1. Sarah Richardson
  2. CloneQC_multi

Overview

Bio::CloneQC

ABOUT

It's about automating the analysis of Sanger sequencing reads.


PREREQUISITES

ON MAC:
Download the Staden macintosh .dmg from  http://sourceforge.net/projects/staden/files/staden/2.0.0b10/staden-2.0.0b10-MacOSX.dmg/download.
Open the image.
Copy the whole disk to /Applications/ as Staden/. That is, now you should have a bin and a lib folder under /Applications/Staden

Edit the staden.profile: open /Applications/Staden/share/staden/staden.profile and comment out line 46. NEVER SET A DYLD_LIBRARY_PATH, GUYS!
			#        export DYLD_LIBRARY_PATH


Add the following to your .bash_profile:
	STADENROOT=/Applications/Staden
	source $STADENROOT/share/staden/staden.profile

Run the otool on some executable in /Applications/Staden/bin to figure out which library its missing.
	otool -L /Applications/Staden/bin/convert_trace

Your output will look like this:
  /Applications/Staden/bin/convert_trace:
  /tmp/staden-2.0.0b10-MacOSX/lib/libstaden-read.1.dylib (compatibility version 6.0.0, current version 6.0.0)
  /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
  /usr/lib/libcurl.4.dylib (compatibility version 5.0.0, current version 5.0.0)
  /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5)
  /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1669.0.0)
  /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)

Obviously we are not keeping libraries in a /tmp/ directory. We will use the install name tool to redirect this mess.
	install_name_tool -change /tmp/staden-2.0.0b10-MacOSX/lib/libstaden-read.1.dylib /Applications/Staden/lib/libstaden-read.1.dylib /Applications/Staden/bin/convert_trace


ON LINUX:
sudo apt-get install staden-io-lib-utils



INSTALLATION

To install this module, run the following commands:

	perl Build.PL
	
Answer the following questions (may differ based on your system, [defaults]):

	Where should scripts be installed? [ /usr/local/bin ] 
	Where should CloneQC write tmp files? [ /tmp ] 

Then run the following:

	./Build
	./Build test
	./Build install

Then enjoy CloneQC.


COPYRIGHT AND LICENSE

Copyright (c) 2013, CloneQC developers
All rights reserved.

Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice, this
list of conditions and the following disclaimer in the documentation and/or
other materials provided with the distribution.

* The names of Johns Hopkins, the Joint Genome Institute, the Lawrence Berkeley
National Laboratory, the Department of Energy, and the GeneDesign developers may
not be used to endorse or promote products derived from this software without
specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.