Commit b06fad96 authored by Holger Brandl's avatar Holger Brandl

modernized used tools

parent a88ffae4
......@@ -22,12 +22,14 @@ append2path(){
export PATH=$1:$PATH
}
append2path ${BIO_BIN_BASE}/bowtie-1.1.2
append2path ${BIO_BIN_BASE}/bowtie2-2.2.5
append2path ${BIO_BIN_BASE}/bowtie-1.2.1.1
append2path ${BIO_BIN_BASE}/bowtie2-2.3.3.1
append2path ${BIO_BIN_BASE}/FastQC_0.11.2
append2path ${BIO_BIN_BASE}/bedtools2-2.25.0/bin
append2path ${BIO_BIN_BASE}/samtools-1.3
append2path ${BIO_BIN_BASE}/samtools-1.5
append2path ${BIO_BIN_BASE}/STAR-2.5.2b/source
# todo this is not an actual tagged release and should be appended differently (if at all)
append2path ${BIO_BIN_BASE}/ucsc
export PATH=/home/$(whoami)/local_bin/R-3.4.0/bin:$PATH
......
......@@ -64,7 +64,7 @@ cd bedtools2
make
########################################################################################################################
## samtools
cd ~/bin
wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2
......@@ -167,16 +167,22 @@ make
## STAR aligner
cd ~/bin
wget https://github.com/alexdobin/STAR/archive/2.5.2b.tar.gz
wget --no-check-certificate https://github.com/alexdobin/STAR/archive/2.5.2b.tar.gz
tar xvf 2.5.2b.tar.gz
cd STAR-2.5.2b/source
make
./STAR
## macos
cd ~/bin/
mkdir -p STAR-2.5.2b/source/
cd STAR-2.5.2b/source/
cmake -DCMAKE_CXX_COMPILER=g++-6 CMakeLists.txt
make
## sratoolkit
cd ~/bin
cd ~/bin/
#wget https://github.com/ncbi/sra-tools/archive/2.8.2-1.tar.gz
#tar xvf 2.8.2-1.tar.gz
#cd sra-tools-2.8.2-1
......@@ -387,4 +393,18 @@ bin/java -help
#bins from http://subread.sourceforge.net/
cd ~/bin/
tar xvf subread-1.5.3-Linux-x86_64.tar.gz
find subread-1.5.3-Linux-x86_64 | grep "featureCounts$"
\ No newline at end of file
find subread-1.5.3-Linux-x86_64 | grep "featureCounts$"
########################################################################################################################
### bowtie2 & bowtie1
umask u=rwx,g=rwx,o=
cd ~/bin/
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.3.1/bowtie2-2.3.3.1-linux-x86_64.zip
unzip bowtie2-2.3.3.1-linux-x86_64.zip
mv bowtie2-2.3.3.1-linux-x86_64 bowtie2-2.3.3.1
mv /projects/bioinfo/bowtie-1.2.1.1-linux-x86_64.zip ~/bin
unzip bowtie-1.2.1.1-linux-x86_64.zip
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