RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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modules not found at runtime when retroseq.pl aliased from its home path #13
My system finds retroseq.pl from an alias to its installation folder.
Due to this, module files were not found even when adding the RetroSeq sub-folder to PERL5LIB
I had to slightly change the lib declare to have the two .pm modules found.
# line 25 of the script
# use lib dirname(__FILE__).'/..';
use lib dirname(Cwd::abs_path(__FILE__)).'/..';
Maybe something to adapt for other users.
Now it works.
Thanks for the great tool
My system finds retroseq.pl from an alias to its installation folder. Due to this, module files were not found even when adding the RetroSeq sub-folder to PERL5LIB I had to slightly change the lib declare to have the two .pm modules found.
Maybe something to adapt for other users. Now it works. Thanks for the great tool