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Old 01-24-2014, 11:44 AM   #3
pag
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Location: CA, USA

Join Date: May 2012
Posts: 72
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My notes to get 8.1 to work within the SMRT analysis pipeline are on this forum. Obviously if running on command-line outside of SMRT analysis, you won't need all of these.

Here are the relevant bits:
#installing current version of wgs...
sudo mv $DOWNLOADPATH/wgs-8.1-Linux-amd64.tar.bz2 $SMRT_HOME/install/smrtanalysis-2.1.1.128549/analysis/bin
cd $SMRT_HOME/install/smrtanalysis-2.1.1.128549/analysis/bin
sudo tar xjf wgs-8.1-Linux-amd64.tar.bz2 #creates wgs-8.1 directory and fills it
mv wgs-7.0/ wgs-7.0.0 #or wgs.old
sudo ln -s wgs wgs-7.0 #points files that depend on wgs7.0 in the path to a generic "wgs" which will be the current version. hopefully pacbio will eventually switch all files to point to a generic/current wgs directory
sudo ln -s wgs-8.1/ wgs #points the generic to the most up-to-date
sudo chown -h smrtanalysis:smrtanalysis wgs* #changes links' ownership
sudo chown -R smrtanalysis:smrtanalysis wgs-8.1/
sudo chmod -R ug=rX,o-rwx wgs-8.1/
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