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Makefile
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Makefile
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PREFIX=~/opt
install_prerequisites:
# sratoolkit
git clone git@github.com:ncbi/ngs.git
pushd ngs
./configure --prefix=${PREFIX}
make
make install
popd
pushd ngs/ngs-sdk
./configure --prefix=${PREFIX}
make
make install
popd
git clone git@github.com:ncbi/ncbi-vdb.git
pushd ncbi-vdb
./configure --prefix=${PREFIX}
make
make install
popd
git clone git@github.com:ncbi/sra-tools.git
cd sra-tools
./configure --prefix=${PREFIX}
make
make install
popd
# bowtie2
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip
unzip bowtie2-2.3.4.1-linux-x86_64.zip
pushd bin
ln -s ../bowtie2-2.3.4.1-linux-x86_64/bowtie2* .
popd
# RSEM
git clone git@github.com:deweylab/RSEM.git
pushd RSEM
make
make install DESTDIR=${PREFIX} prefix=${PREFIX}
popd
make CalCEN:
cp scripts/parameters_template.R parameters.R
Rscript scripts/1_define_runs.R
Rscript scripts/2_download_runs.R
Rscript scripts/3_reference_genome.R
Rscript scripts/4_submit_estimate_expression.R
Rscript scripts/5_gather_estimated_expression.R
Rscript scripts/6.1.1_collect_estimated_expression_meta.R
Rscript scripts/6.1.2_build_coexp_network.R
Rscript scripts/6.1.3_rna_seq_quality_control.R