Index: head/biology/fasta3/Makefile =================================================================== --- head/biology/fasta3/Makefile (revision 385591) +++ head/biology/fasta3/Makefile (revision 385592) @@ -1,76 +1,76 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= fasta3 -PORTVERSION= 36.3.6d -PORTREVISION= 1 +PORTVERSION= 36.3.7a CATEGORIES= biology MASTER_SITES= http://faculty.virginia.edu/wrpearson/fasta/fasta36/ DISTNAME= fasta-${PORTVERSION} DIST_SUBDIR= fasta3/2014-01-29 MAINTAINER= ports@FreeBSD.org COMMENT= Collection of programs for searching DNA and protein databases LICENSE= Fasta LICENSE_NAME= Fasta program copyright W. Pearson and U.Virginia LICENSE_FILE= ${WRKSRC}/COPYRIGHT LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept OPTIONS_DEFINE= DOCS EXAMPLES NO_CDROM= May not be sold or incorporated into a commercial product WRKSRC= ${WRKDIR}/${DISTNAME} BUILD_WRKSRC= ${WRKSRC}/src INSTALL_WRKSRC= ${BUILD_WRKSRC} MAKEFILE= Makefile.freebsd MAKE_ENV= THR_LIBS="-pthread" XDIR="${STAGEDIR}${PREFIX}/bin" \ FASTA_HOST="$$(${UNAME} -n)" SUB_FILES= pkg-message PLIST_SUB= VER="${PORTVERSION:R:R}" MAN1_LINKS= fastf35.1 fasts35.1 fastm35.1 fastx35.1 fasty35.1 \ ggsearch35.1 lalign35.1 ssearch35.1 tfasta35.1 tfastf35.1 \ tfasts35.1 tfastx35.1 tfasty35.1 prfx35.1 prss35.1 MAN1_FILES= fasta36.1 fastf3.1 fasts3.1 prss3.1 map_db.1 ps_lav.1 DOC_FILES= README.versions \ fasta_func.doc readme.* fasta.defaults \ fasta.options fasta_versions.html changes*.html DATA= data/*.mat EXAMPLES= seq/*.aa seq/*.lc seq/*.seq seq/*.lib post-patch: @${CP} ${WRKSRC}/make/${MAKEFILE} ${BUILD_WRKSRC} + @${RM} ${WRKSRC}/bin/README post-install: (cd ${WRKSRC}/bin && ${INSTALL_PROGRAM} * ${STAGEDIR}${PREFIX}/bin) (cd ${WRKSRC}/conf && ${INSTALL_DATA} fastlibs \ ${STAGEDIR}${PREFIX}/etc/fastlibs.sample) @${MKDIR} ${STAGEDIR}${DATADIR} .for data in ${DATA} (cd ${WRKSRC} && ${INSTALL_DATA} ${data} ${STAGEDIR}${DATADIR}) .endfor .for manpage in ${MAN1_FILES} (cd ${WRKSRC}/doc && ${INSTALL_MAN} ${manpage} \ ${STAGEDIR}${MAN1PREFIX}/man/man1) .endfor .for links in ${MAN1_LINKS} (${LN} -sf fasta36.1 ${STAGEDIR}${MAN1PREFIX}/man/man1/${links}) .endfor @${MKDIR} ${STAGEDIR}${DOCSDIR} .for i in COPYRIGHT FASTA_LIST README (cd ${WRKSRC} && ${INSTALL_DATA} ${i} ${STAGEDIR}${DOCSDIR}) .endfor .for docfile in ${DOC_FILES} (cd ${WRKSRC}/doc && ${INSTALL_DATA} ${docfile} ${STAGEDIR}${DOCSDIR}) .endfor @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} .for ex in ${EXAMPLES} (cd ${WRKSRC} && ${INSTALL_DATA} ${ex} ${STAGEDIR}${EXAMPLESDIR}) .endfor .include Index: head/biology/fasta3/distinfo =================================================================== --- head/biology/fasta3/distinfo (revision 385591) +++ head/biology/fasta3/distinfo (revision 385592) @@ -1,2 +1,2 @@ -SHA256 (fasta3/2014-01-29/fasta-36.3.6d.tar.gz) = cab2f530c8d0ebb59ac5e82580d56da14c4c86fcf0a76edb72eeb18c42a79eb6 -SIZE (fasta3/2014-01-29/fasta-36.3.6d.tar.gz) = 969973 +SHA256 (fasta3/2014-01-29/fasta-36.3.7a.tar.gz) = 69d1b8017bb3e4225552686709016405e8f78a3fdf836522c4e57c726f2af87b +SIZE (fasta3/2014-01-29/fasta-36.3.7a.tar.gz) = 1161409 Index: head/biology/fasta3/pkg-plist =================================================================== --- head/biology/fasta3/pkg-plist (revision 385591) +++ head/biology/fasta3/pkg-plist (revision 385592) @@ -1,120 +1,125 @@ bin/fasta%%VER%% bin/fastf%%VER%% bin/fastm%%VER%% bin/fasts%%VER%% bin/fastx%%VER%% bin/fasty%%VER%% bin/ggsearch%%VER%% bin/glsearch%%VER%% bin/lalign%%VER%% -bin/lav2ps -bin/lav2svg bin/map_db bin/ssearch%%VER%% bin/tfastf%%VER%% bin/tfastm%%VER%% bin/tfasts%%VER%% bin/tfastx%%VER%% bin/tfasty%%VER%% etc/fastlibs.sample man/man1/fasta36.1.gz man/man1/fastf3.1.gz man/man1/fastf35.1.gz man/man1/fastm35.1.gz man/man1/fasts3.1.gz man/man1/fasts35.1.gz man/man1/fastx35.1.gz man/man1/fasty35.1.gz man/man1/ggsearch35.1.gz man/man1/lalign35.1.gz man/man1/map_db.1.gz man/man1/prfx35.1.gz man/man1/prss3.1.gz man/man1/prss35.1.gz man/man1/ps_lav.1.gz man/man1/ssearch35.1.gz man/man1/tfasta35.1.gz man/man1/tfastf35.1.gz man/man1/tfasts35.1.gz man/man1/tfastx35.1.gz man/man1/tfasty35.1.gz %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT %%PORTDOCS%%%%DOCSDIR%%/FASTA_LIST %%PORTDOCS%%%%DOCSDIR%%/README %%PORTDOCS%%%%DOCSDIR%%/README.versions %%PORTDOCS%%%%DOCSDIR%%/changes_v34.html %%PORTDOCS%%%%DOCSDIR%%/changes_v35.html %%PORTDOCS%%%%DOCSDIR%%/changes_v36.html %%PORTDOCS%%%%DOCSDIR%%/fasta.defaults %%PORTDOCS%%%%DOCSDIR%%/fasta.options %%PORTDOCS%%%%DOCSDIR%%/fasta_func.doc %%PORTDOCS%%%%DOCSDIR%%/fasta_versions.html %%PORTDOCS%%%%DOCSDIR%%/readme.v30 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t6 %%PORTDOCS%%%%DOCSDIR%%/readme.v30t7 %%PORTDOCS%%%%DOCSDIR%%/readme.v31t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v31t1 %%PORTDOCS%%%%DOCSDIR%%/readme.v32t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v33t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v34t0 %%PORTDOCS%%%%DOCSDIR%%/readme.v35 %%PORTDOCS%%%%DOCSDIR%%/readme.v36 %%PORTDOCS%%%%DOCSDIR%%/readme.w32 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovgh.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/bovprl.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dyr_human.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/egmsmg.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/gst.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/gstt1_drome.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtm1_human.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/gtt1_drome.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/h10_human.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/hahu.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/hsgstm1b.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/humgstd.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lcbo.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/m1r.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/m2.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mchu.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.lc %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgstm1_genclone.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgtt2_x.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ms1.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mu.lib %%PORTEXAMPLES%%%%EXAMPLESDIR%%/musplfm.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwkw.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mwrtc1.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/myosin_bp.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/n0.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/n1.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2_fs.lib %%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2s.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/n2t.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/n_fs.lib %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngt.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ngts.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/oohu.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/prio_atepa.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/prot_test.lib %%PORTEXAMPLES%%%%EXAMPLESDIR%%/qrhuld.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/titin_hum.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.aa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurt8c.lc %%PORTEXAMPLES%%%%EXAMPLESDIR%%/xurtg.aa %%DATADIR%%/blosum45.mat %%DATADIR%%/blosum50.mat %%DATADIR%%/blosum62.mat %%DATADIR%%/blosum80.mat %%DATADIR%%/dna.mat %%DATADIR%%/idn_aa.mat %%DATADIR%%/md_10.mat %%DATADIR%%/md_20.mat %%DATADIR%%/md_40.mat %%DATADIR%%/pam120.mat %%DATADIR%%/pam250.mat %%DATADIR%%/rna.mat %%DATADIR%%/vtml160.mat +%%DATADIR%%/VTML_10.mat +%%DATADIR%%/VTML_120.mat +%%DATADIR%%/VTML_160.mat +%%DATADIR%%/VTML_20.mat +%%DATADIR%%/VTML_200.mat +%%DATADIR%%/VTML_40.mat +%%DATADIR%%/VTML_80.mat