diff -ruN --exclude CVS /usr/ports/biology/embassy/Makefile embassy/Makefile --- /usr/ports/biology/embassy/Makefile Mon Mar 24 11:54:11 2008 +++ embassy/Makefile Fri Aug 17 12:09:48 2007 @@ -3,23 +3,20 @@ # Date created: 1.November.2004 # Whom: Fernan Aguero # -# $FreeBSD: ports/biology/embassy/Makefile,v 1.9 2008/03/23 16:44:05 miwi Exp $ +# $FreeBSD: ports/biology/embassy/Makefile,v 1.6 2006/03/31 09:43:21 thierry Exp $ # PORTNAME= embassy -PORTVERSION= 3.0.0 -PORTREVISION= 2 +PORTVERSION= 5.0.0 CATEGORIES= biology MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ \ - ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ - ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/ DIST_SUBDIR= emboss MAINTAINER= fernan@iib.unsam.edu.ar COMMENT= A collection of contributed EMBOSS applications -LIB_DEPENDS= nucleus.3:${PORTSDIR}/biology/emboss +LIB_DEPENDS= nucleus.5:${PORTSDIR}/biology/emboss PREFIX?= ${LOCALBASE}/emboss NO_MTREE= yes @@ -27,7 +24,9 @@ USE_ICONV= yes USE_GMAKE= yes GNU_CONFIGURE= yes +USE_XLIB= yes USE_MOTIF= yes +USE_LDCONFIG= yes OPTIONS= DOMAINATRIX "Protein domain apps" on \ DOMALIGN "Protein domain apps" on \ @@ -41,7 +40,8 @@ MSE "A multiple sequence screen editor" on \ MYEMBOSS "Examples for developers of EMBOSS apps" on \ PHYLIP "Phylogeny inference" on \ - TOPO "Transmembrane display" on + TOPO "Transmembrane display" on \ + VIENNA "RNA folding" on CONFIGURE_ENV+= CPPFLAGS="-I${PREFIX}/include -I${LOCALBASE}/include" \ LDFLAGS="-L${PREFIX}/lib -L${LOCALBASE}/lib" @@ -50,8 +50,8 @@ DOMAINATRIX_VERSION= 0.1.0 EMNU_VERSION= 1.05 ESIM4_VERSION= 1.0.0 -HMMER_VERSION= 2.1.1 -MEME_VERSION= 2.3.1 +HMMER_VERSION= 2.3.2 +MEME_VERSION= 0.1.0 MSE_VERSION= 1.0.0 TOPO_VERSION= 1.0.0 PHYLIP_VERSION= 3.6b @@ -60,8 +60,10 @@ SIGNATURE_VERSION= 0.1.0 STRUCTURE_VERSION= 0.1.0 MYEMBOSS_VERSION= 3.0.0 -EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP TOPO \ - DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS +VIENNA_VERSION= 1.6 +EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEME MSE PHYLIP \ + TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \ + VIENNA .include @@ -88,9 +90,6 @@ ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \ fi .endfor - -post-patch: - @${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|' do-configure: .for app in ${APPLIST} diff -ruN --exclude CVS /usr/ports/biology/embassy/distinfo embassy/distinfo --- /usr/ports/biology/embassy/distinfo Fri Mar 31 06:43:21 2006 +++ embassy/distinfo Fri Aug 17 12:59:16 2007 @@ -1,39 +1,42 @@ -MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 655f6ec58e0b9dfdac111fd9481359cb -SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 6bc374c5275dead68ef09d8273bf4d73a03bc56990e795d6eddcee4de25c12a0 -SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 349882 -MD5 (emboss/EMNU-1.05.tar.gz) = b3a7fc11e46f7166ddeec11f2fe03d9b -SHA256 (emboss/EMNU-1.05.tar.gz) = d7261d615d6547a9824d3d9e3f82ff756c0db5786e8356bc54cc5fa0c516b26f -SIZE (emboss/EMNU-1.05.tar.gz) = 348924 -MD5 (emboss/ESIM4-1.0.0.tar.gz) = 835393b3246eb4543a694362c6f335ff -SHA256 (emboss/ESIM4-1.0.0.tar.gz) = f8241c9e37ccc17dbd29df2d9c90063ba7caf4e64cc5c368b6878c3aa3895620 -SIZE (emboss/ESIM4-1.0.0.tar.gz) = 384396 -MD5 (emboss/HMMER-2.1.1.tar.gz) = 382594654e45a7e8d5872b4b1016a494 -SHA256 (emboss/HMMER-2.1.1.tar.gz) = 78647dfb7841e8b52b4c3de34400c68d17a877b698956ac9a5ee5e030569cca6 -SIZE (emboss/HMMER-2.1.1.tar.gz) = 561289 -MD5 (emboss/MEME-2.3.1.tar.gz) = 6f4e516e413582268a34e91fb12e21c3 -SHA256 (emboss/MEME-2.3.1.tar.gz) = bec2c8002b8b551ef9c639bcb58633499060cd8a1bfe4754db5ed201a6a0dffa -SIZE (emboss/MEME-2.3.1.tar.gz) = 423966 -MD5 (emboss/MSE-1.0.0.tar.gz) = 3b9810e870937ec32220b5c9fe7a83cd -SHA256 (emboss/MSE-1.0.0.tar.gz) = ddf9092721666d64c56733d9b6d04e749957848cafa8ba4ec6eee083a0ffcab3 -SIZE (emboss/MSE-1.0.0.tar.gz) = 415051 -MD5 (emboss/PHYLIP-3.6b.tar.gz) = 6f2c10438d788acf4a1dff23441b2a2c -SHA256 (emboss/PHYLIP-3.6b.tar.gz) = 32aba94d0be011ee304e974657db11544297c008e53341cd000a1f412eb874e2 -SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1136746 -MD5 (emboss/TOPO-1.0.0.tar.gz) = 7b3355570ba36f7daf57dcbc717215ce -SHA256 (emboss/TOPO-1.0.0.tar.gz) = ff10378b4ecad69ddb374cd47a7d3c7fa5975d6695057f05ea264940258ebaa3 -SIZE (emboss/TOPO-1.0.0.tar.gz) = 351796 -MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = 4332d7de49b27f257b58a90510223eb7 -SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = de66ddfdb72ccf7291be614c9a83fd8fc47363191cb2c045b372de5cc334a594 -SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 347672 -MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = c62f9b69a9ed9580d4489a8de9ea4863 -SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = f4933b62e19ee6b23a78b70c3cf2d5a9a18eff1d7532f92e2d33b1d683877916 -SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 352793 -MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 1e30e12048609a468b7b4d4affb177cf -SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = c6bb252beaccac5256d99301933b15da6ef90af3f20d7f92fed1f78b271785ee -SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 400125 -MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6efc35eb2855738252e0537198f5225d -SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 7142e207987da46cd85c81088ea475abb866da90ff57e4c3ca1c63bd8f209b64 -SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 362563 -MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 15d5bc7b0ce9dfb113777c06c4e18906 -SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = 0a19ebbe52da849fb87799edaea2281a1bf235e6045725789b9b29e58f0a0dc5 -SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 323628 +MD5 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 0be3c59550e1e22924ea2540b11af275 +SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = b81fde3ab329ab75482b341568ef2965d99803765438f3825688a0d2abc05ca6 +SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 420051 +MD5 (emboss/EMNU-1.05.tar.gz) = 64d8b9c2cd1a566aebb3355eb684bd35 +SHA256 (emboss/EMNU-1.05.tar.gz) = 56a55f336b0083ecfd2fd2dae0613f46e802eacb3214c16fc1966e6516795b95 +SIZE (emboss/EMNU-1.05.tar.gz) = 389665 +MD5 (emboss/ESIM4-1.0.0.tar.gz) = ee65d0da0f2d75959f370b13f2218c1c +SHA256 (emboss/ESIM4-1.0.0.tar.gz) = eee1cc8fef40e19fab74b16f1c1cb0883a49561eb9fdc2075f428085c6722bda +SIZE (emboss/ESIM4-1.0.0.tar.gz) = 431329 +MD5 (emboss/HMMER-2.3.2.tar.gz) = 3aa5707db81854f2674bf27aaeb1362e +SHA256 (emboss/HMMER-2.3.2.tar.gz) = 31bbcca1f71b82170a65c4438f9cb9f1dfe3d4e066037a852060b010e3e39b5b +SIZE (emboss/HMMER-2.3.2.tar.gz) = 565223 +MD5 (emboss/MEME-0.1.0.tar.gz) = d304f3b8a8e15af4dfa7b295655d80ec +SHA256 (emboss/MEME-0.1.0.tar.gz) = ed4c02010af036515203661c28776b5e773e77eccad59990b7ac1410399d45ef +SIZE (emboss/MEME-0.1.0.tar.gz) = 448413 +MD5 (emboss/MSE-1.0.0.tar.gz) = 3978a06e3651104f622a5834523c45de +SHA256 (emboss/MSE-1.0.0.tar.gz) = e35560310ece8bb2dec7eeb88e99f39f313bf7366afc445e3b074b687e7f36b2 +SIZE (emboss/MSE-1.0.0.tar.gz) = 445013 +MD5 (emboss/PHYLIP-3.6b.tar.gz) = 760a90bea49872aba95fd7dd2b67570c +SHA256 (emboss/PHYLIP-3.6b.tar.gz) = c2397937f4b827844192a33b31f13271a3560c81045543d912a9c28eb6ad894f +SIZE (emboss/PHYLIP-3.6b.tar.gz) = 1594433 +MD5 (emboss/TOPO-1.0.0.tar.gz) = d45602a1b1f22da50a775c41df5fe672 +SHA256 (emboss/TOPO-1.0.0.tar.gz) = ed1921e92d1bbd9fcc16ab36f2fcbafca9e60cc0d4b4fd1da77660ffd3e7b2f2 +SIZE (emboss/TOPO-1.0.0.tar.gz) = 379381 +MD5 (emboss/DOMALIGN-0.1.0.tar.gz) = e5d004c1223116abaebb6657ae4a80fa +SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = aa61cfc6da3cc478dd7f476537cdc6d966b00b90e2adedc709eb75e39e840c5c +SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 460530 +MD5 (emboss/DOMSEARCH-0.1.0.tar.gz) = 778ab15bce09a6440fc6859b3a27157d +SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = 23e069161ec56df5eab5fc491ca3493c056cfee42f2e05f1b5ef258498792a87 +SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 469776 +MD5 (emboss/SIGNATURE-0.1.0.tar.gz) = 26deae308cc5aac3dee5dd03df2ae9e8 +SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = 9b0529befdbe5d56b3370cfffe0a4b4cc523f350b50ddd4a61dd24776a1770e8 +SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 573992 +MD5 (emboss/STRUCTURE-0.1.0.tar.gz) = 6736b4741b15d4cba488a5422fcfaee1 +SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = 3ed8ea5373232cd80302ff3b8727838b4de2f6b39aa263ab9530bbbe71d730c1 +SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 530874 +MD5 (emboss/MYEMBOSS-3.0.0.tar.gz) = 9c3d6ea80166f62cd6ee63dfcb7e57a4 +SHA256 (emboss/MYEMBOSS-3.0.0.tar.gz) = dc21b1772c2d76ed1c717eba6f8443b86cdf2e3cbcf71e056cdb9723138e4440 +SIZE (emboss/MYEMBOSS-3.0.0.tar.gz) = 354179 +MD5 (emboss/VIENNA-1.6.tar.gz) = 282ed7ac9c1741160fcb1e8d48539311 +SHA256 (emboss/VIENNA-1.6.tar.gz) = 04c4a57486e23c2cc8ef396d9012c396519b2ab1b13b2500199e6457a34cfa58 +SIZE (emboss/VIENNA-1.6.tar.gz) = 635638 diff -ruN --exclude CVS /usr/ports/biology/embassy/pkg-plist embassy/pkg-plist --- /usr/ports/biology/embassy/pkg-plist Fri Mar 31 06:43:21 2006 +++ embassy/pkg-plist Wed Apr 2 13:10:24 2008 @@ -1,201 +1,441 @@ -%%PLIST_DOMAINATRIX%%bin/cathparse -%%PLIST_DOMAINATRIX%%bin/domainnr -%%PLIST_DOMAINATRIX%%bin/domainreso -%%PLIST_DOMAINATRIX%%bin/domainseqs -%%PLIST_DOMAINATRIX%%bin/domainsse -%%PLIST_DOMAINATRIX%%bin/scopparse -%%PLIST_DOMAINATRIX%%bin/ssematch -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/cathparse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainnr.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainreso.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainseqs.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/domainsse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/scopparse.acd -%%PLIST_DOMAINATRIX%%share/EMBOSS/acd/ssematch.acd -%%PLIST_DOMALIGN%%bin/allversusall -%%PLIST_DOMALIGN%%bin/domainalign -%%PLIST_DOMALIGN%%bin/domainrep -%%PLIST_DOMALIGN%%bin/seqalign -%%PLIST_DOMALIGN%%share/EMBOSS/acd/allversusall.acd -%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainalign.acd -%%PLIST_DOMALIGN%%share/EMBOSS/acd/domainrep.acd -%%PLIST_DOMALIGN%%share/EMBOSS/acd/seqalign.acd -%%PLIST_DOMSEARCH%%bin/seqfraggle -%%PLIST_DOMSEARCH%%bin/seqnr -%%PLIST_DOMSEARCH%%bin/seqsearch -%%PLIST_DOMSEARCH%%bin/seqsort -%%PLIST_DOMSEARCH%%bin/seqwords -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd -%%PLIST_EMNU%%bin/emnu -%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd -%%PLIST_HMMER%%bin/ealistat -%%PLIST_HMMER%%bin/ehmmalign -%%PLIST_HMMER%%bin/ehmmbuild -%%PLIST_HMMER%%bin/ehmmcalibrate -%%PLIST_HMMER%%bin/ehmmconvert -%%PLIST_HMMER%%bin/ehmmemit -%%PLIST_HMMER%%bin/ehmmfetch -%%PLIST_HMMER%%bin/ehmmindex -%%PLIST_HMMER%%bin/ehmmpfam -%%PLIST_HMMER%%bin/ehmmsearch -%%PLIST_HMMER%%lib/libhmmer.a -%%PLIST_HMMER%%lib/libhmmer.la -%%PLIST_HMMER%%lib/libhmmer.so -%%PLIST_HMMER%%lib/libhmmer.so.2 -%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd -%%PLIST_MEME%%bin/meme -%%PLIST_MEME%%lib/libmeme.a -%%PLIST_MEME%%lib/libmeme.la -%%PLIST_MEME%%lib/libmeme.so -%%PLIST_MEME%%lib/libmeme.so.2 -%%PLIST_MEME%%share/EMBOSS/acd/meme.acd -%%PLIST_MSE%%bin/mse -%%PLIST_MSE%%lib/libckit.a -%%PLIST_MSE%%lib/libckit.la -%%PLIST_MSE%%lib/libckit.so -%%PLIST_MSE%%lib/libckit.so.1 -%%PLIST_MSE%%share/EMBOSS/acd/mse.acd -%%PLIST_MYEMBOSS%%bin/myseq -%%PLIST_MYEMBOSS%%bin/mytest -%%PLIST_MYEMBOSS%%share/EMBOSS/acd/myseq.acd -%%PLIST_MYEMBOSS%%share/EMBOSS/acd/mytest.acd -%%PLIST_PHYLIP%%bin/fclique -%%PLIST_PHYLIP%%bin/fconsense -%%PLIST_PHYLIP%%bin/fcontml -%%PLIST_PHYLIP%%bin/fcontrast -%%PLIST_PHYLIP%%bin/fdiscboot -%%PLIST_PHYLIP%%bin/fdnacomp -%%PLIST_PHYLIP%%bin/fdnadist -%%PLIST_PHYLIP%%bin/fdnainvar -%%PLIST_PHYLIP%%bin/fdnaml -%%PLIST_PHYLIP%%bin/fdnamlk -%%PLIST_PHYLIP%%bin/fdnamove -%%PLIST_PHYLIP%%bin/fdnapars -%%PLIST_PHYLIP%%bin/fdnapenny -%%PLIST_PHYLIP%%bin/fdollop -%%PLIST_PHYLIP%%bin/fdolmove -%%PLIST_PHYLIP%%bin/fdolpenny -%%PLIST_PHYLIP%%bin/fdrawgram -%%PLIST_PHYLIP%%bin/fdrawtree -%%PLIST_PHYLIP%%bin/ffactor -%%PLIST_PHYLIP%%bin/ffitch -%%PLIST_PHYLIP%%bin/ffreqboot -%%PLIST_PHYLIP%%bin/fgendist -%%PLIST_PHYLIP%%bin/fkitsch -%%PLIST_PHYLIP%%bin/fmix -%%PLIST_PHYLIP%%bin/fmove -%%PLIST_PHYLIP%%bin/fneighbor -%%PLIST_PHYLIP%%bin/fpars -%%PLIST_PHYLIP%%bin/fpenny -%%PLIST_PHYLIP%%bin/fproml -%%PLIST_PHYLIP%%bin/fpromlk -%%PLIST_PHYLIP%%bin/fprotdist -%%PLIST_PHYLIP%%bin/fprotpars -%%PLIST_PHYLIP%%bin/frestboot -%%PLIST_PHYLIP%%bin/frestdist -%%PLIST_PHYLIP%%bin/frestml -%%PLIST_PHYLIP%%bin/fretree -%%PLIST_PHYLIP%%bin/fseqboot -%%PLIST_PHYLIP%%bin/fseqbootall -%%PLIST_PHYLIP%%bin/ftreedist -%%PLIST_PHYLIP%%bin/ftreedistpair -%%PLIST_PHYLIP%%share/EMBOSS/acd/fclique.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fconsense.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontml.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fcontrast.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdiscboot.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnacomp.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnadist.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnainvar.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnaml.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamlk.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnamove.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapars.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdnapenny.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdollop.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolmove.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdolpenny.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawgram.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fdrawtree.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ffactor.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ffitch.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/ffreqboot.acd -%%PLIST_PHYLIP%%share/EMBOSS/acd/fgendist.acd 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