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Makefile
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run-all-experiments-1:
# NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB11004 -with-docker
# NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB11013 -with-docker
# NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB30003 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB40010 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB40014 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0011 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0030 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0065 -with-docker
run-all-experiments-2:
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0117 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0142 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0192 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS12014 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS20002 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS20007 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS20009 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30001 -with-docker
run-all-experiments-3:
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30003 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30015 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30016 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30017 -with-docker
run-all-experiments-4:
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS50005 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BOX122 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BOX132 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BOX212 -with-docker
run-all:
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB11004 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB11013 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB30003 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB40010 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB40014 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0011 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0030 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0065 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0117 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0142 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBA0192 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS12014 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS20002 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS20007 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS20009 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30001 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30003 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30015 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30016 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS30017 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BBS50005 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BOX122 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BOX132 -with-docker
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BOX212 -with-docker
test-run:
NFX_OPTS="-Xms=512m -Xmx=4g" nextflow run main.nf --input_dir ./datasets/BB11013 -with-docker -with-conda -with-report reports/BB11013.html -with-timeline timeline/BB11013.html
run-experiment:
# 1. Coincidences
echo "Coincidences Strategy" > $(INPUT_FASTA_FILE).msasa.timing.log
date +"%Y-%m-%d %H:%M:%S" >> $(INPUT_FASTA_FILE).msasa.timing.log
/usr/bin/time -p python msasa_cli.py $(INPUT_FASTA_FILE) $(INPUT_FASTA_FILE).msasa.1.coincidences.aln \
--log_file $(INPUT_FASTA_FILE).msasa.1.coincidences.log \
--extend \
--temp 10 \
--cooling_rate 0.99 \
--min_temp 0.001 \
--max_no_changes 500 \
--quality_function coincidences 2>> $(INPUT_FASTA_FILE).msasa.timing.log
# 2. Identity
echo "Identity Strategy" >> $(INPUT_FASTA_FILE).msasa.timing.log
date +"%Y-%m-%d %H:%M:%S" >> $(INPUT_FASTA_FILE).msasa.timing.log
/usr/bin/time -p python msasa_cli.py $(INPUT_FASTA_FILE) $(INPUT_FASTA_FILE).msasa.2.identity.aln \
--log_file $(INPUT_FASTA_FILE).msasa.2.identity.log \
--extend \
--temp 5 \
--cooling_rate 0.99 \
--min_temp 0.0001 \
--max_no_changes 500 \
--quality_function identity 2>> $(INPUT_FASTA_FILE).msasa.timing.log
# 3. Similarity
echo "Similarity Strategy (Blosum62)" >> $(INPUT_FASTA_FILE).msasa.timing.log
date +"%Y-%m-%d %H:%M:%S" >> $(INPUT_FASTA_FILE).msasa.timing.log
/usr/bin/time -p python msasa_cli.py $(INPUT_FASTA_FILE) $(INPUT_FASTA_FILE).msasa.3.similarity.aln \
--log_file $(INPUT_FASTA_FILE).msasa.3.similarity.log \
--extend \
--temp 5 \
--cooling_rate 0.99 \
--min_temp 0.01 \
--max_no_changes 500 \
--quality_function similarity 2>> $(INPUT_FASTA_FILE).msasa.timing.log
# 4. Global strategy
echo "Global Strategy" >> $(INPUT_FASTA_FILE).msasa.timing.log
date +"%Y-%m-%d %H:%M:%S" >> $(INPUT_FASTA_FILE).msasa.timing.log
/usr/bin/time -p python msasa_cli.py $(INPUT_FASTA_FILE) $(INPUT_FASTA_FILE).msasa.4.global.aln \
--log_file $(INPUT_FASTA_FILE).msasa.4.global.log \
--extend \
--temp 10 \
--cooling_rate 0.99 \
--min_temp 0.01 \
--max_no_changes 500 \
--quality_function global 2>> $(INPUT_FASTA_FILE).msasa.timing.log
# 5. Local Strategy
echo "Local Strategy" >> $(INPUT_FASTA_FILE).msasa.timing.log
date +"%Y-%m-%d %H:%M:%S" >> $(INPUT_FASTA_FILE).msasa.timing.log
/usr/bin/time -p python msasa_cli.py $(INPUT_FASTA_FILE) $(INPUT_FASTA_FILE).msasa.5.local.aln \
--log_file $(INPUT_FASTA_FILE).msasa.5.local.log \
--extend \
--temp 10 \
--cooling_rate 0.99 \
--min_temp 0.01 \
--max_no_changes 500 \
--quality_function local 2>> $(INPUT_FASTA_FILE).msasa.timing.log