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osX_install_prerequisites.sh
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mkdir bin
#minimap2
cd minimap2 \
&& make \
&& mv minimap2 ../bin \
&& cd ../ \
&& echo minimap2 OK || echo minimap2 FAIL
#htsbox
cd htsbox \
&& make \
&& mv htsbox ../bin \
&& cd ../ \
&& echo htsbox OK || echo htsbox FAIL
#htslib
cd htslib \
&& autoheader \
&& autoconf \
&& ./configure --disable-lzma;make \
&& mv tabix bgzip ../bin/ \
&& cd ../ \
&& echo htslib OK || echo htslib FAIL
#bwa
cd bwa \
&& make \
&& mv bwa ../bin \
&& cd ../ \
&& echo bwahtslib OK || echo bwahtslib FAIL
#bowtie2
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4/bowtie2-2.3.4-macos-x86_64.zip \
&& unzip bowtie2-2.3.4-macos-x86_64.zip \
&& cd bowtie2-2.3.4-macos-x86_64 \
&& mv bowtie2* ../bin \
&& cd ../ \
&& echo bowtie2 OK || echo bowtie2 FAIL
#bcftools
cd bcftools \
&& make \
&& mv bcftools ../bin \
&& cd ../ \
&& echo bcftools OK || echo bcftools FAIL
#samtools
cd samtools \
&& make \
&& mv samtools ../bin \
&& cd ../ \
&& echo samtools OK || echo samtools FAIL
#lofreq
cd lofreq/dist/ \
&& tar -xvf lofreq_star-2.1.3.1_macosx.tgz \
&& mv lofreq_star-2.1.3.1/bin/lofreq ../../bin/ \
&& cd ../../ \
&& echo lofreq OK || echo lofreq FAIL
wget http://pathogenseq.lshtm.ac.uk/downloads/TBProfilerFiles.tgz \
&& tar -xvf TBProfilerFiles.tgz \
&& ./bin/bowtie2-build ref/MTB-h37rv_asm19595v2-eg18.fa ref/MTB-h37rv_asm19595v2-eg18.fa \
&& echo Files OK || echo Files FAIL
python scripts/create_config.py