annotate setup-mac.sh @ 18:eca72016b5b3 draft default tip

Uploaded
author ahosny
date Wed, 07 Sep 2016 09:37:49 -0400
parents 302eb5118a36
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
1 #!/usr/bin/env bash
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
2
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
3 # Homebrew
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
4 ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
5
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
6 # python
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
7 brew install python
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
8
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
9 # pip
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
10 curl -O http://python-distribute.org/distribute_setup.py
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
11 python distribute_setup.py
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
12 curl -O https://raw.github.com/pypa/pip/master/contrib/get-pip.py
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
13 python get-pip.py
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
14
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
15 # wget
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
16 brew install wget
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
17
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
18 # clean after installation
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
19 rm -t tmp
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
20
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
21 # Install pysam library
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
22 pip install pysam
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
23
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
24 # Install Bio Python
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
25 pip install biopython
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
26
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
27 # install bedtools
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
28 brew install homebrew/science/bedtools
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
29
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
30 # install ART
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
31 mkdir cnvsim/ART
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
32 wget -O cnvsim/ART/art.tgz http://www.niehs.nih.gov/research/resources/assets/docs/artsrcgreatsmokymountains041716macostgz.tgz
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
33 tar -xvzf cnvsim/ART/art.tgz -C cnvsim/ART
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
34 rm cnvsim/ART/art.tgz
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
35 mv cnvsim/ART/art_src_GreatSmokyMountains_MacOS/art_illumina cnvsim/ART/art_illumina
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
36 rm -rf cnvsim/ART/art_src_GreatSmokyMountains_MacOS
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
37
e904265469af Uploaded setup script for mac
ahosny
parents:
diff changeset
38