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Makefile
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Makefile
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setup:
pip install -r requirements.txt
npm install
clean-packages:
pip unistall -r requirements.txt
pretty-json:
python -m json.tool ./src/data_dump/output.json
#cat src/data_dump/SGD_1.0.1.4_phenotype.json | python -m json.tool > src/data_dump/SGD_1.0.1.4_phenotype-pretty.json
disease-json:
npm run disease-json
build-disease:
npm run disease-json
build-panther:
npm run panther-json
run-expression:
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_expression.py
run-phenotype:
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_phenotype.py
run-bgi:
# npm run panther-json
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_bgi.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_nongene.py
run-disease:
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_disease_association.py
run-htpdatasamples:
# . env.sh && python ./run_datasets.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_htp_sample_metadata.py
run-htpdatasets:
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_htp_datasets.py
run-agm:
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_agm.py
run-allele:
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_alleles.py
run-refs:
. env.sh && python ./run_references.py
run-resources:
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_resources.py
build-all:
source /data/envs/sgd3/bin/activate && . env.sh && pip install -r requirements.txt
run-all:
#npm run disease-json
#npm run panther-json
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_agm.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_htp_datasets.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_disease_association.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_expression.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_phenotype.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_htp_sample_metadata.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_bgi.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_references.py
source /data/envs/sgd3/bin/activate && . env.sh && python ./run_resources.py
#upload-all:
# run script
# uploads all files to AWS for Alliance to ferret out