It's about automating the analysis of Sanger sequencing reads.
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:
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:
/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
sudo apt-get install staden-io-lib-utils
To install this module, run the following commands:
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:
Then enjoy CloneQC.
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