$ /usr/bin/RepeatMasker -species human -nolow blah.dna RepeatMasker version open-3.2.7 Search engine: Crossmatch Using Master Database: /usr/share/repeatmasker/Libraries/RepeatMaskerLib.embl Building general libraries in: /home/mmokrejs/.RepeatMaskerCache/20090120/general Building species libraries in: /home/mmokrejs/.RepeatMaskerCache/20090120/homo_sapiens analyzing file blah.dna Checking for E. coli insertion elements identifying full-length ALUs in batch 1 of 1 identifying full-length interspersed repeats in batch 1 of 1 identifying remaining ALUs in batch 1 of 1 identifying most interspersed repeats in batch 1 of 1 identifying long interspersed repeats in batch 1 of 1 identifying ancient repeats in batch 1 of 1 identifying retrovirus-like sequences in batch 1 of 1 identifying tough LINE1s in batch 1 of 1 refining SINE/Alu elements in batch 1 of 1 sh: /usr/share/repeatmasker/ProcessRepeats: No such file or directory $
# equery files repeatmasker * Searching for repeatmasker ... * Contents of sci-biology/repeatmasker-3.2.7: /usr /usr/bin /usr/bin/DateRepeats /usr/bin/DupMasker /usr/bin/ProcessRepeats ^^^^^^^^^ I guess in Gentoo REPEATMASKER_DIR is "/usr/share/repeatmasker/" and will never be "/usr/bin". I suspect you will have to create symlinks from the original place or let them be in the default place or patch the real perl code to use another variable for executables.
Thanks for pointing that out, Martin. Fix committed to main tree, please re-merge and test.
fixed, thanks.
