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install.sh
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#!/bin/bash
if [ ! -e ./bin ]; then
mkdir ./bin;
fi
cd bin
unameOut="$(uname -s)"
case "${unameOut}" in
Linux*) machine=Linux;;
Darwin*) machine=Mac;;
#CYGWIN*) machine=Cygwin;;
#MINGW*) machine=MinGw;;
*) machine="UNKNOWN:${unameOut}"
esac
echo ${machine}
if [ ${machine} == "Linux" ]; then
if [ -e axtChain ]; then rm axtChain; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/axtChain
if [ -e blat ]; then rm blat; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
if [ -e gfClient ]; then rm gfClient; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/gfClient
if [ -e gfServer ]; then rm gfServer; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/gfServer
if [ -e chainAntiRepeat ]; then rm chainAntiRepeat; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chainAntiRepeat
if [ -e chainMergeSort ]; then rm chainMergeSort; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chainMergeSort
if [ -e chainNet ]; then rm chainNet; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chainNet
if [ -e chainPreNet ]; then rm chainPreNet; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chainPreNet
if [ -e chainStitchId ]; then rm chainStitchId; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chainStitchId
if [ -e chainSplit ]; then rm chainSplit; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chainSplit
if [ -e faSplit ]; then rm faSplit; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faSplit
if [ -e faToTwoBit ]; then rm faToTwoBit; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit
if [ -e liftOver ]; then rm liftOver; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver
if [ -e liftUp ]; then rm liftUp; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftUp
if [ -e netChainSubset ]; then rm netChainSubset; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/netChainSubset
if [ -e netSyntenic ]; then rm netSyntenic; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/netSyntenic
if [ -e twoBitInfo ]; then rm twoBitInfo; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/twoBitInfo
if [ -e lavToPsl ]; then rm lavToPsl; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/lavToPsl
elif [ ${machine} == "Mac" ]; then
if [ -e axtChain ]; then rm axtChain; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/axtChain
if [ -e blat ]; then rm blat; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/blat/blat
if [ -e gfClient ]; then rm gfClient; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/blat/gfClient
if [ -e gfServer ]; then rm gfServer; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/blat/gfServer
if [ -e chainAntiRepeat ]; then rm chainAntiRepeat; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/chainAntiRepeat
if [ -e chainMergeSort ]; then rm chainMergeSort; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/chainMergeSort
if [ -e chainNet ]; then rm chainNet; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/chainNet
if [ -e chainPreNet ]; then rm chainPreNet; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/chainPreNet
if [ -e chainStitchId ]; then rm chainStitchId; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/chainStitchId
if [ -e chainSplit ]; then rm chainSplit; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/chainSplit
if [ -e faSplit ]; then rm faSplit; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/faSplit
if [ -e faToTwoBit ]; then rm faToTwoBit; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/faToTwoBit
if [ -e liftOver ]; then rm liftOver; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/liftOver
if [ -e liftUp ]; then rm liftUp; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/liftUp
if [ -e netChainSubset ]; then rm netChainSubset; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/netChainSubset
if [ -e netSyntenic ]; then rm netSyntenic; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/netSyntenic
if [ -e twoBitInfo ]; then rm twoBitInfo; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/twoBitInfo
if [ -e lavToPsl ]; then rm lavToPsl; fi; wget https://hgdownload.soe.ucsc.edu/admin/exe/macOSX.x86_64/lavToPsl
fi
# Install lastz
if [ -e lastz ]; then rm lastz; fi
git clone https://github.com/UCSantaCruzComputationalGenomicsLab/lastz.git && \
mv lastz lastz-src && \
cd lastz-src && \
make && \
cp src/lastz ../ && \
cp tools/build_fasta_hsx.py ../ && \
cp tools/hsx_file.py ../ && \
cp tools/hassock_hash.py ../ && \
cd .. && \
rm -rf ./lastz-src
# Install maf-converter from last
if [ -e maf-convert ]; then rm maf-convert; fi;
wget http://last.cbrc.jp/last-1061.zip && unzip last-1061.zip && \
cd ./last-*/ && \
make && \
cd src/ && \
cp lastdb8 lastdb lastal8 lastal last-split8 last-split last-pair-probs last-merge-batches ../../ && \
cd .. && \
mv scripts/* ../ && cd ../ && \
rm -r ./last-*
# Install GSAlign
git clone https://github.com/hsinnan75/GSAlign.git && \
cd GSAlign && \
make all && \
cp bin/* ../ && \
rm -r GSAlign
# Install crossmap
pip install scipy CrossMap
# Install minimap2
if [ ${machine} == "Linux" ]; then
if [ -e minimap2 ]; then rm minimap2 paftools.js k8; fi
wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 && \
tar -xvf minimap2-2.17_x64-linux.tar.bz2 && \
mv minimap2-2.17_x64-linux/minimap2 ./ && mv minimap2-2.17_x64-linux/paftools.js ./ && mv minimap2-2.17_x64-linux/k8 ./ && \
rm -rf ./minimap2-*
fi
# Clean-up
cd ../
chmod a+x ./bin/*