| Previous changeset 8:31047e84cc0d (2016-08-06) Next changeset 10:e904265469af (2016-08-18) |
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Commit message:
Uploaded setup script for linux |
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added:
setup-linux.sh |
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| diff -r 31047e84cc0d -r 382e447d750c setup-linux.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/setup-linux.sh Thu Aug 18 18:41:09 2016 -0400 |
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| @@ -0,0 +1,30 @@ +#!/usr/bin/env bash + +# python +sudo apt-get install python + +# pip +sudo apt-get install python-pip + +# wget +sudo apt-get install wget + +# Install pysam library +sudo pip install pysam + +# Install numpy library +sudo pip install numpy + +# Install Bio Python +sudo pip install biopython + +# install bedtools +sudo apt-get install bedtools + +# install ART +mkdir lib/ART +wget -O cnvsim/ART/art.tgz http://www.niehs.nih.gov/research/resources/assets/docs/artsrcgreatsmokymountains041716linuxtgz.tgz +tar -xvzf cnvsim/ART/art.tgz -C cnvsim/ART +rm cnvsim/ART/art.tgz +mv cnvsim/ART/art_src_GreatSmokyMountains_Linux/art_illumina cnvsim/ART/art_illumina +rm -rf cnvsim/ART/art_src_GreatSmokyMountains_Linux |