Containers for third-party tools used by ProHits-viz
docker build -t nestedcluster -f nestedcluster/Dockerfile .
docker run -v $(pwd):/files/ nestedcluster -m matrix.txt -p parameters.txt
docker build -t rsvg -f rsvg/Dockerfile .
docker run -v $(pwd):/files/ rsvg --format=png --output=./image.png --background-color=white --unlimited ./image.svg
- Generate
requirements.txtfile.
pipreqs utilities/python
- Build
docker build -t pvutilitiespython -f utilities/python/Dockerfile .
- crispr convert:
docker run -v $(pwd):/files/ --user $(id -u):$(id -g) pvutilitiespython /app/crispr_convert/main.py -f folder -t ranks - saint summary statistics:
docker run -v $(pwd):/files/ --user $(id -u):$(id -g) pvutilitiespython /app/saint_stats/main.py -f 0.01 -s saint.txt - saint functional enrichment analysis:
docker run -v $(pwd):/files/ --user $(id -u):$(id -g) pvutilitiespython /app/saint_fea/main.py -f 0.01 -s saint.txt - saint domain enrichment analysis:
docker run -v $(pwd):/files/ --user $(id -u):$(id -g) pvutilitiespython /app/saint_domain_enrich/main.py -b all -d domains.json -f 0.01 -g gene-db.json -i refseqp -s saint.txt - saint specificity:
docker run -v $(pwd):/files/ --user $(id -u):$(id -g) pvutilitiespython /app/saint_specificity/main.py -m fe -s saint.txt - text biogrid network:
docker run -v $(pwd):/files/ --user $(id -u):$(id -g) pvutilitiespython /app/text_biogrid_network/main.py -k $access_key -f file.txt -g gene-db.json - text symbol fix:
docker run -v $(pwd):/files/ --user $(id -u):$(id -g) pvutilitiespython /app/text_symbol_fix/main.py -f file.txt -c "column1|column2"