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Makefile
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PLATFORM = $(shell uname)
ifeq ($(PLATFORM), Darwin)
SMALT = smalt-0.5.7/smalt_MacOSX_i386
BLAST = blast-2.2.25-universal-macosx.tar.gz
endif
ifeq ($(PLATFORM), Linux)
SMALT = smalt-0.5.7/smalt_i686
BLAST = blast-2.2.25-x64-linux.tar.gz
endif
default: ~/cram/db/ ~/cram/bin binaries databases
~/cram/db/:
mkdir -p ~/cram/db/
~/cram/bin:
mkdir -p ~/cram/bin
update:
git pull [email protected]:git/cram.git master
binaries: ~/cram/bin/velvetg ~/cram/bin/prodigal ~/cram/bin/phmmer ~/cram/bin/smalt ~/cram/bin/blastall
databases: ~/cram/db/subsystems2peg ~/cram/db/subsystems2role ~/cram/db/seed.fasta ~/cram/db/taxcollector.fa
~/cram/bin/blastall:
curl -O ftp://ftp.ncbi.nih.gov/blast/executables/release/2.2.25/$(BLAST)
tar -zxvf $(BLAST) blast-2.2.25/bin/formatdb
tar -zxvf $(BLAST) blast-2.2.25/bin/blastall
mv blast-2.2.25/bin/formatdb ~/cram/bin
mv blast-2.2.25/bin/blastall ~/cram/bin
rm -rf blast-2.2.25
rm $(BLAST)
~/cram/bin/velvetg:
curl -O http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.1.05.tgz
tar -zxvf velvet_1.1.05.tgz
make -C velvet_1.1.05 velveth velvetg MAXKMERLENGTH=71 OPENMP=1 LONGSEQUENCES=1
mv velvet_1.1.05/velvetg ~/cram/bin/
mv velvet_1.1.05/velveth ~/cram/bin/
rm -rf velvet_1.1.05*
~/cram/bin/prodigal:
curl -O http://prodigal.googlecode.com/files/prodigal.v2_00.tar.gz
tar -zxvf prodigal.v2_00.tar.gz
make -C prodigal.v2_00
mv prodigal.v2_00/prodigal ~/cram/bin/
rm -rf prodigal.v2_00*
~/cram/bin/phmmer:
curl -O http://selab.janelia.org/software/hmmer3/3.0/hmmer-3.0.tar.gz
tar -zxvf hmmer-3.0.tar.gz
cd hmmer-3.0; ./configure; make; cd -
mv hmmer-3.0/src/phmmer ~/cram/bin/
rm -r hmmer-3.0*
~/cram/bin/smalt:
curl -O ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-0.5.7.tgz
tar -zxvf smalt-0.5.7.tgz
mv $(SMALT) ~/cram/bin/smalt
rm -rf smalt-0.5.7*
~/cram/db/subsystems2peg:
curl ftp://ftp.theseed.org/subsystems/subsystems2peg.gz | gunzip > ~/cram/db/subsystems2peg
~/cram/db/subsystems2role:
curl ftp://ftp.theseed.org/subsystems/subsystems2role.gz | gunzip > ~/cram/db/subsystems2role
~/cram/db/taxcollector.fa:
curl http://microgator.org/taxcollector.fa.gz | gunzip > ~/cram/db/taxcollector.fa
~/cram/db/seed.fasta:
curl ftp://ftp.theseed.org/genomes/SEED/SEED.fasta.gz | gunzip > ~/cram/db/seed.fasta