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make install.sh script take parameters #46

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make install.sh script take parameters #46

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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ project dir:

Install flo's dependencies in `ext/` directory in the project dir:

/path/to/flo/scripts/install.sh
/path/to/flo/scripts/install.sh ucsc-kent parallel genometools

Now edit `opts.yaml` to indicate:
1. Location of source and target assembly in FASTA format (required).
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9 changes: 9 additions & 0 deletions scripts/install.sh
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@@ -1,6 +1,8 @@
#!/usr/bin/env bash

# UCSC-Kent
if [[ "$*" == *"ucsc-kent"* ]] ## Check all the argument to the install.sh script
then
mkdir -p ext/kent/bin; cd ext/kent/bin
tools=(liftUp faSplit liftOver axtChain chainNet blat/blat chainSort faToTwoBit
twoBitInfo chainSplit chainMergeSort netChainSubset)
Expand All @@ -11,8 +13,11 @@ esac
for tool in ${tools[@]}; do wget -c "${ftp_dir}/${tool}"; done
chmod +x *
cd -
fi

# GNU parallel
if [[ "$*" == *"parallel"* ]] ## Check all the argument to the install.sh script
then
cd ext
wget -c http://ftp.gnu.org/gnu/parallel/parallel-20150722.tar.bz2
tar xvf parallel-20150722.tar.bz2
Expand All @@ -21,11 +26,15 @@ cd parallel-20150722
./configure
make
cd ../..
fi

# Genometools
if [[ "$*" == *"genometools"* ]] ## Check all the argument to the install.sh script
then
cd ext
wget -c https://github.com/genometools/genometools/archive/refs/tags/v1.6.2.tar.gz -O v1.6.2.tar.gz
tar xvf v1.6.2.tar.gz
rm v1.6.2.tar.gz
cd genometools-1.6.2
make cairo=no errorcheck=no
fi