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get_dependencies_slim_v0.6.2.sh
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get_dependencies_slim_v0.6.2.sh
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#!/bin/sh
if [ ! -d "lib" ]; then
mkdir lib
fi
cd lib/
# jquery autocomplete
if [ ! -d "jquery-autocomplete" ]; then
mkdir jquery-autocomplete
# git clone https://github.com/devbridge/jQuery-Autocomplete.git jquery-autocomplete
cd jquery-autocomplete
# git pull
curl -OL https://github.com/devbridge/jQuery-Autocomplete/archive/v1.4.7.tar.gz
tar -xzvf v1.4.7.tar.gz
mv jQuery-Autocomplete-1.4.7/* .
cd ..
else
echo "jQuery already there..."
fi
# Papaparser
if [ ! -d "papa" ]; then
mkdir papa
#git clone https://github.com/mholt/PapaParse.git papa
cd papa
#git pull
curl -OL https://github.com/mholt/PapaParse/archive/4.4.0.tar.gz
tar -xzvf 4.4.0.tar.gz
mv PapaParse-4.4.0/* .
cd ..
else
echo "PAPAparser already there..."
fi
# Demultiplexing tool # no stable release yet... oops
if [ ! -d "DTD" ]; then
mkdir DTD
cd DTD
# git clone https://github.com/yoann-dufresne/DoubleTagDemultiplexer.git DTD/
curl -OL https://github.com/yoann-dufresne/DoubleTagDemultiplexer/archive/f687329ac846193605af97ef2b3f65d1bf5bce04.zip
unzip f687329ac846193605af97ef2b3f65d1bf5bce04.zip
mv DoubleTagDemultiplexer-f687329ac846193605af97ef2b3f65d1bf5bce04/* .
# git pull
cd ..
else
echo "DTD is already there..."
fi
# Pandaseq
if [ ! -d "pandaseq" ]; then
mkdir pandaseq
#git clone https://github.com/neufeld/pandaseq.git pandaseq/
cd pandaseq
#git pull
curl -OL https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz
tar -xzvf v2.11.tar.gz
mv pandaseq-2.11/* .
cd ..
else
echo "PANDAseq is already there..."
fi
# Vsearch
if [ ! -d "vsearch" ]; then
mkdir vsearch
# git clone https://github.com/torognes/vsearch.git vsearch/
cd vsearch
curl -OL https://github.com/torognes/vsearch/archive/v2.8.0.tar.gz
tar -xzvf v2.8.0.tar.gz
mv vsearch-2.8.0/* .
# git pull
cd ..
else
echo "VSEARCH is already there..."
fi
# QIIME 2
# docker pull qiime2/core:201
# Casper # no repos... oops
cd casper
if [ ! -d "casper_v0.8.2" ]; then
tar -xf casper_v0.8.2.tar.xz
fi
cd ..
# Swarm
if [ ! -d "swarm" ]; then
mkdir swarm
# git clone https://github.com/torognes/swarm.git swarm/
cd swarm
#git pull
curl -OL https://github.com/torognes/swarm/archive/v2.2.2.tar.gz
tar -xzvf v2.2.2.tar.gz
mv swarm-2.2.2/* .
cd ..
else
echo "SWARM is already there..."
fi