diff options
author | Baptiste Daroussin <bapt@FreeBSD.org> | 2014-09-01 11:37:14 +0000 |
---|---|---|
committer | Baptiste Daroussin <bapt@FreeBSD.org> | 2014-09-01 11:37:14 +0000 |
commit | a76b6b5c50aa5c419d596103d4340492d94f09c3 (patch) | |
tree | 9b7b27b9d470ff8bf9122de83a9fa8e69dda28eb /biology | |
parent | Remove *.la files (diff) |
Remove non staged ports without pending PR from b*
Notes
Notes:
svn path=/head/; revision=366862
Diffstat (limited to 'biology')
-rw-r--r-- | biology/Makefile | 3 | ||||
-rw-r--r-- | biology/blast/Makefile | 77 | ||||
-rw-r--r-- | biology/blast/distinfo | 2 | ||||
-rw-r--r-- | biology/blast/files/pkg-message.in | 15 | ||||
-rw-r--r-- | biology/blast/pkg-descr | 18 | ||||
-rw-r--r-- | biology/blast/pkg-plist | 219 | ||||
-rw-r--r-- | biology/embassy/Makefile | 131 | ||||
-rw-r--r-- | biology/embassy/distinfo | 34 | ||||
-rw-r--r-- | biology/embassy/pkg-descr | 14 | ||||
-rw-r--r-- | biology/embassy/pkg-plist | 515 | ||||
-rw-r--r-- | biology/pymol/Makefile | 49 | ||||
-rw-r--r-- | biology/pymol/distinfo | 2 | ||||
-rw-r--r-- | biology/pymol/files/patch-setup.py | 31 | ||||
-rw-r--r-- | biology/pymol/pkg-descr | 9 | ||||
-rw-r--r-- | biology/pymol/pkg-plist | 854 |
15 files changed, 0 insertions, 1973 deletions
diff --git a/biology/Makefile b/biology/Makefile index 458c72813d4e..14f7b8a61350 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -9,14 +9,12 @@ SUBDIR += babel SUBDIR += biococoa SUBDIR += biojava - SUBDIR += blast SUBDIR += blat SUBDIR += boinc-simap SUBDIR += chemeq SUBDIR += clustalw SUBDIR += consed SUBDIR += crux - SUBDIR += embassy SUBDIR += emboss SUBDIR += fasta SUBDIR += fasta3 @@ -74,7 +72,6 @@ SUBDIR += py-biopython SUBDIR += pycogent SUBDIR += pyfasta - SUBDIR += pymol SUBDIR += python-nexus SUBDIR += recombine SUBDIR += ruby-bio diff --git a/biology/blast/Makefile b/biology/blast/Makefile deleted file mode 100644 index 30fc47cd1ca3..000000000000 --- a/biology/blast/Makefile +++ /dev/null @@ -1,77 +0,0 @@ -# Created by: Fernan Aguero <fernan@iib.unsam.edu.ar> -# $FreeBSD$ - -PORTNAME= wu-blast -PORTVERSION= 2.0 -PORTREVISION= 20060322 # YYYYMMDD -CATEGORIES= biology -MASTER_SITES= # -EXTRACT_SUFX= .tar.Z - -MAINTAINER= ports@FreeBSD.org -COMMENT= WU BLAST, a software package for sequence similarity searches - -BROKEN= Mark as broken: no checksum provided - -DEPRECATED= Rights to BLAST 2.0 (WU-BLAST) have been acquired by Advanced Biocomputing, LLC -EXPIRATION_DATE=2014-09-04 - -RESTRICTED= License does not allow redistribution of binaries. You should first register for the software, which is free for academic use. -ONLY_FOR_ARCHS= i386 amd64 - -NO_BUILD= yes -DOWNLOAD_URL= http://blast.wustl.edu/licensing - -NO_WRKSUBDIR= yes - -PORTDOCS= COPYRIGHT FAQ-Indexing.html HISTORY LICENSE Memory.html \ - README.html parameters.html tabular.html -BINS= blasta gb2fasta gt2fasta memfile nrdb pam patdb \ - pir2fasta sp2fasta xdformat xdget -SCRIPTS= wu-blastall wu-formatdb -BLASTA_LINKS= blastn blastp blastx tblastn tblastx -XDFORMAT_LINKS= setdb pressdb -SUB_FILES= pkg-message - -NO_STAGE= yes -.include <bsd.port.pre.mk> - -.if ${ARCH} == amd64 -DISTNAME= blast${PORTVERSION:S/.0//}.freebsd-6.x-x64 -.else -DISTNAME= blast${PORTVERSION:S/.0//}.freebsd-6.x-i686 -.endif - -.if !exists(${DISTDIR}/${DISTNAME}${EXTRACT_SUFX}) -IGNORE= You must manually fetch ${PORTNAME}${PORTVERSION:S/.0//} for the FreeBSD platform (${DISTNAME}${EXTRACT_SUFX}) from ${DOWNLOAD_URL}, place it in ${DISTDIR} and then run make again -.endif - -do-install: -.for bin in ${BINS} - ${INSTALL_PROGRAM} ${WRKSRC}/${bin} ${PREFIX}/bin -.endfor -.for script in ${SCRIPTS} - ${INSTALL_SCRIPT} ${WRKSRC}/${script} ${PREFIX}/bin -.endfor - ${CHMOD} a-rw,a+x ${PREFIX}/bin/blasta -.for blink in ${BLASTA_LINKS} - @(cd ${PREFIX}/bin && ${LN} -s blasta ${blink}) -.endfor -.for xlink in ${XDFORMAT_LINKS} - @(cd ${PREFIX}/bin && ${LN} -s xdformat ${xlink}) -.endfor -.if ${PORT_OPTIONS:MDOCS} - @${MKDIR} ${DOCSDIR} -.for doc in ${PORTDOCS} - ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} -.endfor -.endif - ${MKDIR} ${DATADIR} - ${CP} -R ${WRKSRC}/matrix ${DATADIR} - ${CP} -R ${WRKSRC}/filter ${DATADIR} - ${CP} ${WRKSRC}/sysblast.sample ${DATADIR} - -post-install: - @${CAT} ${PKGMESSAGE} - -.include <bsd.port.post.mk> diff --git a/biology/blast/distinfo b/biology/blast/distinfo deleted file mode 100644 index 6d040eaf212e..000000000000 --- a/biology/blast/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (blast2.freebsd-6.x-i686.tar.Z) = IGNORE -SHA256 (blast2.freebsd-6.x-x64.tar.Z) = IGNORE diff --git a/biology/blast/files/pkg-message.in b/biology/blast/files/pkg-message.in deleted file mode 100644 index c2fa0c29be37..000000000000 --- a/biology/blast/files/pkg-message.in +++ /dev/null @@ -1,15 +0,0 @@ -====================================================================== - -A sample configuration file has been installed in %%DATADIR%% and named -sysblast.sample. Edit it to suit your needs, rename it to 'sysblast' and -place it under /etc so that it can be recognized at runtime by the blast -executable. - -Matrix files and filter executables have been placed in -%%DATADIR%%/matrix and %%DATADIR%%/filter, respectively. -You should set environment variables WUBLASTMAT and WUBLASTFILTER -(pointing to the respective directories) so that the blast executable -can find them. - -====================================================================== - diff --git a/biology/blast/pkg-descr b/biology/blast/pkg-descr deleted file mode 100644 index 902e6fbcb5be..000000000000 --- a/biology/blast/pkg-descr +++ /dev/null @@ -1,18 +0,0 @@ -Washington University BLAST (WU BLAST) version 2.0 is a powerful -software package for gene and protein identification, using sensitive, -selective and rapid similarity searches of protein and nucleotide -sequence databases. WU BLAST 2.0 builds upon WU BLAST 1.4, which in turn -was based on the public domain NCBI BLAST version 1.4. While NCBI BLAST -and WU BLAST 1.4 are in the public domain, WU BLAST 2.0 contains -significant new features and extended capabilities, the development of -which began in late 1994, at Washington University in Saint Louis. First -released in May 1996, or more than a year ahead of the NCBI, WU BLAST -2.0 is the original gapped BLAST with statistics and is known for -setting higher standards for sensitivity, speed, correctness and -accuracy, scalability and reliability than competing programs and -implementations. WU BLAST is neither a re-hashed nor "Mac-ified" version -of NCBI BLAST, although WU BLAST in many ways is easier to use. WU BLAST -essentially shares no code with NCBI BLAST, except for portions that -both packages derived from ungapped NCBI BLAST 1.4. - -WWW: http://blast.wustl.edu diff --git a/biology/blast/pkg-plist b/biology/blast/pkg-plist deleted file mode 100644 index 0933560e1e2e..000000000000 --- a/biology/blast/pkg-plist +++ /dev/null @@ -1,219 +0,0 @@ -bin/blasta -bin/gb2fasta -bin/gt2fasta -bin/memfile -bin/nrdb -bin/pam -bin/patdb -bin/pir2fasta -bin/sp2fasta -bin/xdformat -bin/xdget -bin/wu-blastall -bin/wu-formatdb -bin/blastn -bin/blastp -bin/blastx -bin/tblastn -bin/tblastx -bin/setdb -bin/pressdb -%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT -%%PORTDOCS%%%%DOCSDIR%%/FAQ-Indexing.html -%%PORTDOCS%%%%DOCSDIR%%/HISTORY -%%PORTDOCS%%%%DOCSDIR%%/LICENSE -%%PORTDOCS%%%%DOCSDIR%%/Memory.html -%%PORTDOCS%%%%DOCSDIR%%/README.html -%%PORTDOCS%%%%DOCSDIR%%/parameters.html -%%PORTDOCS%%%%DOCSDIR%%/parameters.pdf -%%PORTDOCS%%%%DOCSDIR%%/tabular.html -%%DATADIR%%/matrix/aa/nuc.4.4 -%%DATADIR%%/matrix/aa/BLOSUM30 -%%DATADIR%%/matrix/aa/BLOSUM35 -%%DATADIR%%/matrix/aa/BLOSUM40 -%%DATADIR%%/matrix/aa/BLOSUM45 -%%DATADIR%%/matrix/aa/BLOSUM50 -%%DATADIR%%/matrix/aa/BLOSUM55 -%%DATADIR%%/matrix/aa/BLOSUM60 -%%DATADIR%%/matrix/aa/BLOSUM62 -%%DATADIR%%/matrix/aa/BLOSUM65 -%%DATADIR%%/matrix/aa/BLOSUM70 -%%DATADIR%%/matrix/aa/BLOSUM75 -%%DATADIR%%/matrix/aa/BLOSUM80 -%%DATADIR%%/matrix/aa/BLOSUM85 -%%DATADIR%%/matrix/aa/BLOSUM90 -%%DATADIR%%/matrix/aa/BLOSUMN -%%DATADIR%%/matrix/aa/blosum100 -%%DATADIR%%/matrix/aa/blosum30 -%%DATADIR%%/matrix/aa/blosum35 -%%DATADIR%%/matrix/aa/blosum40 -%%DATADIR%%/matrix/aa/blosum45 -%%DATADIR%%/matrix/aa/blosum50 -%%DATADIR%%/matrix/aa/blosum55 -%%DATADIR%%/matrix/aa/blosum60 -%%DATADIR%%/matrix/aa/blosumn -%%DATADIR%%/matrix/aa/blosum62 -%%DATADIR%%/matrix/aa/blosum65 -%%DATADIR%%/matrix/aa/blosum70 -%%DATADIR%%/matrix/aa/blosum75 -%%DATADIR%%/matrix/aa/blosum80 -%%DATADIR%%/matrix/aa/blosum85 -%%DATADIR%%/matrix/aa/DAYHOFF -%%DATADIR%%/matrix/aa/GONNET -%%DATADIR%%/matrix/aa/IDENTITY -%%DATADIR%%/matrix/aa/MATCH -%%DATADIR%%/matrix/aa/PAM10 -%%DATADIR%%/matrix/aa/NUC.4.2 -%%DATADIR%%/matrix/aa/NUC.4.4 -%%DATADIR%%/matrix/aa/PAM100 -%%DATADIR%%/matrix/aa/PAM110 -%%DATADIR%%/matrix/aa/PAM120 -%%DATADIR%%/matrix/aa/PAM130 -%%DATADIR%%/matrix/aa/PAM120.cdi -%%DATADIR%%/matrix/aa/PAM140 -%%DATADIR%%/matrix/aa/PAM150 -%%DATADIR%%/matrix/aa/PAM160 -%%DATADIR%%/matrix/aa/PAM170 -%%DATADIR%%/matrix/aa/PAM160.cdi -%%DATADIR%%/matrix/aa/PAM180 -%%DATADIR%%/matrix/aa/PAM190 -%%DATADIR%%/matrix/aa/PAM20 -%%DATADIR%%/matrix/aa/PAM200 -%%DATADIR%%/matrix/aa/PAM200.cdi -%%DATADIR%%/matrix/aa/PAM210 -%%DATADIR%%/matrix/aa/PAM220 -%%DATADIR%%/matrix/aa/PAM230 -%%DATADIR%%/matrix/aa/PAM240 -%%DATADIR%%/matrix/aa/PAM250 -%%DATADIR%%/matrix/aa/PAM250.cdi -%%DATADIR%%/matrix/aa/PAM260 -%%DATADIR%%/matrix/aa/PAM270 -%%DATADIR%%/matrix/aa/PAM280 -%%DATADIR%%/matrix/aa/PAM290 -%%DATADIR%%/matrix/aa/PAM30 -%%DATADIR%%/matrix/aa/PAM300 -%%DATADIR%%/matrix/aa/PAM310 -%%DATADIR%%/matrix/aa/PAM320 -%%DATADIR%%/matrix/aa/PAM330 -%%DATADIR%%/matrix/aa/PAM340 -%%DATADIR%%/matrix/aa/PAM350 -%%DATADIR%%/matrix/aa/PAM360 -%%DATADIR%%/matrix/aa/PAM370 -%%DATADIR%%/matrix/aa/PAM380 -%%DATADIR%%/matrix/aa/PAM390 -%%DATADIR%%/matrix/aa/PAM40 -%%DATADIR%%/matrix/aa/PAM40.cdi -%%DATADIR%%/matrix/aa/PAM400 -%%DATADIR%%/matrix/aa/PAM410 -%%DATADIR%%/matrix/aa/PAM420 -%%DATADIR%%/matrix/aa/PAM430 -%%DATADIR%%/matrix/aa/PAM440 -%%DATADIR%%/matrix/aa/PAM450 -%%DATADIR%%/matrix/aa/PAM460 -%%DATADIR%%/matrix/aa/PAM470 -%%DATADIR%%/matrix/aa/PAM480 -%%DATADIR%%/matrix/aa/PAM490 -%%DATADIR%%/matrix/aa/PAM50 -%%DATADIR%%/matrix/aa/PAM500 -%%DATADIR%%/matrix/aa/PAM60 -%%DATADIR%%/matrix/aa/PAM70 -%%DATADIR%%/matrix/aa/PAM80 -%%DATADIR%%/matrix/aa/PAM80.cdi -%%DATADIR%%/matrix/aa/PAM90 -%%DATADIR%%/matrix/aa/blosum90 -%%DATADIR%%/matrix/aa/pam120.cdi -%%DATADIR%%/matrix/aa/pam160.cdi -%%DATADIR%%/matrix/aa/dayhoff -%%DATADIR%%/matrix/aa/gonnet -%%DATADIR%%/matrix/aa/identity -%%DATADIR%%/matrix/aa/match -%%DATADIR%%/matrix/aa/pam10 -%%DATADIR%%/matrix/aa/pam100 -%%DATADIR%%/matrix/aa/pam110 -%%DATADIR%%/matrix/aa/pam120 -%%DATADIR%%/matrix/aa/pam130 -%%DATADIR%%/matrix/aa/pam140 -%%DATADIR%%/matrix/aa/pam150 -%%DATADIR%%/matrix/aa/pam160 -%%DATADIR%%/matrix/aa/pam170 -%%DATADIR%%/matrix/aa/pam180 -%%DATADIR%%/matrix/aa/pam190 -%%DATADIR%%/matrix/aa/pam20 -%%DATADIR%%/matrix/aa/pam200 -%%DATADIR%%/matrix/aa/pam250.cdi -%%DATADIR%%/matrix/aa/pam210 -%%DATADIR%%/matrix/aa/pam220 -%%DATADIR%%/matrix/aa/pam230 -%%DATADIR%%/matrix/aa/pam240 -%%DATADIR%%/matrix/aa/pam250 -%%DATADIR%%/matrix/aa/pam40.cdi -%%DATADIR%%/matrix/aa/pam260 -%%DATADIR%%/matrix/aa/pam270 -%%DATADIR%%/matrix/aa/pam280 -%%DATADIR%%/matrix/aa/pam290 -%%DATADIR%%/matrix/aa/pam30 -%%DATADIR%%/matrix/aa/pam300 -%%DATADIR%%/matrix/aa/pam310 -%%DATADIR%%/matrix/aa/pam320 -%%DATADIR%%/matrix/aa/pam330 -%%DATADIR%%/matrix/aa/pam340 -%%DATADIR%%/matrix/aa/pam350 -%%DATADIR%%/matrix/aa/pam360 -%%DATADIR%%/matrix/aa/pam370 -%%DATADIR%%/matrix/aa/pam380 -%%DATADIR%%/matrix/aa/pam390 -%%DATADIR%%/matrix/aa/pam40 -%%DATADIR%%/matrix/aa/pam80.cdi -%%DATADIR%%/matrix/aa/pam400 -%%DATADIR%%/matrix/aa/pam410 -%%DATADIR%%/matrix/aa/pam420 -%%DATADIR%%/matrix/aa/pam430 -%%DATADIR%%/matrix/aa/pam440 -%%DATADIR%%/matrix/aa/pam450 -%%DATADIR%%/matrix/aa/pam460 -%%DATADIR%%/matrix/aa/pam470 -%%DATADIR%%/matrix/aa/pam480 -%%DATADIR%%/matrix/aa/pam490 -%%DATADIR%%/matrix/aa/pam50 -%%DATADIR%%/matrix/aa/pam500 -%%DATADIR%%/matrix/aa/pam60 -%%DATADIR%%/matrix/aa/pam70 -%%DATADIR%%/matrix/aa/pam80 -%%DATADIR%%/matrix/aa/pam90 -%%DATADIR%%/matrix/aa/pam200.cdi -%%DATADIR%%/matrix/aa/PHAT_T70_B66 -%%DATADIR%%/matrix/aa/PHAT_T75_B73 -%%DATADIR%%/matrix/aa/PHAT_T80_B78 -%%DATADIR%%/matrix/aa/PHAT_T85_B82 -%%DATADIR%%/matrix/aa/phat_t70_b66 -%%DATADIR%%/matrix/aa/phat_t75_b73 -%%DATADIR%%/matrix/aa/phat_t80_b78 -%%DATADIR%%/matrix/aa/phat_t85_b82 -%%DATADIR%%/matrix/aa/nuc.4.2 -%%DATADIR%%/matrix/aa/BLOSUM100 -%%DATADIR%%/matrix/nt/PUPY.4.4 -%%DATADIR%%/matrix/nt/IDENTITY.4.2 -%%DATADIR%%/matrix/nt/IDENTITY.4.4 -%%DATADIR%%/matrix/nt/identity.4.2 -%%DATADIR%%/matrix/nt/pupy.4.2 -%%DATADIR%%/matrix/nt/pupy.4.4 -%%DATADIR%%/matrix/nt/PUPY.4.2 -%%DATADIR%%/matrix/nt/identity.4.4 -%%DATADIR%%/matrix/README -%%DATADIR%%/filter/seg -%%DATADIR%%/filter/seg+xnu -%%DATADIR%%/filter/xnu+seg -%%DATADIR%%/filter/nseg -%%DATADIR%%/filter/dust -%%DATADIR%%/filter/nmerge -%%DATADIR%%/filter/xnu -%%DATADIR%%/filter/pmerge -%%DATADIR%%/filter/pseg -%%DATADIR%%/filter/README -%%DATADIR%%/sysblast.sample -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%DATADIR%%/matrix/aa -@dirrm %%DATADIR%%/matrix/nt -@dirrm %%DATADIR%%/matrix -@dirrm %%DATADIR%%/filter -@dirrm %%DATADIR%% diff --git a/biology/embassy/Makefile b/biology/embassy/Makefile deleted file mode 100644 index 1655a08677b5..000000000000 --- a/biology/embassy/Makefile +++ /dev/null @@ -1,131 +0,0 @@ -# Created by: Fernan Aguero <fernan@iib.unsamn.edu.ar> -# $FreeBSD$ - -PORTNAME= embassy -PORTVERSION= 6.2.0 -PORTREVISION= 2 -CATEGORIES= biology -MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ -DIST_SUBDIR= emboss - -MAINTAINER= ports@FreeBSD.org -COMMENT= Collection of contributed EMBOSS applications - -BROKEN= does not fetch - -LIB_DEPENDS= libnucleus.so:${PORTSDIR}/biology/emboss - -PREFIX?= ${LOCALBASE}/emboss -NO_MTREE= yes -USE_SUBMAKE= yes -USES= iconv gmake motif -GNU_CONFIGURE= yes -USE_XORG= x11 -USE_LDCONFIG= yes - -OPTIONS_DEFINE= DOMAINATRIX DOMALIGN DOMSEARCH SIGNATURE STRUCTURE \ - EMNU ESIM4 HMMER MEMENEW MSE MYEMBOSS PHYLIPNEW TOPO \ - VIENNA MIRA IPRSCAN CBSTOOLS - -DOMAINATRIX_DESC= Protein domain apps -DOMALIGN_DESC= Protein domain apps -DOMSEARCH_DESC= Protein domain apps -SIGNATURE_DESC= Protein domain apps -STRUCTURE_DESC= Protein domain apps -EMNU_DESC= EMBOSS simple menu -ESIM4_DESC= Align cDNA/EST to genome -HMMER_DESC= HMM alignment and searches -MEMENEW_DESC= Motif detection -MSE_DESC= A multiple sequence screen editor -MYEMBOSS_DESC= Examples for developers of EMBOSS apps -PHYLIPNEW_DESC= Phylogeny inference -TOPO_DESC= Transmembrane display -VIENNA_DESC= RNA folding -MIRA_DESC= Whole Genome shotgun and EST assembler -IPRSCAN_DESC= InterPro scan -CBSTOOLS_DESC= CBS Tools - -OPTIONS_DEFAULT= DOMAINATRIX DOMALIGN DOMSEARCH SIGNATURE STRUCTURE \ - EMNU ESIM4 HMMER MEMENEW MSE MYEMBOSS PHYLIPNEW TOPO \ - VIENNA MIRA IPRSCAN CBSTOOLS - -CPPFLAGS+= -I${PREFIX}/include -I${LOCALBASE}/include -I${LOCALBASE}/emboss/include -LDFLAGS+= -L${PREFIX}/lib -L${LOCALBASE}/lib -L${LOCALBASE}/emboss/lib - -CONFIGURE_ENV= CPPFLAGS="${CPPFLAGS}" LDFLAGS="${LDFLAGS}" - -EMBASSY_WRKDIR= ${WRKSRC}/EMBASSY -DOMAINATRIX_VERSION= 0.1.0 -EMNU_VERSION= 1.05 -ESIM4_VERSION= 1.0.0 -HMMER_VERSION= 2.3.2 -MEMENEW_VERSION= 4.0.0 -MSE_VERSION= 3.0.0 -TOPO_VERSION= 2.0.0 -PHYLIPNEW_VERSION= 3.69 -DOMALIGN_VERSION= 0.1.0 -DOMSEARCH_VERSION= 0.1.0 -SIGNATURE_VERSION= 0.1.0 -STRUCTURE_VERSION= 0.1.0 -MYEMBOSS_VERSION= 6.2.0 -VIENNA_VERSION= 1.7.2 -MIRA_VERSION= 2.8.2 -IPRSCAN_VERSION= 4.3.1 -CBSTOOLS_VERSION= 1.0.0 -EMBASSY_APPS= DOMAINATRIX EMNU ESIM4 HMMER MEMENEW MSE PHYLIPNEW \ - TOPO DOMALIGN DOMSEARCH SIGNATURE STRUCTURE MYEMBOSS \ - VIENNA MIRA IPRSCAN CBSTOOLS - -NO_STAGE= yes -.include <bsd.port.options.mk> - -.for app in ${EMBASSY_APPS} -.if ${PORT_OPTIONS:M${app}} -APPLIST+= ${app} -${app}_WRKSRC= ${EMBASSY_WRKDIR}/${app}-${${app}_VERSION} -${app}_DISTFILE=${app}-${${app}_VERSION}${EXTRACT_SUFX} -DISTFILES+= ${${app}_DISTFILE} -PLIST_${app}= "" -.else -PLIST_${app}= "@comment " -.endif -PLIST_SUB+= PLIST_${app}=${PLIST_${app}} -.endfor - -do-extract: -.for app in ${APPLIST} - @ ${MKDIR} ${EMBASSY_WRKDIR} - @ cd ${EMBASSY_WRKDIR} && ${TAR} ${EXTRACT_BEFORE_ARGS} \ - ${_DISTDIR}/${${app}_DISTFILE} ${EXTRACT_AFTER_ARGS} - @ if [ `id -u` = 0 ]; then \ - ${CHMOD} -R ug-s ${${app}_WRKSRC}; \ - ${CHOWN} -R 0:0 ${${app}_WRKSRC}; \ - fi -.endfor - -post-extract: - @${REINPLACE_CMD} -e 's#emboss_doc##g' ${EMBASSY_WRKDIR}/MIRA-2.8.2/Makefile.in - -post-patch: - @${FIND} ${WRKSRC} -name configure | ${XARGS} ${REINPLACE_CMD} -e 's|echo aout|echo elf|' - -do-configure: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} -.endfor - -do-build: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} -.endfor - -do-install: -.for app in ${APPLIST} - @ cd ${${app}_WRKSRC} && \ - ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_FLAGS} ${MAKEFILE} \ - ${MAKE_ARGS} ${INSTALL_TARGET} -.endfor - -.include <bsd.port.mk> diff --git a/biology/embassy/distinfo b/biology/embassy/distinfo deleted file mode 100644 index c2a406355c43..000000000000 --- a/biology/embassy/distinfo +++ /dev/null @@ -1,34 +0,0 @@ -SHA256 (emboss/DOMAINATRIX-0.1.0.tar.gz) = 53b1633d8a4fec4335ffe96fff309ef2e61b38140dad916b042522e1a48d5e02 -SIZE (emboss/DOMAINATRIX-0.1.0.tar.gz) = 407290 -SHA256 (emboss/EMNU-1.05.tar.gz) = ccad2f9572b2667b2522e47aa8256b2f17e33a31f74f75991424af0c49ca651d -SIZE (emboss/EMNU-1.05.tar.gz) = 368599 -SHA256 (emboss/ESIM4-1.0.0.tar.gz) = 8c02b53105f9bb95fd0acda15133ad4ac736e720df93c06ffaa6fe54b9baad10 -SIZE (emboss/ESIM4-1.0.0.tar.gz) = 406757 -SHA256 (emboss/HMMER-2.3.2.tar.gz) = fd60908ffe8fea41259480701d64c3442a6a469945dbe03fdfa5677b1a3dc6a6 -SIZE (emboss/HMMER-2.3.2.tar.gz) = 559938 -SHA256 (emboss/MEMENEW-4.0.0.tar.gz) = f5dab1527612e060e6230f579b3243e0da2da086df7ba0e280d0efbb99d5d973 -SIZE (emboss/MEMENEW-4.0.0.tar.gz) = 507901 -SHA256 (emboss/MSE-3.0.0.tar.gz) = 1fc5f5313cede53ad95122afeb69b4b588f3b564567bff9855a9691b92eea701 -SIZE (emboss/MSE-3.0.0.tar.gz) = 425691 -SHA256 (emboss/PHYLIPNEW-3.69.tar.gz) = ae0fd57a5b87961d12df8579298d5ec02a147d6678ead4b561dff2c57c5dba67 -SIZE (emboss/PHYLIPNEW-3.69.tar.gz) = 1652212 -SHA256 (emboss/TOPO-2.0.0.tar.gz) = 15f1106800ba803e2c5d79dbfa79b5d521e9ed0ca9da0ceaa77e15366613e915 -SIZE (emboss/TOPO-2.0.0.tar.gz) = 377565 -SHA256 (emboss/DOMALIGN-0.1.0.tar.gz) = 33a12d28c16039663467f34d930b2a0a6ab2ef7d987db94fd8ed4abd02b1bf9f -SIZE (emboss/DOMALIGN-0.1.0.tar.gz) = 430542 -SHA256 (emboss/DOMSEARCH-0.1.0.tar.gz) = af2e408dcd29b9330df7c310d64c888f53d225ebb0bb5402237891fdcdea7ce3 -SIZE (emboss/DOMSEARCH-0.1.0.tar.gz) = 447445 -SHA256 (emboss/SIGNATURE-0.1.0.tar.gz) = e24bda9ff60ef9940f603f4c65b7e5673d6b81ef0c19d53b294197e98bb2497c -SIZE (emboss/SIGNATURE-0.1.0.tar.gz) = 559082 -SHA256 (emboss/STRUCTURE-0.1.0.tar.gz) = c555e1fc16b377109a1bef21116bfe0907709fb2f629d7cbb4add455bc871050 -SIZE (emboss/STRUCTURE-0.1.0.tar.gz) = 521708 -SHA256 (emboss/MYEMBOSS-6.2.0.tar.gz) = 13edbea0d11a14f67631a4cf6c69985f42c97383d8182f8815e294be03c5ebae -SIZE (emboss/MYEMBOSS-6.2.0.tar.gz) = 322935 -SHA256 (emboss/VIENNA-1.7.2.tar.gz) = e2288e6a2f4538cce916033208ab12f0ffb8a92bb1d3ab89fae302b785171fb7 -SIZE (emboss/VIENNA-1.7.2.tar.gz) = 649028 -SHA256 (emboss/MIRA-2.8.2.tar.gz) = 9d2a64fdb1b95bb6e2ac280be3352740e9b5f498f2ff17157374a2ca9744601d -SIZE (emboss/MIRA-2.8.2.tar.gz) = 347282 -SHA256 (emboss/IPRSCAN-4.3.1.tar.gz) = 179513e2473dc31e5b6153c29670773e7bceaaf84315156961baf8f1e292a289 -SIZE (emboss/IPRSCAN-4.3.1.tar.gz) = 345907 -SHA256 (emboss/CBSTOOLS-1.0.0.tar.gz) = 100131d86d4efeafbd63fc712c82bf493e9d174f0bc505e37bdd35ffb56182ff -SIZE (emboss/CBSTOOLS-1.0.0.tar.gz) = 385340 diff --git a/biology/embassy/pkg-descr b/biology/embassy/pkg-descr deleted file mode 100644 index 8a04b6c0ec88..000000000000 --- a/biology/embassy/pkg-descr +++ /dev/null @@ -1,14 +0,0 @@ -EMBASSY is a collection of contributed EMBOSS software. From the web -pages: - - "EMBOSS is GPL licensed. The libraries are under the Lesser GPL (LGPL). - Programs which have been included from third parties who have their own - licencing terms are kept apart under the EMBASSY grouping. - - This allows the EMBOSS libraries to link to other software, and only - requires that software to have an LGPL-compatible licence. Phylip, for - example, fits this model. - - But, to the user they do look exactly like EMBOSS aplications." - -WWW: http://emboss.sourceforge.net/apps/#Embassy diff --git a/biology/embassy/pkg-plist b/biology/embassy/pkg-plist deleted file mode 100644 index ff9b9963614d..000000000000 --- a/biology/embassy/pkg-plist +++ /dev/null @@ -1,515 +0,0 @@ -%%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_DOMAINATRIX%%share/EMBOSS/doc/programs/text/cathparse.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainnr.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainreso.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainseqs.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/domainsse.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/scopparse.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/programs/text/ssematch.txt -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/index.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/cathparse.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainnr.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainreso.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainseqs.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/domainsse.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/scopparse.html -%%PLIST_DOMAINATRIX%%share/EMBOSS/doc/html/embassy/domainatrix/ssematch.html -%%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%%@dirrm share/EMBOSS/doc/html/embassy/domainatrix -%%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_DOMALIGN%%share/EMBOSS/doc/programs/text/allversusall.txt -%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/domainalign.txt -%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/domainrep.txt -%%PLIST_DOMALIGN%%share/EMBOSS/doc/programs/text/seqalign.txt -%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/index.html -%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/allversusall.html -%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/domainalign.html -%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/domainrep.html -%%PLIST_DOMALIGN%%share/EMBOSS/doc/html/embassy/domalign/seqalign.html -%%PLIST_DOMALIGN%%@dirrm share/EMBOSS/doc/html/embassy/domalign -%%PLIST_DOMALIGN%%bin/allversusall -%%PLIST_DOMALIGN%%bin/domainalign -%%PLIST_DOMALIGN%%bin/domainrep -%%PLIST_DOMALIGN%%bin/seqalign -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqnr.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsearch.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqfraggle.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqsort.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/acd/seqwords.acd -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqfraggle.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqnr.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsearch.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqsort.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/programs/text/seqwords.txt -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/index.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqfraggle.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqnr.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsearch.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqsort.html -%%PLIST_DOMSEARCH%%share/EMBOSS/doc/html/embassy/domsearch/seqwords.html -%%PLIST_DOMSEARCH%%@dirrm share/EMBOSS/doc/html/embassy/domsearch -%%PLIST_DOMSEARCH%%bin/seqnr -%%PLIST_DOMSEARCH%%bin/seqsearch -%%PLIST_DOMSEARCH%%bin/seqfraggle -%%PLIST_DOMSEARCH%%bin/seqsort -%%PLIST_DOMSEARCH%%bin/seqwords -%%PLIST_SIGNATURE%%share/EMBOSS/acd/libgen.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/matgen3d.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocplot.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/rocon.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggen.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/siggenlig.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscan.acd -%%PLIST_SIGNATURE%%share/EMBOSS/acd/sigscanlig.acd -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/libgen.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/matgen3d.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/rocon.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/rocplot.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/siggen.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/siggenlig.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/sigscan.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/programs/text/sigscanlig.txt -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/index.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/libgen.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/matgen3d.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/rocon.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/rocplot.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/siggen.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/siggenlig.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscan.html -%%PLIST_SIGNATURE%%share/EMBOSS/doc/html/embassy/signature/sigscanlig.html -%%PLIST_SIGNATURE%%@dirrm share/EMBOSS/doc/html/embassy/signature -%%PLIST_SIGNATURE%%bin/libgen -%%PLIST_SIGNATURE%%bin/matgen3d -%%PLIST_SIGNATURE%%bin/rocplot -%%PLIST_SIGNATURE%%bin/rocon -%%PLIST_SIGNATURE%%bin/siggen -%%PLIST_SIGNATURE%%bin/siggenlig -%%PLIST_SIGNATURE%%bin/sigscan -%%PLIST_SIGNATURE%%bin/sigscanlig -%%PLIST_STRUCTURE%%share/EMBOSS/acd/contacts.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/domainer.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/hetparse.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/interface.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbparse.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbplus.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/pdbtosp.acd -%%PLIST_STRUCTURE%%share/EMBOSS/acd/sites.acd -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/contacts.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/domainer.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/hetparse.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/interface.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbparse.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbplus.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/pdbtosp.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/programs/text/sites.txt -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/index.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/contacts.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/domainer.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/hetparse.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/interface.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbparse.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbplus.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/pdbtosp.html -%%PLIST_STRUCTURE%%share/EMBOSS/doc/html/embassy/structure/sites.html -%%PLIST_STRUCTURE%%@dirrm share/EMBOSS/doc/html/embassy/structure -%%PLIST_STRUCTURE%%bin/contacts -%%PLIST_STRUCTURE%%bin/domainer -%%PLIST_STRUCTURE%%bin/hetparse -%%PLIST_STRUCTURE%%bin/interface -%%PLIST_STRUCTURE%%bin/pdbparse -%%PLIST_STRUCTURE%%bin/pdbplus -%%PLIST_STRUCTURE%%bin/pdbtosp -%%PLIST_STRUCTURE%%bin/sites -%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd -%%PLIST_EMNU%%share/EMBOSS/doc/programs/text/emnu.txt -%%PLIST_EMNU%%share/EMBOSS/doc/html/embassy/emnu/index.html -%%PLIST_EMNU%%share/EMBOSS/doc/html/embassy/emnu/emnu.html -%%PLIST_EMNU%%@dirrm share/EMBOSS/doc/html/embassy/emnu -%%PLIST_EMNU%%bin/emnu -%%PLIST_ESIM4%%share/EMBOSS/acd/esim4.acd -%%PLIST_ESIM4%%share/EMBOSS/doc/programs/text/esim4.txt -%%PLIST_ESIM4%%share/EMBOSS/doc/html/embassy/esim4/index.html -%%PLIST_ESIM4%%share/EMBOSS/doc/html/embassy/esim4/esim4.html -%%PLIST_ESIM4%%@dirrm share/EMBOSS/doc/html/embassy/esim4 -%%PLIST_ESIM4%%bin/esim4 -%%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/ehmmbuild.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd -%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmalign.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmbuild.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmcalibrate.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmconvert.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmemit.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmfetch.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmindex.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmpfam.txt -%%PLIST_HMMER%%share/EMBOSS/doc/programs/text/ehmmsearch.txt -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/index.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmalign.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmbuild.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmcalibrate.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmconvert.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmemit.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmfetch.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmindex.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmpfam.html -%%PLIST_HMMER%%share/EMBOSS/doc/html/embassy/hmmernew/ehmmsearch.html -%%PLIST_HMMER%%@dirrm share/EMBOSS/doc/html/embassy/hmmernew -%%PLIST_HMMER%%bin/ehmmcalibrate -%%PLIST_HMMER%%bin/ehmmconvert -%%PLIST_HMMER%%bin/ehmmemit -%%PLIST_HMMER%%bin/ehmmfetch -%%PLIST_HMMER%%bin/ehmmindex -%%PLIST_HMMER%%bin/ehmmbuild -%%PLIST_HMMER%%bin/ehmmalign -%%PLIST_HMMER%%bin/ehmmpfam -%%PLIST_HMMER%%bin/ehmmsearch -%%PLIST_MEMENEW%%share/EMBOSS/acd/emast.acd -%%PLIST_MEMENEW%%share/EMBOSS/acd/ememe.acd -%%PLIST_MEMENEW%%share/EMBOSS/acd/ememetext.acd -%%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/emast.txt -%%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememe.txt -%%PLIST_MEMENEW%%share/EMBOSS/doc/programs/text/ememetext.txt -%%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/index.html -%%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/emast.html -%%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememe.html -%%PLIST_MEMENEW%%share/EMBOSS/doc/html/embassy/memenew/ememetext.html -%%PLIST_MEMENEW%%@dirrm share/EMBOSS/doc/html/embassy/memenew -%%PLIST_MEMENEW%%bin/emast -%%PLIST_MEMENEW%%bin/ememe -%%PLIST_MEMENEW%%bin/ememetext -%%PLIST_MSE%%share/EMBOSS/acd/mse.acd -%%PLIST_MSE%%share/EMBOSS/doc/programs/text/mse.txt -%%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/index.html -%%PLIST_MSE%%share/EMBOSS/doc/html/embassy/mse/mse.html -%%PLIST_MSE%%@dirrm share/EMBOSS/doc/html/embassy/mse -%%PLIST_MSE%%lib/libckit.so.1 -%%PLIST_MSE%%lib/libckit.so -%%PLIST_MSE%%lib/libckit.la -%%PLIST_MSE%%lib/libckit.a -%%PLIST_MSE%%bin/mse -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fclique.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fconsense.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fcontml.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fcontrast.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdiscboot.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnacomp.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnadist.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnainvar.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnaml.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnamlk.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnamove.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnapars.acd -%%PLIST_PHYLIPNEW%%share/EMBOSS/acd/fdnapenny.acd 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-@dirrm share/EMBOSS/doc/html/embassy -@dirrmtry share/EMBOSS/doc/html -@dirrmtry share/EMBOSS/doc -@dirrmtry share/EMBOSS -@dirrmtry share diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile deleted file mode 100644 index 11d56ac81f93..000000000000 --- a/biology/pymol/Makefile +++ /dev/null @@ -1,49 +0,0 @@ -# Created by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> -# $FreeBSD$ - -PORTNAME= pymol -PORTVERSION= ${VERSION}.${SVNREVISION} -PORTREVISION= 3 -CATEGORIES= biology python -MASTER_SITES= ${MASTER_SITE_LOCAL:S|%SUBDIR%|maho/pymol|} - -MAINTAINER= ports@FreeBSD.org -COMMENT= Free and Open-Source molecular modeling system - -BUILD_DEPENDS= ${PYNUMERIC} -RUN_DEPENDS= ${PYNUMERIC} \ - ${PYTHON_SITELIBDIR}/Pmw:${PORTSDIR}/x11-toolkits/py-Pmw -LIB_DEPENDS= libpng15.so:${PORTSDIR}/graphics/png \ - libfreetype.so:${PORTSDIR}/print/freetype2 - -VERSION= 1.5.0.1 -SVNREVISION= 3978 - -WRKSRC= ${WRKDIR}/pymol-${PORTVERSION} -USE_GL= glut glew -USES= gmake tar:bzip2 -USE_PYTHON= yes -PLIST_SUB= PYMOL_VER=${VERSION} PYTHON_VER=${PYTHON_VER} - -NO_STAGE= yes -pre-build: - @${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+" ${WRKSRC}/setup.py - -#do build process actually installs some files, so omitted. -do-build: - -do-install: - @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} install) - @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup2.py install) - @${INSTALL_SCRIPT} ${WRKSRC}/pymol ${PREFIX}/bin/pymol - -#maintainance -do-fetch-svn: - #svn ls https://pymol.svn.sourceforge.net/svnroot/pymol/tags - #http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/ - ${RM} -rf pymol-${VERSION}.${SVNREVISION} - svn -r ${SVNREVISION} export http://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-${VERSION}.${SVNREVISION} - tar cvfj pymol-${VERSION}.${SVNREVISION}.tar.bz2 pymol-${VERSION}.${SVNREVISION} - scp pymol-${VERSION}.${SVNREVISION}.tar.bz2 freefall.freebsd.org:public_distfiles/pymol/ - -.include <bsd.port.mk> diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo deleted file mode 100644 index 509273172d80..000000000000 --- a/biology/pymol/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (pymol-1.5.0.1.3978.tar.bz2) = 76ff4a6bc126f3fd4dccb62c2345fea3b2a007ecc687d89f7fe21b8f5a0496fc -SIZE (pymol-1.5.0.1.3978.tar.bz2) = 9730397 diff --git a/biology/pymol/files/patch-setup.py b/biology/pymol/files/patch-setup.py deleted file mode 100644 index 105d89d8a732..000000000000 --- a/biology/pymol/files/patch-setup.py +++ /dev/null @@ -1,31 +0,0 @@ ---- setup.py 2012-02-14 04:02:02.000000000 +0900 -+++ setup.py 2012-02-15 13:09:38.000000000 +0900 -@@ -159,7 +159,8 @@ - "layer3", - "layer4", - "layer5", -- "/usr/include/freetype2", -+ "%%LOCALBASE%%/include/freetype2", -+ "%%LOCALBASE%%/include", - # VMD plugin support - # "contrib/uiuc/plugins/include", - # "contrib/uiuc/plugins/molfile_plugin/src", -@@ -181,7 +181,7 @@ - "GLU", - "glut", - "GLEW"] -- lib_dirs = [ "/usr/X11R6/lib64", ] -+ lib_dirs = [ "%%LOCALBASE%%/lib", ] - def_macros = [ ("_PYMOL_MODULE",None), - ("_PYMOL_INLINE",None), - ("_PYMOL_FREETYPE",None), -@@ -201,7 +202,7 @@ - "-funroll-loops", - "-O3", - "-g" ] -- ext_link_args = [] -+ ext_link_args = [ "-L%%LOCALBASE%%/lib" ] - - - distribution = setup ( # Distribution meta-data - diff --git a/biology/pymol/pkg-descr b/biology/pymol/pkg-descr deleted file mode 100644 index dfd8cdfb4d4f..000000000000 --- a/biology/pymol/pkg-descr +++ /dev/null @@ -1,9 +0,0 @@ -PyMOL is a molecular graphics system with an embedded Python interpreter -designed for real-time visualization and rapid generation of -high-quality molecular graphics images and animations. It is fully extensible -and available free to everyone via the "Python" license. -PyMOL can be used to create images and animations with unprecedented ease. -It can also perform many other valuable tasks (such as editing PDB files) -to assist you in your research. - -WWW: http://pymol.sourceforge.net/ diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist deleted file mode 100644 index fb7eabf7b538..000000000000 --- a/biology/pymol/pkg-plist +++ /dev/null @@ -1,854 +0,0 @@ -bin/pymol -%%PYTHON_SITELIBDIR%%/chempy/__init__.py -%%PYTHON_SITELIBDIR%%/chempy/__init__.pyc -%%PYTHON_SITELIBDIR%%/chempy/arc.py -%%PYTHON_SITELIBDIR%%/chempy/arc.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.py -%%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/commands.py -%%PYTHON_SITELIBDIR%%/chempy/bmin/commands.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.py -%%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.pyc -%%PYTHON_SITELIBDIR%%/chempy/bmin/state.py 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