This page was last updated on Wednesday, 11-Jan-2017 12:18:46 CST

Installation notes for ALLMAPS version 0.6.9

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Prerequisites

Python libraries Biopython, Numpy, DEAP, NetworkX, and Matplotlib
Install with
$ sudo pip install biopython numpy deap networkx matplotlib

Concorde

1. $ cd /programinstallers/
2. $ wget http://www.math.uwaterloo.ca/tsp/concorde/downloads/codes/linux24/concorde.gz
3. $ gunzip concorde.gz
4. $ chmod +x concorde
5. $ sudo mv concorde /usr/local/bin/

Kent utilities faSize and liftOver

1. $ cd /programinstallers/
2. $ wget -N http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faSize
3. $ wget -N http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
4. $ chmod +x faSize liftOver
5. $ sudo mv faSize liftOver /usr/local/bin/

Installation

1. $ cd /programinstallers/
2. $ sudo pip install jcvi
3. Test sample data
   $ wget https://dl.dropboxusercontent.com/u/15937715/Data/ALLMAPS/ALLMAPS-testdata.zip
4. $ unzip ALLMAPS-testdata.zip
5. $ cd ALLMAPS-testdata
6. $ sh run.sh
7. Cleanup
   $ cd /programinstallers/ && rm ALLMAPS-testdata -rf
8. To determine version number I did this
   $ ls /usr/local/lib/python2.7/dist-packages
   …
   drwxr-sr-x 12 root staff 4,096 Jan 11 10:56 jcvi
   drwxr-sr-x 2 root staff 4,096 Jan 11 10:57 jcvi-0.6.9.egg-info
   …