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Old 09-08-2010, 09:44 AM   #35
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Location: Phoenix, AZ

Join Date: Mar 2010
Posts: 279

Time to Git a Linux Machine

I'm slowly getting back up and running after moving from my post-doc to an independent position. Other than learning how damn expensive everything is I'm slowly deciding that I should swear off the idea of a new MacPro workstation for a Linux workstation given all the issues I seem to run into with the "not quite so standard Mac OSX10.6 implementation of Unix". But with the idea of sharing my ongoing experiences and a trail I can follow to build my next machine I thought I'd update my thread. I hope some people have found it useful...

Some new idea's and an update

1) I'm becoming increasing certain that I'm getting good enough at command line issues to REALLY mess up my system
2) My list of used programs continues to increase as I try each new sequencing method
3) As per issue 1 - I'm also not reading instructions very well. New Rule - If at first you don't succeed...Go back and read the damn instructions again because most likely you didn't follow them correctly!

New Applications to Install

As previously stated in the post if you are using a Mac OS environment you need to do a couple of special things

A) Install Xcode on your system (See earlier post)
B) Install Fink on your system (See earlier post)
- install the following fink packages:md5deep and pkgconfig
- "fink install md5deep" (needed for bfast install)
- "fink install pkgconfig" (needed for fastx-toolkit install)
C) Install Git on your system (
D) Create a $PATH Directory and update this directory in your .profile (See earlier post for instructions)
- In my case "$HOME/local/bin"

1) Install FASTX-Toolkit (

***Why did I get this package***
Because I have some illumina mate-pair data that I want to analyze with BWA using sampe but the reads need to be reverse complemented to work correctly by my understanding so I'm using the fastx_reverse_complement application in the package that seems to be very fast and correctly reverse complements the reads and reverses the quality values

- Go to download page and download the following:
a) fastx_toolkit-0.0.13.tar.bz2
b) libgtextutils-0.6.tar.bz2
- Move both to ngs/applications folder and unpack both packages
- In Terminal navigate the libgtextutils folder "cd ngs/applications/libtestutils-0.6"
- Install the package as follows:
sudo make install (this will ask for your password, must be admin level privileged set)

- Move to fastx_toolkit folder "cd ../fastx_toolkit-0.0.13"
- Install the package as follows:
./configure --prefix=$HOME/local/bin
make install

- Test install by typing "fastx_uncollapser -h", this should pop up a usage documentation for this app

2) Install Bfast, DNAA, and Breakway

*** Why these packages***
As you might guess from the above install I now have some mate-pair data and want to try out the Breakway package from the UCLA group but it depends on two of their other packages Bfast and DNAA

Bfast - This package seems to be the vain of my existence but thankfully Nils and the helplist have been amazingly helpful

Mac Related Issues:
a) You must have fink and have installed the md5deep package otherwise "make check" will fail
b) The current sourceforge version (0.6.4e) does not install correctly thought the previous version does, however, this is a known issue and has been fixed in the master branch (if that's a new term to you we are in the same boat) but this mean you need to use the git repository version
c) Using ".configure -prefix=$HOME/local" works but makes DNAA mad when you install it so use sudo (time to be superman again)

a) In Terminal navigate to ngs/applications
b) Get current Bfast version from Git (restart Terminal after git installation)
- type "git clone git://"
- this will create a folder called "bfast" in the current directory
- Move into the directory "cd bfast"
- Install bfast by typing the following:
make check
sudo make install (requests a password with admin level privileges)

- Test install and check current version by typing "bfast" in Terminal

c) Navigate back to ngs directory by typing "cd ../"
d) Get current version of DNAA from Git
- type "git clone git:// dnaa"
- this will create a directory named "dnaa" in the current directory (ngs/applications)
- move into the the dnaa directory by typing "cd dnaa"
e) Because this package depends on both BFAST and SAMTOOLS you need to provide links to these application directories even though you already have them in a $PATH directory (/usr/local/bin and $HOME/local/bin repectively)
- create a link to the BFAST package you just installed by typing "ln -s ../bfast bfast"
- create a link to your current SAMTOOLS package by typing "ln -s ../samtools-0.1.8 samtools"
f) Install DNAA by typing the following:
sudo make install (requests a password with admin level privileges)

g) Download current version of BREAKWAY from sourceforge (, move it to the ngs/applications folder and unpack it and you should be ready to go

Last edited by Jon_Keats; 02-17-2011 at 09:18 PM. Reason: found typo in url
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