diff --git a/Makefile b/Makefile index 014e5f2..3a712a0 100644 --- a/Makefile +++ b/Makefile @@ -5,12 +5,14 @@ default: haskell all: find_tree_matches.exe haskell +GHC=ghc-7.4.2 + haskell: - ghc -O2 --make Main.hs -o phybin.exe + $(GHC) -O2 --make Main.hs -o phybin.exe strip phybin.exe win: - ghc -DWIN32 --make Bio/Phylogeny/PhyBin/Main.hs -o phybin.exe + $(GHC) -DWIN32 --make Bio/Phylogeny/PhyBin/Main.hs -o phybin.exe release: haskell upx phybin.exe diff --git a/vary_branchlen.sh b/vary_branchlen.sh index 9adfe96..b358463 100755 --- a/vary_branchlen.sh +++ b/vary_branchlen.sh @@ -5,7 +5,10 @@ if [ "$2" == "" ]; then echo "ERR: Two args required!"; exit 1; fi taxa=$1 dataset=$2 -branchlens="0.0001 0.001 0.01 0.05 0.1 0.5 1.0 5.0" +# 12 settings: +branchlens="0.0001 0.001 0.01 0.02 0.03 0.05 0.1 0.2 0.3 0.5 1.0 5.0" + +DOGRAPH="-g" echo Wiping "$dataset/phybin_output/" ... rm -rf "$dataset/phybin_output/" @@ -15,7 +18,7 @@ echo "[parallel] Starting jobs..." for bl in $branchlens; do echo "Running with branch len $bl" echo "==============================" - PHYBIN="./phybin.exe -b $bl -g -n $taxa" + PHYBIN="./phybin.exe -b $bl $DOGRAPH -n $taxa" outdir="$dataset/phybin_output/brlen$bl/" LOG="$dataset/phybin_output/brlen$bl.log" @@ -25,7 +28,7 @@ for bl in $branchlens; do # ASSUMPTION2! We likewise expect the inputs in a certain spot. RENAMER="$dataset/renaming_table.txt" echo " RUNNING: $PHYBIN -m $RENAMER -s '_' -o $outdir" - $PHYBIN -m $RENAMER -s '_' -o $outdir $dataset/final_trees/*BranchLab*.out | tee $LOG + ($PHYBIN -m $RENAMER -s '_' -o $outdir $dataset/final_trees/*BranchLab*.out | tee $LOG) & done echo "[parallel] Waiting for outstanding jobs"