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Makefile
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include wdl/.env
export
run_on_cori_jaws:
#jaws list-sites
#[
# {
# "max_ram_gb": "2048",
# "site_id": "CORI"
# },
# {
# "max_ram_gb": "250",
# "site_id": "JGI"
# },
# {
# "max_ram_gb": "376",
# "site_id": "TAHOMA"
# }
#]
jaws submit wdl/test.wdl storage/input_local.json TAHOMA
run_on_cori_local:
java -Dconfig.file=cromwell_shifter.conf \
-Dbackend.providers.Local.config.dockerRoot=$(pwd)/cromwell-executions \
-jar /global/cfs/projectdirs/jaws/cromwell/cromwell.jar run wdl/test.wdl -i storage/input_local.json
run_test:
java -jar wdl/cromwell/cromwell-66.jar run wdl/workflow/docker/main.wdl -i storage/input_local.json
validate_wdl:
java -jar wdl/cromwell/womtool-66.jar validate wdl/workflow/docker/main.wdl -i storage/input_local.json
spit_dag:
java -jar wdl/cromwell/womtool-66.jar womgraph wdl/workflow/docker/main.wdl
run_wdl:
java -jar wdl/cromwell/cromwell-66.jar run wdl/workflow/docker/main.wdl -i storage/input_local.json
run_on_prismweb_with_conf:
# -o options.json
~/cromwell/jdk-12.0.1/bin/java -Dconfig.file=cromwell_docker.conf \
-jar ~/cromwell/cromwell-66.jar run wdl/workflow/docker/main.wdl -i storage/input.json
run_on_prismweb_server_mode:
# doesn't work!
# start the server with call-caching turned on
~/cromwell/jdk-12.0.1/bin/java -Dconfig.file=cromwell_docker.conf -jar ~/cromwell/cromwell-66.jar server &
# submit the WDL to Cromwell. Call-caching is turned on via config file.
curl -X POST --header "Accept: application/json" --header "Accept: application/x-zip" -v "localhost:50011/api/workflows/v1" -F workflowSource=@wdl/workflow/docker/main.wdl -F workflowInputs=@storage/input.json -F workflowDependencies=@wdl/workflow/docker/archive.zip #-F [email protected]
# submit with call-caching turned off
curl -X POST --header "Accept: application/json" --header "Accept: application/x-zip" -v "localhost:50011/api/workflows/v1" -F workflowSource=@wdl/workflow/docker/main.wdl -F workflowInputs=@storage/input.json -F workflowDependencies=@wdl/workflow/docker/archive.zip -F [email protected]
# see the metadata to check if call caching was on or off
# use fq to parse the json
curl --header "Accept: application/json" -v "localhost:8088/api/workflows/v1/${wid}/metadata" | jq '.calls."test.hello"[0].callCaching'
run_on_local_server_mode:
# start the server with call-caching turned on
java -Dconfig.file=cromwell_docker.conf -jar ~/cromwell/cromwell-66.jar server &
# submit the WDL to Cromwell. Call-caching is turned on via config file.
curl -X POST --header "Accept: application/json" -v "localhost:50011/api/workflows/v1" -F workflowSource=@wdl/workflow/docker/main.wdl -F workflowInputs=@storage/input.json #-F [email protected]
# submit with call-caching turned off
curl -X POST --header "Accept: application/json" -v "localhost:50011/api/workflows/v1" -F [email protected] -F [email protected] -F [email protected]
# see the metadata to check if call caching was on or off
# use fq to parse the json
curl --header "Accept: application/json" -v "localhost:8088/api/workflows/v1/${wid}/metadata" | jq '.calls."test.hello"[0].callCaching'
run_on_prismweb:
~/cromwell/jdk-12.0.1/bin/java -jar ~/cromwell/cromwell-66.jar run wdl/workflow/docker/main.wdl -i storage/input.json
run_wdl_on_cori:
java -jar /global/cfs/projectdirs/jaws/cromwell/cromwell-66.jar run wdl/workflow/shifter_at_cori/run_job_analysis.wdl -i /global/homes/a/anubhav/storage/input.json
prepare-your-input:
wdl/scripts/prepare_input.sh
all-build:
@docker-compose -f wdl/docker-compose.yml build
all-build-up:
@docker-compose -f wdl/docker-compose.yml up --detach --build
just-pull-all:
wdl/scripts/pull_spin_containers.sh
push-all-images:
#@docker image tag wdl_msconvert:latest microbiomedata/metapro-msconvert:latest
@docker push microbiomedata/metapro-msconvert:latest
#@docker image tag wdl_masic_console:latest microbiomedata/metapro-masic:$(MASIC_VERSION)
@docker push microbiomedata/metapro-masic:$(MASIC_VERSION)
#@docker image tag wdl_mzidtotsvconverter:latest microbiomedata/metapro-mzidtotsvconverter:$(MZID2TSV_VERSION)
@docker push microbiomedata/metapro-mzidtotsvconverter:$(MZID2TSV_VERSION)
#@docker image tag wdl_msgfplus:latest microbiomedata/metapro-msgfplus:$(MSGFPLUS_VERSION)
@docker push microbiomedata/metapro-msgfplus:$(MSGFPLUS_VERSION)
#@docker image tag wdl_fastafilesplitter:latest microbiomedata/metapro-fastafilesplitter:$(Fasta_File_Splitter_VERSION)
@docker push microbiomedata/metapro-fastafilesplitter:$(Fasta_File_Splitter_VERSION)
#@docker image tag wdl_validatefastafile:latest microbiomedata/metapro-validatefastafile:$(VALIDATE_FASTA_FILE_VERSION)
@docker push microbiomedata/metapro-validatefastafile:$(VALIDATE_FASTA_FILE_VERSION)
#@docker image tag wdl_masicresultsmerge:latest microbiomedata/metapro-masicresultsmerge:$(MASICResultsMerge_VERSION)
@docker push microbiomedata/metapro-masicresultsmerge:$(MASICResultsMerge_VERSION)
#@docker image tag wdl_proteindigestionsimulator:latest microbiomedata/metapro-proteindigestionsimulator:$(PDS_VERSION)
@docker push microbiomedata/metapro-proteindigestionsimulator:$(PDS_VERSION)
#@docker image tag wdl_mzidmerger:latest microbiomedata/metapro-mzidmerger:$(MzidMerger_VERSION)
@docker push microbiomedata/metapro-mzidmerger:$(MzidMerger_VERSION)
#@docker image tag wdl_peptidehitresultsprocrunner:latest microbiomedata/metapro-peptidehitresultsprocrunner:$(PHRP_VERSION)
@docker push microbiomedata/metapro-peptidehitresultsprocrunner:$(PHR #@docker image tag wdl_msconvert:latest microbiomedata/metapro-msconvert:latest
@docker push microbiomedata/metapro-msconvert:latest
#@docker image tag wdl_masic_console:latest microbiomedata/metapro-masic:$(MASIC_VERSION)
@docker push microbiomedata/metapro-masic:$(MASIC_VERSION)
#@docker image tag wdl_mzidtotsvconverter:latest microbiomedata/metapro-mzidtotsvconverter:$(MZID2TSV_VERSION)
@docker push microbiomedata/metapro-mzidtotsvconverter:$(MZID2TSV_VERSION)
#@docker image tag wdl_msgfplus:latest microbiomedata/metapro-msgfplus:$(MSGFPLUS_VERSION)
@docker push microbiomedata/metapro-msgfplus:$(MSGFPLUS_VERSION)
#@docker image tag wdl_fastafilesplitter:latest microbiomedata/metapro-fastafilesplitter:$(Fasta_File_Splitter_VERSION)
@docker push microbiomedata/metapro-fastafilesplitter:$(Fasta_File_Splitter_VERSION)
#@docker image tag wdl_validatefastafile:latest microbiomedata/metapro-validatefastafile:$(VALIDATE_FASTA_FILE_VERSION)
@docker push microbiomedata/metapro-validatefastafile:$(VALIDATE_FASTA_FILE_VERSION)
#@docker image tag wdl_masicresultsmerge:latest microbiomedata/metapro-masicresultsmerge:$(MASICResultsMerge_VERSION)
@docker push microbiomedata/metapro-masicresultsmerge:$(MASICResultsMerge_VERSION)
#@docker image tag wdl_proteindigestionsimulator:latest microbiomedata/metapro-proteindigestionsimulator:$(PDS_VERSION)
@docker push microbiomedata/metapro-proteindigestionsimulator:$(PDS_VERSION)
#@docker image tag wdl_mzidmerger:latest microbiomedata/metapro-mzidmerger:$(MzidMerger_VERSION)
@docker push microbiomedata/metapro-mzidmerger:$(MzidMerger_VERSION)
#@docker image tag wdl_peptidehitresultsprocrunner:latest microbiomedata/metapro-peptidehitresultsprocrunner:$(PHRP_VERSION)
@docker push microbiomedata/metapro-peptidehitresultsprocrunner:$(PHRP_VERSION)
#@docker image tag wdl_metadatacollection:latest microbiomedata/metapro-metadatacollection:2.0.1
@docker push microbiomedata/metapro-metadatacollection:2.0.1
#@docker image tag wdl_post-processing:latest microbiomedata/metapro-post-processing:2.0.1
@docker push microbiomedata/metapro-post-processing:2.0.1
#-------------
#@docker image tag wdl_metadatacollection:latest microbiomedata/metapro-metadatacollection:2.0.1
@docker push microbiomedata/metapro-metadatacollection:2.0.1
#@docker image tag wdl_post-processing:latest microbiomedata/metapro-post-processing:2.0.1
@docker push microbiomedata/metapro-post-processing:2.0.1
#-------------
build_unified:
docker-compose up --build
build_unified_fast:
docker-compose build --parallel
docker-compose up
run_workflow:
bash run_task.sh
#-------------