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|
default: haskell
all: find_tree_matches.exe haskell
# GHC=ghc-7.4.2
GHC=ghc-7.6.3
release: haskell
upx phybin.exe
du -h phybin.exe
haskell:
cabal configure
cabal build
cp ./dist/build/phybin/phybin phybin.exe
du -h phybin.exe
strip phybin.exe
du -h phybin.exe
win:
$(GHC) -DWIN32 --make Main.hs -o phybin.exe
find_tree_matches.exe: find_tree_matches.ss
mzc --exe find_tree_matches.exe find_tree_matches.ss
clean:
rm -f phybin *.exe *.hi *.o Bio/Phylogeny/PhyBin/*.o Bio/Phylogeny/PhyBin/*.hi
################################################################################
#launch: clean release doc distro push upload
launch: doc distro push upload
doc:
pandoc -s -S --toc -c website.css README.md -o website/index.html
release_website:
cp website/* ~/.hyplan/projects/phybin/
distro:
cabal sdist
cp -v dist/*.tar.gz website/
# HASKELLSRV=haskell.intel
HASKELLSRV=community.haskell.org
################################################################################
# Collecting shortcuts for running different datasets:
# LOCALSETS=~/newton_and_newton_local/datasets
LOCALSETS=.
rhizobia:
rm -rf $(LOCALSETS)/rhizobia/phybin_outputs
mkdir $(LOCALSETS)/rhizobia/phybin_outputs
./phybin.exe $(LOCALSETS)/rhizobia/gde/*.dnd -o $(LOCALSETS)/rhizobia/phybin_output/ -p 2 -n 7 -g -v
#yersinia_test_names:
# ./phybin.exe -w ~/newton_and_newton_local/datasets/yersinia/yersinia_trees/111.dnd -s . -m ../datasets/yersinia/name_table_hack_yersinia.txt
yersinia:
rm -rf $(LOCALSETS)/yersinia/phybin_outputs
mkdir $(LOCALSETS)/yersinia/phybin_outputs
./phybin.exe $(LOCALSETS)/yersinia/yersinia_trees/ -o $(LOCALSETS)/yersinia/phybin_outputs/ -m ../datasets/yersinia/name_table_hack_yersinia.txt -s . -n 9 -g
legionella:
rm -rf $(LOCALSETS)/legionella/phybin_outputs
mkdir $(LOCALSETS)/legionella/phybin_outputs
./phybin.exe $(LOCALSETS)/legionella/legionella_orthologs_aa/ -o $(LOCALSETS)/legionella/phybin_outputs/ -m ../datasets/legionella/name_table_hack_legionella.txt -s 0123456789 -n 4 -g
# Newer ones [2012.11.19]:
newbatch: rickettsia rickettsiales wolbachia
# BRANCHTHRESH=0.01
BRANCHTHRESH=0.05
PHYBIN= ./phybin.exe -b $(BRANCHTHRESH) -g
#------------------------------------------------------------
rickettsia: $(LOCALSETS)/Rickettsia/renaming_table.txt
rm -rf $(LOCALSETS)/Rickettsia/phybin_outputs
mkdir $(LOCALSETS)/Rickettsia/phybin_outputs
$(PHYBIN) -n 15 -m $(LOCALSETS)/Rickettsia/renaming_table.txt -s '_' -o $(LOCALSETS)/Rickettsia/phybin_output/ $(LOCALSETS)/Rickettsia/final_trees/*BranchLab*.out
$(LOCALSETS)/Rickettsia/renaming_table.txt: $(LOCALSETS)/Rickettsia/Rickettsia_orthololgs.txt
runghc stripTable.hs $^ > $@
#------------------------------------------------------------
rickettsiales: $(LOCALSETS)/Rickettsiales/renaming_table.txt
rm -rf $(LOCALSETS)/Rickettsiales/phybin_outputs
mkdir $(LOCALSETS)/Rickettsiales/phybin_outputs
$(PHYBIN) -n 29 -m $(LOCALSETS)/Rickettsiales/renaming_table.txt -s '_' -o $(LOCALSETS)/Rickettsiales/phybin_output/ $(LOCALSETS)/Rickettsiales/final_trees/*BranchLab*.out
$(LOCALSETS)/Rickettsiales/renaming_table.txt: $(LOCALSETS)/Rickettsiales/Rickettsiales_orthologs.txt
runghc stripTable.hs $^ > $@
#------------------------------------------------------------
wolbachia: $(LOCALSETS)/Wolbachia/renaming_table.txt
rm -rf $(LOCALSETS)/Wolbachia/phybin_outputs
mkdir $(LOCALSETS)/Wolbachia/phybin_outputs
$(PHYBIN) -n 4 -m $(LOCALSETS)/Wolbachia/renaming_table.txt -s '_' -o $(LOCALSETS)/Wolbachia/phybin_output/ $(LOCALSETS)/Wolbachia/final_trees/*BranchLab*.out
$(LOCALSETS)/Wolbachia/renaming_table.txt: $(LOCALSETS)/Wolbachia/Wolbachia_orthologs.txt
runghc stripTable.hs $^ > $@
vary_branchlen: $(LOCALSETS)/Rickettsia/renaming_table.txt $(LOCALSETS)/Rickettsiales/renaming_table.txt $(LOCALSETS)/Wolbachia/renaming_table.txt
./vary_branchlen.sh 15 Rickettsia
./vary_branchlen.sh 29 Rickettsiales
./vary_branchlen.sh 4 Wolbachia
temp:
./phybin.exe ~/newton_and_newton_local/datasets/rhizobia/gde/*.dnd -o temp -p 2 -n 7
|
