The workflow was built from the manual construction notes of FORUM
- docker
- conda
- bc
``nextflow.config
TESTDEV
to false for a release production- entrez
. /local/env/envconda.sh
conda create -p ~/env-forum
conda create -p ~/env-forum openjdk
cd forum-diseases-chem-nextflow
# -p bigmem 3 To RAM
srun --cpus-per-task=8 --mem=50G --pty bash
. /local/env/envconda.sh
conda activate ~/env-forum
alias ll='ls -ail'
curl -s https://get.nextflow.io | bash
export TESTDEV="true"
./nextflow run forum.nf -resume
#!/bin/bash
. /local/env/envnextflow-22.10.4.sh
export NXF_EXECUTOR=slurm
export NXF_OPTS="-Xms500M -Xmx2G"
nextflow run forum.nf --rdfoutdir /scratch/$USER/forum-data
sbatch script.sh
./nextflow run forum-vocabularies.nf -entry forum_vocabularies -bg
./nextflow run forum-MeSH.nf -entry forum_mesh -bg
./nextflow run forum-MetaNetX.nf -entry forum_MetaNetX -bg
./nextflow run forum-PubChem-min.nf -entry forum_PubChemMin -bg
./nextflow run forum-PMID-CID.nf -entry forum_PMID_CID -bg
./nextflow run forum-SBML_Human.nf -entry forum_SBML_Human -bg
./nextflow run forum-chemont.nf -entry forum_Chemont -bg
- 3d 17h 41m 56s nextflow run forum-PMID-CID.nf -entry forum_PMID_CID
- 14d 5h 58m 56s nextflow run forum-chemont.nf -entry forum_Chemont
- 2d 17h 14m 4s nextflow run forum-PMID-CID.nf -entry forum_PMID_CID
- tweak forum_Chemont
# if the vocabularies workflow is not built.
./nextflow run forum-vocabularies.nf -entry forum_vocabularies
# and then...
./nextflow run forum-computation-test-virtuoso.nf -entry test_upload_vocab -c nextflow-test.config
docker logs forum_virtuoso_9980 -f
docker rm -f forum_virtuoso_9980
./nextflow run forum-computation-cid-mesh.nf -entry computation_cid_mesh
./nextflow run forum-computation-chebi-mesh.nf -entry computation_chebi_mesh