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lasca.sh
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68 lines (52 loc) · 5.46 KB
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#!/bin/bash
touch lasca.log
#touch lasca_download.log
#touch lasca_process.log
#touch lasca_py.log
#exec > lasca_download.log 2>&1
#wget -P ./../primary/ https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_insitu_primary_30.hic &
#wget -P ./../replicate/ https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_GM12878_insitu_replicate_30.hic &
#wget -P ./../K562/ https://ftp.ncbi.nlm.nih.gov/geo/series/GSE63nnn/GSE63525/suppl/GSE63525_K562_combined_30.hic &
#wait
#exec > lasca.log 2>&1
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/primary/GSE63525_GM12878_insitu_primary_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/primary/lasca/GSE63525_GM12878_insitu_primary_30_5K_chr1.cool --resolutions 5000 --chromosome 1 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/primary/GSE63525_GM12878_insitu_primary_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/primary/lasca/GSE63525_GM12878_insitu_primary_30_5K_chr6.cool --resolutions 5000 --chromosome 6 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/primary/GSE63525_GM12878_insitu_primary_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/primary/lasca/GSE63525_GM12878_insitu_primary_30_10K_chr1.cool --resolutions 10000 --chromosome 1 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/primary/GSE63525_GM12878_insitu_primary_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/primary/lasca/GSE63525_GM12878_insitu_primary_30_10K_chr6.cool --resolutions 10000 --chromosome 6 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/replicate/GSE63525_GM12878_insitu_replicate_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/replicate/lasca/GSE63525_GM12878_insitu_replicate_30_5K_chr1.cool --resolutions 5000 --chromosome 1 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/replicate/GSE63525_GM12878_insitu_replicate_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/replicate/lasca/GSE63525_GM12878_insitu_replicate_30_5K_chr6.cool --resolutions 5000 --chromosome 6 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/replicate/GSE63525_GM12878_insitu_replicate_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/replicate/lasca/GSE63525_GM12878_insitu_replicate_30_10K_chr1.cool --resolutions 10000 --chromosome 1 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/replicate/GSE63525_GM12878_insitu_replicate_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/replicate/lasca/GSE63525_GM12878_insitu_replicate_30_10K_chr6.cool --resolutions 10000 --chromosome 6 &
#wait
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/K562/GSE63525_K562_combined_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/K562/lasca/GSE63525_K562_combined_30_5K_chr1.cool --resolutions 5000 --chromosome 1 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/K562/GSE63525_K562_combined_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/K562/lasca/GSE63525_K562_combined_30_5K_chr6.cool --resolutions 10000 --chromosome 6 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/K562/GSE63525_K562_combined_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/K562/lasca/GSE63525_K562_combined_30_10K_chr1.cool --resolutions 5000 --chromosome 1 &
#hicConvertFormat -m /home/ubuntu/loop_analyzer/data/hub/K562/GSE63525_K562_combined_30.hic --inputFormat hic --outputFormat cool -o /home/ubuntu/loop_analyzer/data/hub/K562/lasca/GSE63525_K562_combined_30_10K_chr6.cool --resolutions 10000 --chromosome 6 &
#wait
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_primary_30_chr1_10000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_replicate_30_chr1_10000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_K562_combined_30_chr1_10000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_primary_30_chr6_10000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_replicate_30_chr6_10000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_K562_combined_30_chr6_10000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_primary_30_chr1_5000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_replicate_30_chr1_5000.cool &
wait
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_K562_combined_30_chr1_5000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_primary_30_chr6_5000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_GM12878_insitu_replicate_30_chr6_5000.cool &
cooler balance /home/ubuntu/loop_analyzer/data/hub/lasca/GSE63525_K562_combined_30_chr6_5000.cool &
wait
exec > lasca.log 2>&1
python3 lasca.py
#!/bin/bash
exec > lasca.log 2>&1
python3 lasca.py
cooler balance GM12878_primary_30_KR_5000.cool &
cooler balance GM12878_primary_30_KR_10000.cool &
wait
python3 lasca.py &
cooler balance GM12878_primary_30_KR_25000.cool &
cooler balance GM12878_primary_30_KR_50000.cool &
cooler balance GM12878_primary_30_KR_100000.cool &
wait