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Alan Christie
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Merge remote-tracking branch 'origin/master'
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‎Dockerfile-obabel‎

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# We should create an Open Babel implementation of pipeline_utils that handles the basic I/O for
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# structure files so that the dependency on RDKit can be removed.
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# See https://github.com/InformaticsMatters/pipelines-obabel/issues/1
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FROM informaticsmatters/obabel:latest
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LABEL maintainer="Tim Dudgeon<[email protected]>"
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USER root
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# Copy the obabel pipeline implementation into the image
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COPY src/python /opt/python-obabel
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RUN apt-get install -y --no-install-recommends python-setuptools gzip python-pip && pip install -e /opt/python-obabel
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# And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
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RUN pip install im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*
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USER obabel
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‎Dockerfile-pli‎

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@@ -3,7 +3,7 @@ LABEL maintainer="Tim Dudgeon<[email protected]>"
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USER root
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RUN apt-get install zlib1g-dev make gcc git -y
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RUN apt-get update -y && apt-get install zlib1g-dev make gcc git -y
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RUN mkdir -p /usr/local/
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WORKDIR /usr/local/
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RUN git clone https://bitbucket.org/AstexUK/pli.git

‎Dockerfile-rdkit-centos‎

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FROM informaticsmatters/rdkit-python-centos:latest
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LABEL maintainer="Tim Dudgeon<[email protected]>"
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USER root
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# install required packages
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RUN yum -y update && yum -y install zip unzip python-devel python2-pip python-setuptools python2-matplotlib
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# Copy the pipeline implementation into the image
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COPY src/python /opt/python
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RUN pip install -e /opt/python
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# And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
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# NOTE: matplotlib is missing
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RUN pip install molvs standardiser im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*

‎Dockerfile-smog‎

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@@ -3,7 +3,10 @@ LABEL maintainer="Tim Dudgeon<[email protected]>"
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USER root
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RUN apt-get install libopenbabel-dev g++ -y
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RUN echo 'deb http://deb.debian.org/debian experimental main' >> /etc/apt/sources.list
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RUN apt-get update -y && apt-get install -t experimental libopenbabel-dev g++ -y
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WORKDIR /usr/local
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RUN wget https://sourceforge.net/projects/opengrowth/files/SMoG2016.tar.gz/download -O smog.tar.gz &&\

‎build.gradle‎

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@@ -84,18 +84,28 @@ task buildSmogImage(type: DockerBuildImage) {
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tag = "informaticsmatters/smog:latest"
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}
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task buildSdPosterDockerImage(type: DockerBuildImage) {
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task buildSdPosterImage(type: DockerBuildImage) {
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description 'Builds the pipelines SD-poster Docker image'
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dockerFile = file('Dockerfile-sdposter')
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inputDir = file('.')
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tag = "squonk/rdkit-${pipeline}-sdposter:latest"
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}
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task buildObabelImage(type: DockerBuildImage) {
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// TODO - remove this once the pipelines-obabel project becomes active
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description 'Builds the obabel Docker image'
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dockerFile = file('Dockerfile-obabel')
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inputDir = file('.')
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tag = "informaticsmatters/pipelines-obabel:latest"
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}
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task buildDockerImages() {
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dependsOn buildPliImage // that one depends on buildPipelinesImage
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dependsOn buildSmogImage // and so does this one
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dependsOn buildSdPosterDockerImage
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dependsOn buildSdPosterImage
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dependsOn buildObabelImage
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group 'Docker'
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description 'Builds all the project Docker images'

‎src/nextflow/docking/plip.nsd.nf‎

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@@ -12,6 +12,7 @@ protein = file(params.protein)
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process splitter {
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container 'informaticsmatters/pli:latest'
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beforeScript 'chmod g+w .'
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input:
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*/
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process pli_scoring {
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container 'informaticsmatters/pli:latest'
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beforeScript 'chmod g+w .'
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input:
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process joiner {
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container 'informaticsmatters/pli:latest'
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beforeScript 'chmod g+w .'
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publishDir baseDir, mode: 'link'
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‎src/nextflow/docking/smog.nsd.nf‎

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process splitter {
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container 'informaticsmatters/smog:latest'
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beforeScript 'chmod g+w .'
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input:
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*/
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process smog_scoring {
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container 'informaticsmatters/smog:latest'
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beforeScript 'chmod g+w .'
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input:
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process joiner {
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container 'informaticsmatters/smog:latest'
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beforeScript 'chmod g+w .'
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publishDir baseDir, mode: 'link'
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‎src/python/pipelines/docking/obabel_prepare_pdb.dsd.json‎

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{ "@class":"org.squonk.core.DockerServiceDescriptor",
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{ "@class": "org.squonk.core.DockerServiceDescriptor",
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"serviceConfig": {
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"id": "pipelines.xchem.obabel.prepare.pdb.v1",
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"name": "OBabelPreparePDB",
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"description": "Prepare PDB file uisng Open Babel",
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"tags": [ "rdkit", "xchem", "docker", "openbabel", "obabel", "prepare", "pdb", "convert"],
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"resourceUrl": null,
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"icon": "icons/transform_molecule.png",
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"id": "pipelines.xchem.obabel.prepare.pdb.v1",
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"name": "OBabelPreparePDB",
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"description": "Prepare PDB file using Open Babel",
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"tags": [ "rdkit", "xchem", "docker", "openbabel", "obabel", "prepare", "pdb", "convert", "protein"],
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"resourceUrl": null,
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"icon": "icons/transform_molecule.png",
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"inputDescriptors": [
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{
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"primaryType": "org.squonk.types.PDBFile",
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"mediaType": "chemical/x-pdb",
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"name": "pdb"
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}
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],
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"outputDescriptors": [
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{
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"primaryType": "org.squonk.types.Mol2File",
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"mediaType": "chemical/x-mol2",
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"name": "mol2"
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}
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],
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"inputDescriptors": [
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{
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"primaryType": "org.squonk.types.PDBFile",
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"mediaType": "chemical/x-pdb",
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"name": "pdb"
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}
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],
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"outputDescriptors": [
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{
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"primaryType": "org.squonk.types.Mol2File",
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"mediaType": "chemical/x-mol2",
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"name": "mol2"
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}
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],
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"optionDescriptors": [
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{
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"modes": [
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"User"
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],
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"editable": true,
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"@class": "org.squonk.options.OptionDescriptor",
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"typeDescriptor": {
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"type": "java.lang.Float",
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"@class": "org.squonk.options.SimpleTypeDescriptor"
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},
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"key": "arg.protonate",
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"label": "Protonate at pH",
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"description": "Optionally protonate side chains at this pH",
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"visible": true,
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"minValues": 0,
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"maxValues": 1
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}
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],
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"executorClassName": "org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep"
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"optionDescriptors": [
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{
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"modes": [
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"User"
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],
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"editable": true,
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"@class": "org.squonk.options.OptionDescriptor",
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"typeDescriptor": {
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"type": "java.lang.Float",
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"@class": "org.squonk.options.SimpleTypeDescriptor"
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},
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"key": "arg.protonate",
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"label": "Protonate at pH",
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"description": "Optionally protonate side chains at this pH",
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"visible": true,
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"minValues": 0,
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"maxValues": 1
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}
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],
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"executorClassName": "org.squonk.execution.steps.impl.ThinDatasetDockerExecutorStep"
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},
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"inputRoutes": [ {"route": "FILE"} ],
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"outputRoutes": [ {"route": "FILE"} ],
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"imageName": "informaticsmatters/rdkit_pipelines",
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"command": "python -m pipelines.docking.obabel_prepare_pdb -i ${PIN}pdb.pdb.gz -o ${POUT}mol2 -mol2${protonate ? ' -prot ' + protonate : ''} --meta"
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"imageName": "informaticsmatters/pipelines-obabel:latest",
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"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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}

‎src/python/pipelines/docking/obabel_prepare_pdb.py‎

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#!/usr/bin/env python
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# Copyright 2017 Informatics Matters Ltd.
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# Copyright 2018 Informatics Matters Ltd.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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def execute(input, output, extension, format, ph, noGzip):
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# TODO - convert this to use the Python API rather than an external process
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filename = output + "." + extension
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base_args = ["obabel", "-ipdb", input, format, "-O", filename]
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if ph:
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base_args.append("-p")
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base_args.append("ph")
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base_args.append(str(ph))
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utils.log("Command: " + " ".join(base_args))
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subprocess.check_call(base_args, stdout=sys.stderr, stderr=sys.stderr)
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# NOTE the -z argument does not seem to work correctly with obabel (truncted files generated) so we
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# NOTE the -z argument does not seem to work correctly with obabel (truncated files generated) so we
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# fall back to good old gzip to handle the compression once the uncompressed file is created
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if not noGzip:
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subprocess.check_call(['gzip', filename], stdout=sys.stderr, stderr=sys.stderr)

‎src/python/pipelines/rdkit/o3dAlign.dsd.json‎

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},
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"@class": "org.squonk.options.OptionDescriptor"
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},
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{
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"modes": [
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"User"
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],
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"editable": true,
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"visible": true,
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"description": "Use Crippen (logP) contributions",
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"label": "Use Crippen (logP) contributions",
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"key": "arg.crippen",
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"minValues": 1,
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"maxValues": 1,
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"typeDescriptor": {
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"type": "java.lang.Boolean",
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"@class": "org.squonk.options.SimpleTypeDescriptor"
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},
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"@class": "org.squonk.options.OptionDescriptor"
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},
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{
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"@class": "org.squonk.options.OptionDescriptor",
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"modes": [
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}
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],
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"imageName": "informaticsmatters/rdkit_pipelines",
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"command": "python -m pipelines.rdkit.o3dAlign queryMol.data.gz -i ${PIN}input.data.gz -o ${POUT}output -of json${binding.variables.containsKey('qmolidx') ? ' --qmolidx ' + binding.variables.get('qmolidx') : ''}${binding.variables.containsKey('num') ? ' --num ' + binding.variables.get('num') : ''}${binding.variables.containsKey('threshold') ? ' --threshold ' + binding.variables.get('threshold') : ''} --meta"
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"command": "python -m pipelines.rdkit.o3dAlign queryMol.data.gz -i ${PIN}input.data.gz -o ${POUT}output -of json${binding.variables.containsKey('qmolidx') ? ' --qmolidx ' + binding.variables.get('qmolidx') : ''}${binding.variables.containsKey('num') ? ' --num ' + binding.variables.get('num') : ''}${binding.variables.containsKey('threshold') ? ' --threshold ' + binding.variables.get('threshold') : ''}${crippen ? ' --crippen' : ''} --meta"
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}

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