Thursday, August 29, 2013

Update Stacks installation

Julian Catchen has written a very useful piece of software called Stacks for analysis of restriction site associated DNA (RAD) data. The stacksToVCF code that I recently wrote may have exposed a bug in how Stacks processes the CIGAR string from read alignments with indels, and I'm updating my Stacks installation to test a fix pushed out by Julian.

The following is only for updating, not for a fresh installation.

Note that you need to have Google's sparsehash and samtools' bam library and header available for these instructions. For this case, I compiled both sparsehash and samtools from source, and installed sparsehash via make install. Since I didn't do that for the bam header and library, I have to specify them below.
#Get the most recent version (1.06 in this case):
wget http://creskolab.uoregon.edu/stacks/source/stacks-1.06.tar.gz

#Unarchive and decompress the .tar.gz:
tar -zxvf stacks-1.06.tar.gz

#Move to the directory and configure:
cd stacks-1.06
./configure --enable-sparsehash --enable-bam \
--with-bam-include-path=/path/to/directory/with/samtools_bam.h \
--with-bam-lib-path=/path/to/directory/with/samtools_bam.o

#make
make

#install
sudo make install
Then you need to reconfigure the stacks_export_notify.pl file to be able to send email:
sudo vim /usr/local/bin/stacks_export_notify.pl
And modify the configurations to suit your system. For my case, it's just modifying the url variable to point to my server. All other settings can be left as they are. You can test that this was successful by invoking the version option for any of the component programs:
$ ref_map.pl -v
ref_map.pl 1.06

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