0.23.* |
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--- | ||
"@class": org.squonk.core.DockerServiceDescriptor | ||
serviceConfig: | ||
id: pipelines.dmpk.sygnature.tmax_cmax_sim.1 | ||
name: TmaxCmaxSimulation | ||
description: Simulation of Tmax and Cmax | ||
tags: | ||
- sygnature | ||
- dmpk | ||
- pk | ||
- cmax | ||
- tmax | ||
- simulation | ||
- prediction | ||
- docker | ||
resourceUrl: | ||
icon: icons/program.png | ||
outputDescriptors: | ||
- primaryType: org.squonk.types.PngImageFile | ||
mediaType: image/png | ||
name: output | ||
optionDescriptors: | ||
- modes: | ||
- User | ||
editable: true | ||
visible: true | ||
description: Half life(elim)(hr) | ||
label: Half life(elim)(hr) | ||
key: arg.halfLife | ||
minValues: 1 | ||
maxValues: 1 | ||
typeDescriptor: | ||
type: java.lang.Float | ||
"@class": org.squonk.options.SimpleTypeDescriptor | ||
"@class": org.squonk.options.OptionDescriptor | ||
- modes: | ||
- User | ||
editable: true | ||
visible: true | ||
description: Half life(abs)(hr) | ||
label: Half life(abs)(hr) | ||
key: arg.absorption | ||
minValues: 1 | ||
maxValues: 1 | ||
typeDescriptor: | ||
type: java.lang.Float | ||
"@class": org.squonk.options.SimpleTypeDescriptor | ||
"@class": org.squonk.options.OptionDescriptor | ||
- modes: | ||
- User | ||
editable: true | ||
visible: true | ||
description: Dose(mg) | ||
label: Dose(mg) | ||
key: arg.dose | ||
minValues: 1 | ||
maxValues: 1 | ||
typeDescriptor: | ||
type: java.lang.Float | ||
"@class": org.squonk.options.SimpleTypeDescriptor | ||
"@class": org.squonk.options.OptionDescriptor | ||
- modes: | ||
- User | ||
editable: true | ||
visible: true | ||
description: AUC(mg/L.hr) | ||
label: AUC(mg/L.hr) | ||
key: arg.auc | ||
minValues: 1 | ||
maxValues: 1 | ||
typeDescriptor: | ||
type: java.lang.Float | ||
"@class": org.squonk.options.SimpleTypeDescriptor | ||
"@class": org.squonk.options.OptionDescriptor | ||
- modes: | ||
- User | ||
editable: true | ||
visible: true | ||
description: Simulation Time Length(hr) | ||
label: Simulation Time Length(hr) | ||
key: arg.time | ||
minValues: 1 | ||
maxValues: 1 | ||
typeDescriptor: | ||
type: java.lang.Float | ||
"@class": org.squonk.options.SimpleTypeDescriptor | ||
"@class": org.squonk.options.OptionDescriptor | ||
executorClassName: org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep | ||
outputRoutes: | ||
- route: FILE | ||
imageName: informaticsmatters/rdkit_pipelines | ||
command: >- | ||
python -m pipelines.dmpk.pk_tmax_cmax_sim -o ${POUT}output --half-life $halfLife | ||
--absorption $absorption --dose $dose --auc $auc --time $time |
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--- | ||
"@class": org.squonk.core.DockerServiceDescriptor | ||
serviceConfig: | ||
id: pipelines.xchem.obabel.prepare.pdb.v1 | ||
name: OBabelPreparePDB | ||
description: Prepare PDB file using Open Babel | ||
tags: | ||
- rdkit | ||
- xchem | ||
- docker | ||
- openbabel | ||
- obabel | ||
- prepare | ||
- pdb | ||
- convert | ||
- protein | ||
resourceUrl: | ||
icon: icons/transform_molecule.png | ||
inputDescriptors: | ||
- primaryType: org.squonk.types.PDBFile | ||
mediaType: chemical/x-pdb | ||
name: pdb | ||
outputDescriptors: | ||
- primaryType: org.squonk.types.Mol2File | ||
mediaType: chemical/x-mol2 | ||
name: mol2 | ||
optionDescriptors: | ||
- modes: | ||
- User | ||
editable: true | ||
"@class": org.squonk.options.OptionDescriptor | ||
typeDescriptor: | ||
type: java.lang.Float | ||
"@class": org.squonk.options.SimpleTypeDescriptor | ||
key: arg.protonate | ||
label: Protonate at pH | ||
description: Optionally protonate side chains at this pH | ||
visible: true | ||
minValues: 0 | ||
maxValues: 1 | ||
executorClassName: org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep | ||
inputRoutes: | ||
- route: FILE | ||
outputRoutes: | ||
- route: FILE | ||
imageName: informaticsmatters/pipelines-obabel:latest | ||
command: >- | ||
python -m pipelines.docking.obabel_prepare_pdb -i ${PIN}pdb.pdb.gz -o ${POUT}mol2 -mol2 | ||
${binding.variables.containsKey('protonate') ? '-prot ' + protonate : ''} | ||
--meta |
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