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10570c91c8
This patch brings EMBOSS up to date with the current version. i. The patches included in files/ are bugfixes for files in EMBOSS-3.0.0 that appeared after the release. They are documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README This is just 'for the record' so that we remember to remove these patches in the next update. ii. EMBOSS is now installed by default in LOCALBASE/emboss This is to avoid CONFLICTS with other ports that install files with the same names. Installing EMBOSS to another PREFIX is also possible. iii. now EMBASSY and EMBOSS both store their distfiles in the same DIST_SUBDIR iv. use built-in PKGMESSAGE and SUB_FILES instead of doing it the old (manual) way For EMBASSY: This update brings embassy in sync with the update of EMBOSS to 3.0.0. Things that changed from previous version of the port: i. embassy now installs by default in $LOCALBASE/emboss (the new default PREFIX for emboss as well). ii. changed DIST_SUBDIR so that all the distfiles are put together with emboss. This makes sense(TM) iii. incorporated new EMBASSY apps (this accounts for the changes in OPTIONS and pkg-plist) iv. removed obsoleted patches Finally, I included a sample text that could go in UPDATING. PR: 93053 Submitted by: Fernan Aguero <fernan (at) iib.unsam.edu.ar> (maintainer)
202 lines
7.5 KiB
Plaintext
202 lines
7.5 KiB
Plaintext
%%PLIST_DOMAINATRIX%%bin/cathparse
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%%PLIST_DOMAINATRIX%%bin/domainnr
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%%PLIST_DOMAINATRIX%%bin/domainreso
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%%PLIST_DOMAINATRIX%%bin/domainseqs
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%%PLIST_DOMAINATRIX%%bin/domainsse
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%%PLIST_DOMAINATRIX%%bin/scopparse
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%%PLIST_DOMAINATRIX%%bin/ssematch
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd
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%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd
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%%PLIST_DOMALIGN%%bin/allversusall
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%%PLIST_DOMALIGN%%bin/domainalign
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%%PLIST_DOMALIGN%%bin/domainrep
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%%PLIST_DOMALIGN%%bin/seqalign
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%%PLIST_DOMALIGN%%share/EMBOSS/acd/allversusall.acd
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%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainalign.acd
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%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainrep.acd
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%%PLIST_DOMALIGN%%share/EMBOSS/acd/seqalign.acd
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%%PLIST_DOMSEARCH%%bin/seqfraggle
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%%PLIST_DOMSEARCH%%bin/seqnr
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%%PLIST_DOMSEARCH%%bin/seqsearch
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%%PLIST_DOMSEARCH%%bin/seqsort
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%%PLIST_DOMSEARCH%%bin/seqwords
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%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd
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%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd
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%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd
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%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd
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%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd
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%%PLIST_EMNU%%bin/emnu
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%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
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%%PLIST_HMMER%%bin/ealistat
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%%PLIST_HMMER%%bin/ehmmalign
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%%PLIST_HMMER%%bin/ehmmbuild
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%%PLIST_HMMER%%bin/ehmmcalibrate
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%%PLIST_HMMER%%bin/ehmmconvert
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%%PLIST_HMMER%%bin/ehmmemit
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%%PLIST_HMMER%%bin/ehmmfetch
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%%PLIST_HMMER%%bin/ehmmindex
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%%PLIST_HMMER%%bin/ehmmpfam
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%%PLIST_HMMER%%bin/ehmmsearch
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%%PLIST_HMMER%%lib/libhmmer.a
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%%PLIST_HMMER%%lib/libhmmer.la
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%%PLIST_HMMER%%lib/libhmmer.so
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%%PLIST_HMMER%%lib/libhmmer.so.2
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%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
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%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
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%%PLIST_MEME%%bin/meme
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%%PLIST_MEME%%lib/libmeme.a
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%%PLIST_MEME%%lib/libmeme.la
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%%PLIST_MEME%%lib/libmeme.so
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%%PLIST_MEME%%lib/libmeme.so.2
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%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
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%%PLIST_MSE%%bin/mse
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%%PLIST_MSE%%lib/libckit.a
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%%PLIST_MSE%%lib/libckit.la
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%%PLIST_MSE%%lib/libckit.so
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%%PLIST_MSE%%lib/libckit.so.1
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%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
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%%PLIST_MYEMBOSS%%bin/myseq
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%%PLIST_MYEMBOSS%%bin/mytest
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%%PLIST_MYEMBOSS%%share/EMBOSS/acd/myseq.acd
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%%PLIST_MYEMBOSS%%share/EMBOSS/acd/mytest.acd
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%%PLIST_PHYLIP%%bin/fclique
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%%PLIST_PHYLIP%%bin/fconsense
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%%PLIST_PHYLIP%%bin/fcontml
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%%PLIST_PHYLIP%%bin/fcontrast
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%%PLIST_PHYLIP%%bin/fdiscboot
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%%PLIST_PHYLIP%%bin/fdnacomp
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%%PLIST_PHYLIP%%bin/fdnadist
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%%PLIST_PHYLIP%%bin/fdnainvar
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%%PLIST_PHYLIP%%bin/fdnaml
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%%PLIST_PHYLIP%%bin/fdnamlk
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%%PLIST_PHYLIP%%bin/fdnamove
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%%PLIST_PHYLIP%%bin/fdnapars
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%%PLIST_PHYLIP%%bin/fdnapenny
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%%PLIST_PHYLIP%%bin/fdollop
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%%PLIST_PHYLIP%%bin/fdolmove
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%%PLIST_PHYLIP%%bin/fdolpenny
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%%PLIST_PHYLIP%%bin/fdrawgram
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%%PLIST_PHYLIP%%bin/fdrawtree
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%%PLIST_PHYLIP%%bin/ffactor
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%%PLIST_PHYLIP%%bin/ffitch
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%%PLIST_PHYLIP%%bin/ffreqboot
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%%PLIST_PHYLIP%%bin/fgendist
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%%PLIST_PHYLIP%%bin/fkitsch
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%%PLIST_PHYLIP%%bin/fmix
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%%PLIST_PHYLIP%%bin/fmove
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%%PLIST_PHYLIP%%bin/fneighbor
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%%PLIST_PHYLIP%%bin/fpars
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%%PLIST_PHYLIP%%bin/fpenny
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%%PLIST_PHYLIP%%bin/fproml
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%%PLIST_PHYLIP%%bin/fpromlk
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%%PLIST_PHYLIP%%bin/fprotdist
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%%PLIST_PHYLIP%%bin/fprotpars
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%%PLIST_PHYLIP%%bin/frestboot
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%%PLIST_PHYLIP%%bin/frestdist
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%%PLIST_PHYLIP%%bin/frestml
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%%PLIST_PHYLIP%%bin/fretree
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%%PLIST_PHYLIP%%bin/fseqboot
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%%PLIST_PHYLIP%%bin/fseqbootall
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%%PLIST_PHYLIP%%bin/ftreedist
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%%PLIST_PHYLIP%%bin/ftreedistpair
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fclique.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fconsense.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontml.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontrast.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdiscboot.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnacomp.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnadist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnainvar.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnaml.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamlk.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamove.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapars.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapenny.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdollop.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolmove.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolpenny.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawgram.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawtree.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ffactor.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ffitch.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ffreqboot.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fgendist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fkitsch.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fmix.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fmove.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fneighbor.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fpars.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fpenny.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fproml.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fpromlk.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fprotdist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fprotpars.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/frestboot.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/frestdist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/frestml.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fretree.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fseqboot.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/fseqbootall.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedist.acd
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%%PLIST_PHYLIP%%share/EMBOSS/acd/ftreedistpair.acd
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%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font1
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%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font2
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%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font3
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%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font4
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%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font5
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%%PLIST_PHYLIP%%share/PHYLIP/data/phylipnew/font6
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%%PLIST_PHYLIP%%@dirrm share/PHYLIP/data/phylipnew
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%%PLIST_PHYLIP%%@dirrm share/PHYLIP/data
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%%PLIST_PHYLIP%%@dirrm share/PHYLIP
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%%PLIST_SIGNATURE%%bin/libgen
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%%PLIST_SIGNATURE%%bin/matgen3d
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%%PLIST_SIGNATURE%%bin/rocon
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%%PLIST_SIGNATURE%%bin/rocplot
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%%PLIST_SIGNATURE%%bin/siggen
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%%PLIST_SIGNATURE%%bin/siggenlig
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%%PLIST_SIGNATURE%%bin/sigscan
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%%PLIST_SIGNATURE%%bin/sigscanlig
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/libgen.acd
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/matgen3d.acd
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocon.acd
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocplot.acd
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggen.acd
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggenlig.acd
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscan.acd
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%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscanlig.acd
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%%PLIST_ESIM4%%bin/esim4
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%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd
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%%PLIST_STRUCTURE%%bin/contacts
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%%PLIST_STRUCTURE%%bin/domainer
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%%PLIST_STRUCTURE%%bin/hetparse
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%%PLIST_STRUCTURE%%bin/interface
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%%PLIST_STRUCTURE%%bin/pdbparse
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%%PLIST_STRUCTURE%%bin/pdbplus
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%%PLIST_STRUCTURE%%bin/pdbtosp
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%%PLIST_STRUCTURE%%bin/sites
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/contacts.acd
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/domainer.acd
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/hetparse.acd
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/interface.acd
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbparse.acd
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbplus.acd
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbtosp.acd
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%%PLIST_STRUCTURE%%share/EMBOSS/acd/sites.acd
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%%PLIST_TOPO%%bin/topo
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%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
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@dirrmtry share/EMBOSS/acd
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@dirrmtry share/EMBOSS
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