mkdir ./bin >> setup.log 2>&1 mkdir ./bin/cora >> setup.log 2>&1 wget -q --directory-prefix ./bin/cora http://groups.csail.mit.edu/cb/cora/CORA.v1.1.4b.zip >> setup.log 2>&1 unzip ./bin/cora/CORA.v1.1.4b.zip -d ./bin/cora >> setup.log 2>&1 rm ./bin/cora/CORA.v1.1.4b.zip >> setup.log 2>&1 chmod 755 ./bin/cora/* >> setup.log 2>&1 mkdir ./ref >> setup.log 2>&1 wget -q --directory-prefix ./ref http://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr21_gl000210_random.fa.gz >> setup.log 2>&1 gunzip ./ref/chr21_gl000210_random.fa.gz ./ref/ >> setup.log 2>&1 mkdir ./read >> setup.log 2>&1 wget -q --directory-prefix ./read http://groups.csail.mit.edu/cb/cora/sample_1.0.0.tgz >> setup.log 2>&1 tar -xf ./read/sample_1.0.0.tgz -C ./read/ >> setup.log 2>&1 rm ./read/sample_1.0.0.tgz >> setup.log 2>&1 mkdir ./bin/samtools/ >> setup.log 2>&1 wget -q --directory-prefix ./bin/samtools/ http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2 >> setup.log 2>&1 tar -jxf ./bin/samtools/samtools-0.1.19.tar.bz2 -C ./bin/samtools/ >> setup.log 2>&1 rm ./bin/samtools/samtools-0.1.19.tar.bz2 >> setup.log 2>&1 make -C ./bin/samtools/samtools-0.1.19/ >> setup.log 2>&1 ./bin/samtools/samtools-0.1.19/samtools faidx ./ref/chr21_gl000210_random.fa >> setup.log 2>&1 mkdir ./bin/bwa/ >> setup.log 2>&1 wget -q --directory-prefix ./bin/bwa/ http://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.5a.tar.bz2 >> setup.log 2>&1 tar -jxf ./bin/bwa/bwa-0.7.5a.tar.bz2 -C ./bin/bwa/ >> setup.log 2>&1 rm ./bin/bwa/bwa-0.7.5a.tar.bz2 >> setup.log 2>&1 make -C ./bin/bwa/bwa-0.7.5a/ >> setup.log 2>&1 mkdir ./bin/bowtie2/ >> setup.log 2>&1 wget -q --directory-prefix ./bin/bowtie2 http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip >> setup.log 2>&1 unzip ./bin/bowtie2/bowtie2-2.1.0-source.zip -d ./bin/bowtie2/ >> setup.log 2>&1 rm ./bin/bowtie2/bowtie2-2.1.0-source.zip >> setup.log 2>&1 make -C ./bin/bowtie2/bowtie2-2.1.0/ >> setup.log 2>&1 wget -q http://groups.csail.mit.edu/cb/cora/sample_runs >> setup.log 2>&1