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tdudgeontdudgeon
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updates to nextflow workflows
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‎Dockerfile-smog‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,10 @@ RUN wget https://sourceforge.net/projects/opengrowth/files/SMoG2016.tar.gz/downl
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g++ -O3 -Wall -std=c++11 -Wno-uninitialized -I/usr/include/openbabel-2.0 -lm -c /usr/local/SMoG2016/SMoG2016.cpp -o /usr/local/SMoG2016/SMoG2016.o &&\
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g++ /usr/local/SMoG2016/SMoG2016.o -o /usr/local/SMoG2016/SMoG2016.exe -rdynamic /usr/lib/libopenbabel.so -Wl,-rpath,/usr/lib
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RUN useradd -u 1001 -g 0 -m smog
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USER 1001
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ARG USERID=1001
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RUN useradd -u $USERID -g 0 -m smog
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USER $USERID
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WORKDIR /home/smog

‎src/nextflow/README.md‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -138,7 +138,7 @@ When Squonk executes your pipeline it does the following:
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* copies your `*.nsd.conf` file to the file `nextflow.conf` in this directory
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* creates a simple `execute` bash script that will executes the pipeline with the options provided by the user and as specified
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in the service descriptor
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* Runs a container using the `informaticsmatters/nextflow` Docker image, mounting in the working directory and running the
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* Runs a container using the `informaticsmatters/nextflow-docker` Docker image, mounting in the working directory and running the
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`execute` script
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* After execution grabs the expected output files and as the results of execution
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* deletes the temporary working directory (unless working in debug mode)

‎src/nextflow/docking/plip.nsd.nf‎

Lines changed: 5 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -48,38 +48,23 @@ process pli_scoring {
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process joiner {
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beforeScript 'chmod g+w .'
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publishDir baseDir, pattern: "{output.data.gz,output.metadata}"
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input:
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file parts from scored_parts.collect()
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output:
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file 'output_metrics.txt' into joiner_metrics
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file 'output.data.gz'
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"""
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cat scored_part*.sdf | python -m pipelines_utils_rdkit.filter -if sdf -of json -o output --meta --thin
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"""
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}
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process metrics_meta {
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beforeScript 'chmod g+w .'
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publishDir baseDir
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publishDir baseDir, mode: 'link'
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input:
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file parts from scored_parts.collect()
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file 'splitter_metrics.txt' from splitter_metrics
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file 'joiner_metrics.txt' from joiner_metrics
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output:
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file 'output.data.gz'
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file 'output_metrics.txt'
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file 'output.metadata'
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"""
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cat scored_part*.sdf | python -m pipelines_utils_rdkit.filter -if sdf -of json -o output --meta --thin
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mv output_metrics.txt joiner_metrics.txt
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grep '__InputCount__' splitter_metrics.txt | sed s/__InputCount__/PLI/ > output_metrics.txt
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grep '__InputCount__' splitter_metrics.txt >> output_metrics.txt
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grep '__OutputCount__' joiner_metrics.txt >> output_metrics.txt
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echo '{"type":"org.squonk.types.BasicObject","valueClassMappings":{"pliff_cscore":"java.lang.Float","pliff_iscore":"java.lang.Float","pliff_tscore":"java.lang.Float","pliff_gscore":"java.lang.Float","pliff_score":"java.lang.Float","pliff_nb_score":"java.lang.Float"}}' > output.metadata
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"""
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}
85-

‎src/nextflow/docking/rdock.nsd.nf‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -27,7 +27,7 @@ receptorzip = file(params.receptor)
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process unzip_config {
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beforeScript 'chmod g+w .'
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container 'informaticsmatters/rdkit_pipelines'
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container 'informaticsmatters/rdkit_pipelines:latest'
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input:
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file receptorzip
@@ -48,7 +48,7 @@ process unzip_config {
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process splitter {
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beforeScript 'chmod g+w .'
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container 'informaticsmatters/rdkit_pipelines'
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container 'informaticsmatters/rdkit_pipelines:latest'
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input:
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file ligands
@@ -89,7 +89,7 @@ process rdock {
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*/
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process results {
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container 'informaticsmatters/rdock'
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container 'informaticsmatters/rdock-mini'
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// change permissions - see above
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beforeScript 'chmod g+w .'
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@@ -108,9 +108,9 @@ process results {
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process metrics {
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beforeScript 'chmod g+w .'
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container 'informaticsmatters/rdkit_pipelines'
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container 'informaticsmatters/rdkit_pipelines:latest'
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publishDir baseDir
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publishDir baseDir, mode: 'link'
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input:
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file 'results.sdf' from results

‎src/nextflow/docking/smog.nsd.nf‎

Lines changed: 9 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -48,39 +48,23 @@ process smog_scoring {
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process joiner {
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beforeScript 'chmod g+w .'
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publishDir baseDir, pattern: "{output.data.gz,output.metadata}"
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publishDir baseDir, mode: 'link'
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input:
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file parts from scored_parts.collect()
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file parts from scored_parts.collect()
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file 'splitter_metrics.txt' from splitter_metrics
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output:
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file 'output_metrics.txt' into joiner_metrics
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file 'output_metrics.txt'
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file 'output.data.gz'
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file 'output.metadata'
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"""
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cat scored_part*.sdf | python -m pipelines_utils_rdkit.filter -if sdf -of json -o output --meta --thin
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"""
63-
}
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process metrics_meta {
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beforeScript 'chmod g+w .'
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publishDir baseDir
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input:
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file 'splitter_metrics.txt' from splitter_metrics
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file 'joiner_metrics.txt' from joiner_metrics
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output:
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file 'output_metrics.txt'
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file 'output.metadata'
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"""
80-
grep '__InputCount__' splitter_metrics.txt | sed s/__InputCount__/PLI/ > output_metrics.txt
64+
mv output_metrics.txt joiner_metrics.txt
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grep '__InputCount__' splitter_metrics.txt | sed s/__InputCount__/SMOG/ > output_metrics.txt
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grep '__InputCount__' splitter_metrics.txt >> output_metrics.txt
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grep '__OutputCount__' joiner_metrics.txt >> output_metrics.txt
83-
echo '{"type":"org.squonk.types.BasicObject","valueClassMappings":{"pliff_cscore":"java.lang.Float","pliff_iscore":"java.lang.Float","pliff_tscore":"java.lang.Float","pliff_gscore":"java.lang.Float","pliff_score":"java.lang.Float","pliff_nb_score":"java.lang.Float"}}' > output.metadata
84-
"""
68+
echo '{"type":"org.squonk.types.BasicObject","valueClassMappings":{"SMoG2016_SCORE":"java.lang.Float","EmbedRMS":"java.lang.Float"}}' > output.metadata
69+
"""
8570
}
86-

‎src/python/pipelines/dmpk/pk_tmax_cmax_sim.dsd.json‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -10,6 +10,7 @@
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"cmax",
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"tmax",
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"simulation",
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"prediction",
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"docker"
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],
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"resourceUrl": null,

‎test-nextflow.sh‎

Lines changed: 19 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -24,38 +24,35 @@ nextflow run src/nextflow/docking/rdock.nf -c src/nextflow/docking/rdock.config
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echo 'Running SMoG2016 in squonk mode'
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sudo rm -rf tmp/*
27-
cp src/nextflow/docking/smog.nsd.nf tmp/nextflow.nf
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cp src/nextflow/docking/smog.nsd.config tmp/nextflow.config
29-
gzip -c data/smog/DCP2_1.pdb > tmp/protein.pdb.gz
30-
cp data/smog/confs.data.gz tmp/ligands.data.gz
31-
cp data/smog/confs.metadata tmp/ligands.metadata
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cd tmp
33-
docker run -it --rm -v $PWD:$PWD:z -w $PWD -v /var/run/docker.sock:/var/run/docker.sock informaticsmatters/nextflow sh -c 'nextflow run nextflow.nf -c nextflow.config --score 100.0 -with-docker'
28+
ln ../src/nextflow/docking/smog.nsd.nf nextflow.nf
29+
ln ../src/nextflow/docking/smog.nsd.config nextflow.config
30+
gzip -c ../data/smog/DCP2_1.pdb > protein.pdb.gz
31+
ln ../data/smog/confs.data.gz ligands.data.gz
32+
ln ../data/smog/confs.metadata ligands.metadata
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docker run -it --rm -v $PWD:$PWD:z -w $PWD -v /var/run/docker.sock:/var/run/docker.sock informaticsmatters/nextflow-docker:0.30.2 sh -c 'nextflow run nextflow.nf -c nextflow.config --score 100.0 -with-docker'
3434
cd ..
35-
sudo rm -rf tmp/*
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echo 'Running PLI in squonk mode'
3937
sudo rm -rf tmp/*
40-
cp src/nextflow/docking/plip.nsd.nf tmp/nextflow.nf
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cp src/nextflow/docking/plip.nsd.config tmp/nextflow.config
42-
gzip -c data/smog/DCP2_1.pdb > tmp/protein.pdb.gz
43-
cp data/smog/confs.data.gz tmp/ligands.data.gz
44-
cp data/smog/confs.metadata tmp/ligands.metadata
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cd tmp
46-
docker run -it --rm -v $PWD:$PWD:z -w $PWD -v /var/run/docker.sock:/var/run/docker.sock informaticsmatters/nextflow sh -c 'nextflow run nextflow.nf -c nextflow.config --score 100.0 -with-docker'
39+
ln ../src/nextflow/docking/plip.nsd.nf nextflow.nf
40+
ln ../src/nextflow/docking/plip.nsd.config nextflow.config
41+
gzip -c ../data/smog/DCP2_1.pdb > protein.pdb.gz
42+
ln ../data/smog/confs.data.gz ligands.data.gz
43+
ln ../data/smog/confs.metadata ligands.metadata
44+
docker run -it --rm -v $PWD:$PWD:z -w $PWD -v /var/run/docker.sock:/var/run/docker.sock informaticsmatters/nextflow-docker:0.30.2 sh -c 'nextflow run nextflow.nf -c nextflow.config --score 100.0 -with-docker'
4745
cd ..
48-
sudo rm -rf tmp/*
49-
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5147
echo 'Running rDock in squonk mode'
5248
sudo rm -rf tmp/*
53-
cp src/nextflow/docking/rdock.nsd.nf tmp/nextflow.nf
54-
cp src/nextflow/docking/rdock.nsd.config tmp/nextflow.config
55-
cp data/hivpr.config.zip tmp/config.zip
56-
cp data/dhfr_3d.data.gz tmp/ligands.data.gz
57-
cp data/dhfr_3d.metadata tmp/ligands.metadata
5849
cd tmp
59-
docker run -it --rm -v $PWD:$PWD:z -w $PWD -v /var/run/docker.sock:/var/run/docker.sock informaticsmatters/nextflow sh -c 'nextflow run nextflow.nf -c nextflow.config --num_dockings 1 --limit 40 --chunk 5 -with-docker'
50+
ln ../src/nextflow/docking/rdock.nsd.nf nextflow.nf
51+
ln ../src/nextflow/docking/rdock.nsd.config nextflow.config
52+
ln ../data/hivpr.config.zip config.zip
53+
ln ../data/dhfr_3d.data.gz ligands.data.gz
54+
ln ../data/dhfr_3d.metadata ligands.metadata
55+
docker run -it --rm -v $PWD:$PWD:z -w $PWD -v /var/run/docker.sock:/var/run/docker.sock informaticsmatters/nextflow-docker:0.30.2 sh -c 'nextflow run nextflow.nf -c nextflow.config --num_dockings 1 --limit 40 --chunk 5 -with-docker'
6056
cd ..
57+
6158
sudo rm -rf tmp/*

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