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comparison setup-linux.sh @ 9:382e447d750c draft

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Uploaded setup script for linux
author ahosny
date Thu, 18 Aug 2016 18:41:09 -0400
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8:31047e84cc0d 9:382e447d750c
1 #!/usr/bin/env bash
2
3 # python
4 sudo apt-get install python
5
6 # pip
7 sudo apt-get install python-pip
8
9 # wget
10 sudo apt-get install wget
11
12 # Install pysam library
13 sudo pip install pysam
14
15 # Install numpy library
16 sudo pip install numpy
17
18 # Install Bio Python
19 sudo pip install biopython
20
21 # install bedtools
22 sudo apt-get install bedtools
23
24 # install ART
25 mkdir lib/ART
26 wget -O cnvsim/ART/art.tgz http://www.niehs.nih.gov/research/resources/assets/docs/artsrcgreatsmokymountains041716linuxtgz.tgz
27 tar -xvzf cnvsim/ART/art.tgz -C cnvsim/ART
28 rm cnvsim/ART/art.tgz
29 mv cnvsim/ART/art_src_GreatSmokyMountains_Linux/art_illumina cnvsim/ART/art_illumina
30 rm -rf cnvsim/ART/art_src_GreatSmokyMountains_Linux