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Update Makefile #2

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21 changes: 11 additions & 10 deletions scripts/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -16,20 +16,21 @@ trimmomatic:
rm Trimmomatic-0.32.zip
mv Trimmomatic-0.32/ plugins/
Pfam:
wget http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz
tar -zxf hmmer-3.1b1-linux-intel-x86_64.tar.gz
cd hmmer-3.1b1-linux-intel-x86_64 && ./configure && $(MAKE) -j6 && $(MAKE) -j6 check
cp hmmer-3.1b1-linux-intel-x86_64/src/hmmpress .
cp hmmer-3.1b1-linux-intel-x86_64/src/hmmscan .
cp hmmer-3.1b1-linux-intel-x86_64/src/hmmsearch .
cp hmmer-3.1b1-linux-intel-x86_64/src/hmmstat .
wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
tar -zxf hmmer-3.1b2-linux-intel-x86_64.tar.gz
cd hmmer-3.1b2-linux-intel-x86_64 && ./configure && $(MAKE) -j6 && $(MAKE) -j6 check
cp hmmer-3.1b2-linux-intel-x86_64/src/hmmpress .
cp hmmer-3.1b2-linux-intel-x86_64/src/hmmscan .
cp hmmer-3.1b2-linux-intel-x86_64/src/hmmsearch .
cp hmmer-3.1b2-linux-intel-x86_64/src/hmmstat .
#The file bellow was not found in the url bellow, could you provide this file?
wget http://sourceforge.net/projects/transdecoder/files/Pfam-AB.hmm.bin
hmmpress Pfam-AB.hmm.bin
GRCm38:
wget ftp://ftp.ensembl.org/pub/release-71/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.71.cdna.all.fa.gz
gzip -d Mus_musculus.GRCm38.71.cdna.all.fa.gz
clean:
rm trimmomatic-0.32.jar express hmmer-3.1b1-linux-intel-x86_64.tar.gz Pfam-A.hmm* Mus_musculus.GRCm38.71.cdna.all.fa
rm -fr plugins/* hmmer-3.1b1-linux-intel-x86_64
rm trimmomatic-0.32.jar express hmmer-3.1b2-linux-intel-x86_64.tar.gz Pfam-A.hmm* Mus_musculus.GRCm38.71.cdna.all.fa
rm -fr plugins/* hmmer-3.1b2-linux-intel-x86_64
clean_check:
rm -fr unit_test/*
rm -fr unit_test/*