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Copy path2_copy_star_cdp_pipeline2.sh
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2_copy_star_cdp_pipeline2.sh
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#!/bin/bash
export PROJDIR="/fs/cbcb-lab/ekmolloy/jdai123/star-study/"
# Pipeline 2 Star-CDP
OUT="$PROJDIR/bio-result/prune-deprune-deduplicate-bio-result/star_cdp"
PDD="prune-deprune-deduplicate-bio-result"
DATA="3515_Lkb1_T1_Fam"
# Pipeline 2a
IN="$PROJDIR/H_bio_result_Full/star_cdp"
cp $IN/$DATA/one_sol_branch_trees.nwk $OUT/$DATA/one_sol_branch_trees.nwk
cp $IN/$DATA/rand_sol_branch_trees.nwk $OUT/$DATA/rand_sol_branch_trees.nwk
cp $IN/$DATA/sc_branch_trees.nwk $OUT/$DATA/sc_branch_trees.nwk
cp $IN/$DATA/one_sol_sh_branch_trees.nwk $OUT/$DATA/one_sol_sh_branch_trees.nwk
cp $IN/$DATA/rand_sol_branch_trees.nwk $OUT/$DATA/rand_sol_branch_trees.nwk
cp $IN/$DATA/sc_sh_branch_trees.nwk $OUT/$DATA/sc_sh_branch_trees.nwk
cp $IN/$DATA/star_cdp_usage.log $OUT/$DATA/
# Pipeline 2b
IN="$PROJDIR/H_bio_result_Full/star_cdp"
cp $IN/$DATA/one_sol_sh_branch_resolve_poly_ckpt.txt $OUT/$DATA/
cp $IN/$DATA/rand_sol_sh_branch_resolve_poly_ckpt.txt $OUT/$DATA/
cp $IN/$DATA/sc_sh_branch_resolve_poly_ckpt.txt $OUT/$DATA/
DATA="3513_NT_T1_Fam"
# Pipeline 2a
IN="$PROJDIR/G_bio_result_pruned_deduplicate/star_cdp"
cp $IN/$DATA/one_sol_branch_trees.nwk $OUT/$DATA/
cp $IN/$DATA/rand_sol_branch_trees.nwk $OUT/$DATA
cp $IN/$DATA/sc_branch_trees.nwk $OUT/$DATA/
cp $IN/$DATA/one_sol_branch_sh_trees.nwk $OUT/$DATA/one_sol_sh_branch_trees.nwk
cp $IN/$DATA/rand_sol_branch_sh_trees.nwk $OUT/$DATA/rand_sol_sh_branch_trees.nwk
cp $IN/$DATA/sc_branch_sh_trees.nwk $OUT/$DATA/sc_sh_branch_trees.nwk
cp $PROJDIR/E_bio_result_pruned/star_cdp/$DATA/consensus_star_cdp_usage.log $OUT/$DATA/star_cdp_usage.log
# Pipeline 2b
IN="$PROJDIR/H_bio_result_Full/star_cdp"
cp $IN/$DATA/one_sol_sh_branch_resolve_poly_trees.nwk $OUT/$DATA/
cp $IN/$DATA/one_sol_sh_branch_resolve_poly_usage.log $OUT/$DATA/
cp $IN/$DATA/rand_sol_sh_branch_resolve_poly_trees.nwk $OUT/$DATA/
cp $IN/$DATA/rand_sol_sh_branch_resolve_poly_usage.log $OUT/$DATA/
cp $IN/$DATA/sc_sh_branch_resolve_poly_trees.nwk $OUT/$DATA/
cp $IN/$DATA/sc_sh_branch_resolve_poly_usage.log $OUT/$DATA/
DATA="3724_NT_All"
# Pipeline 2a
IN="$PROJDIR/G_bio_result_pruned_deduplicate/star_cdp"
cp $IN/$DATA/one_sol_branch_trees.nwk $OUT/$DATA/
cp $IN/$DATA/rand_sol_branch_trees.nwk $OUT/$DATA
cp $IN/$DATA/sc_branch_trees.nwk $OUT/$DATA/
cp $IN/$DATA/one_sol_branch_sh_trees.nwk $OUT/$DATA/one_sol_sh_branch_trees.nwk
cp $IN/$DATA/rand_sol_branch_sh_trees.nwk $OUT/$DATA/rand_sol_sh_branch_trees.nwk
cp $IN/$DATA/sc_branch_sh_trees.nwk $OUT/$DATA/sc_sh_branch_trees.nwk
cp $PROJDIR/E_bio_result_pruned/star_cdp/$DATA/consensus_star_cdp_usage.log $OUT/$DATA/star_cdp_usage.log
# Pipeline 2b
IN="$PROJDIR/H_bio_result_Full/star_cdp"
cp $IN/$DATA/one_sol_sh_branch_resolve_poly_trees.nwk $OUT/$DATA/
cp $IN/$DATA/one_sol_sh_branch_resolve_poly_usage.log $OUT/$DATA/
cp $IN/$DATA/rand_sol_sh_branch_resolve_poly_trees.nwk $OUT/$DATA/
cp $IN/$DATA/rand_sol_sh_branch_resolve_poly_usage.log $OUT/$DATA/
cp $IN/$DATA/sc_sh_branch_resolve_poly_trees.nwk $OUT/$DATA/
cp $IN/$DATA/sc_sh_branch_resolve_poly_usage.log $OUT/$DATA/
##### PIPELINE 2c
DATA="3513_NT_T1_Fam"
IN="G_bio_result_pruned_deduplicate/laml/star_cdp_one_sol/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_one_sol"
cp $IN/laml_output_trees.nwk $OUT/one_sol_branch_trees.nwk
cp $IN/laml_output_usage.log $OUT/one_sol_usage.log
IN="G_bio_result_pruned_deduplicate/laml/star_cdp_rand_sol/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_rand_sol"
cp $IN/laml_output_trees.nwk $OUT/one_sol_branch_trees.nwk
cp $IN/laml_output_usage.log $OUT/one_sol_usage.log
IN="G_bio_result_pruned_deduplicate/laml/star_cdp_sc/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_sc"
cp $IN/laml_output_trees.nwk $OUT/one_sol_branch_trees.nwk
cp $IN/laml_output_usage.log $OUT/one_sol_usage.log
#####################
DATA="3724_NT_All"
IN="G_bio_result_pruned_deduplicate/laml/star_cdp_one_sol/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_one_sol"
cp $IN/laml_output_trees.nwk $OUT/one_sol_branch_trees.nwk
cp $IN/laml_output_usage.log $OUT/one_sol_usage.log
IN="G_bio_result_pruned_deduplicate/laml/star_cdp_rand_sol/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_rand_sol"
cp $IN/laml_output-24hrs_trees.nwk $OUT/one_sol_branch_trees.nwk
cp $IN/laml_output-24hrs_usage.log $OUT/one_sol_usage.log
IN="G_bio_result_pruned_deduplicate/laml/star_cdp_sc/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_sc"
cp $IN/laml_output-24hrs_ckpt.txt $OUT/one_sol_ckpt.txt
cp $IN/24hrs-best_branch_trees.nwk $OUT/one_sol_branch_trees.nwk
#################
DATA="3515_Lkb1_T1_Fam"
IN="H_bio_result_Full/laml/star_cdp_one_sol/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_one_sol"
cp $IN/one_sol_ckpt.txt $OUT/one_sol_ckpt.txt
IN="H_bio_result_Full/laml/star_cdp_rand_sol/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_rand_sol"
cp $IN/one_sol_ckpt.txt $OUT/one_sol_ckpt.txt
IN="H_bio_result_Full/laml/star_cdp_sc/$DATA"
OUT="bio-result/$PDD/laml/$DATA/star_cdp_sc"
cp $IN/one_sol_ckpt.txt $OUT/one_sol_ckpt.txt