diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 24862d3e1732..fed3bdc4df4e 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -1,61 +1,65 @@ # Created by: Johann Visagie PORTNAME= emboss PORTVERSION= 6.6.0 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= biology MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/ DISTNAME= ${PORTNAME:tu}-${PORTVERSION} DIST_SUBDIR= ${PORTNAME} MAINTAINER= wen@FreeBSD.org COMMENT= Collection of open source tools for genetic sequence analysis LICENSE= GPLv2 BUILD_DEPENDS= clustalw:biology/clustalw \ primer3:biology/primer3 LIB_DEPENDS= libgd.so:graphics/gd \ libpng.so:graphics/png USES= gmake libtool iconv mysql pgsql ssl USE_SUBMAKE= yes CONFLICTS= qmail-ldap-[0-9]* digest-[0-9]* PREFIX?= ${LOCALBASE}/emboss NO_MTREE= yes GNU_CONFIGURE= yes USE_LDCONFIG= yes SUB_FILES= pkg-message emboss-shell SUB_LIST= PREFIX=${PREFIX} DATADIR=${DATADIR} LDFLAGS+= -L${LOCALBASE}/lib CONFIGURE_ARGS+=${ICONV_CONFIGURE_ARG} INSTALL_TARGET= install-strip DOCSDIR= ${PREFIX}/share/${PORTNAME:tu}/doc DATADIR= ${PREFIX}/share/${PORTNAME:tu} OPTIONS_DEFINE= DOCS X11 OPTIONS_DEFAULT= X11 DOCS_CONFIGURE_ON= --with-docroot=${DOCSDIR} X11_USES= motif xorg X11_USE= XORG=x11 X11_LIB_DEPENDS= libgd.so:graphics/gd \ libpng.so:graphics/png X11_CONFIGURE_OFF= --without-x CONFIG_FILE= ${WRKSRC}/emboss/emboss.default.template post-patch: @${REINPLACE_CMD} -e 's/-liconv/${ICONV_LIB}/' ${WRKSRC}/configure +post-build: + ${CC} -DEMBOSS_PREFIX="\"${PREFIX}\"" ${FILESDIR}/emboss.c -o ${WRKDIR}/emboss + pre-install: @ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${PREFIX}/share/${PORTNAME:tu}#' ${CONFIG_FILE} post-install: @${MKDIR} ${STAGEDIR}${LOCALBASE}/bin ${INSTALL_SCRIPT} ${WRKDIR}/emboss-shell ${STAGEDIR}${LOCALBASE}/bin ${INSTALL_DATA} ${CONFIG_FILE} ${STAGEDIR}${DATADIR} + ${INSTALL_PROGRAM} ${WRKDIR}/emboss ${STAGEDIR}${LOCALBASE}/bin .include diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index ea7511984c28..a8e5c23c1cc6 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1630940920 +TIMESTAMP = 1632518858 SHA256 (emboss/EMBOSS-6.6.0.tar.gz) = 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SIZE (emboss/EMBOSS-6.6.0.tar.gz) = 117962028 diff --git a/biology/emboss/files/emboss.c b/biology/emboss/files/emboss.c new file mode 100644 index 000000000000..1b6f1deca5df --- /dev/null +++ b/biology/emboss/files/emboss.c @@ -0,0 +1,59 @@ +/*************************************************************************** + * Description: + * Wrapper to turn emboss commands into subcommands. The emboss suite + * contains executables that conflict with multiple other software + * packages and therefore cannot be safely installed directly under a + * standard prefix. This wrapper can be installed under the standard + * PATH and used to to execute emboss commands installed under a + * private prefix, without altering PATH, activating a special + * environment, opening a container, etc. This sub-command paradigm + * is already familiar to bioinformaticians thanks to other suites + * like samtools, bedtools, etc. + * + * Example: + * + * emboss seqret args + * + * instead of one of the following: + * + * prefix/bin/seqret args + * + * env PATH=prefix/bin:$PATH seqret args + * + * conda activate emboss + * seqret args + * + * Arguments: + * The full emboss command you would use if it were in PATH. + * + * Compile with EMBOSS_PREFIX set to the parent of the bin directory + * containing the emboss binaries. + * + * History: + * Date Name Modification + * 2021-09-13 Jason Bacon Begin + ***************************************************************************/ + +#include +#include +#include +#include + +#ifndef EMBOSS_PREFIX +#define EMBOSS_PREFIX "/usr/local/emboss" +#endif + +int main(int argc,char *argv[]) + +{ + char cmd[PATH_MAX + 1]; + + if ( argc < 2 ) + { + fprintf(stderr, "Usage: %s emboss-command [args]\n", argv[0]); + return EX_USAGE; + } + + snprintf(cmd, PATH_MAX, "%s/bin/%s", EMBOSS_PREFIX, argv[1]); + execv(cmd, argv + 1); +} diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index 281c02c28196..f2b9e61952fd 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -1,2317 +1,2318 @@ bin/aaindexextract bin/abiview bin/acdc bin/acdgalaxy bin/acdlog bin/acdpretty bin/acdtable bin/acdtrace bin/acdvalid bin/aligncopy bin/aligncopypair bin/antigenic bin/assemblyget bin/backtranambig bin/backtranseq bin/banana bin/biosed bin/btwisted bin/cachedas bin/cachedbfetch bin/cacheebeyesearch bin/cacheensembl bin/cai bin/chaos bin/charge bin/checktrans bin/chips bin/cirdna bin/codcmp bin/codcopy bin/coderet bin/compseq bin/cons bin/consambig bin/cpgplot bin/cpgreport bin/cusp bin/cutgextract bin/cutseq bin/dan bin/dbiblast bin/dbifasta bin/dbiflat bin/dbigcg bin/dbtell bin/dbxcompress bin/dbxedam bin/dbxfasta bin/dbxflat bin/dbxgcg bin/dbxobo bin/dbxreport bin/dbxresource bin/dbxstat bin/dbxtax bin/dbxuncompress bin/degapseq bin/density bin/descseq bin/diffseq bin/distmat bin/dotmatcher bin/dotpath bin/dottup bin/dreg bin/drfinddata bin/drfindformat bin/drfindid bin/drfindresource bin/drget bin/drtext bin/edamdef bin/edamhasinput bin/edamhasoutput bin/edamisformat bin/edamisid bin/edamname bin/edialign bin/einverted +%%LOCALBASE%%/bin/emboss %%LOCALBASE%%/bin/emboss-shell bin/embossdata bin/embossupdate bin/embossversion bin/emma bin/emowse bin/entret bin/epestfind bin/eprimer3 bin/eprimer32 bin/equicktandem bin/est2genome bin/etandem bin/extractalign bin/extractfeat bin/extractseq bin/featcopy bin/featmerge bin/featreport bin/feattext bin/findkm bin/freak bin/fuzznuc bin/fuzzpro bin/fuzztran bin/garnier bin/geecee bin/getorf bin/godef bin/goname bin/helixturnhelix bin/hmoment bin/iep bin/infoalign bin/infoassembly bin/infobase bin/inforesidue bin/infoseq bin/isochore bin/jaspextract bin/jaspscan bin/jembossctl bin/lindna bin/listor bin/makenucseq bin/makeprotseq bin/marscan bin/maskambignuc bin/maskambigprot bin/maskfeat bin/maskseq bin/matcher bin/megamerger bin/merger bin/msbar bin/mwcontam bin/mwfilter bin/needle bin/needleall bin/newcpgreport bin/newcpgseek bin/newseq bin/nohtml bin/noreturn bin/nospace bin/notab bin/notseq bin/nthseq bin/nthseqset bin/octanol bin/oddcomp bin/ontocount bin/ontoget bin/ontogetcommon bin/ontogetdown bin/ontogetobsolete bin/ontogetroot bin/ontogetsibs bin/ontogetup bin/ontoisobsolete bin/ontotext bin/palindrome bin/pasteseq bin/patmatdb bin/patmatmotifs bin/pepcoil bin/pepdigest bin/pepinfo bin/pepnet bin/pepstats bin/pepwheel bin/pepwindow bin/pepwindowall bin/plotcon bin/plotorf bin/polydot bin/preg bin/prettyplot bin/prettyseq bin/primersearch bin/printsextract bin/profit bin/prophecy bin/prophet bin/prosextract bin/pscan bin/psiphi bin/rebaseextract bin/recoder bin/redata bin/refseqget bin/remap bin/restover bin/restrict bin/revseq bin/runJemboss.sh bin/seealso bin/seqcount bin/seqmatchall bin/seqret bin/seqretsetall bin/seqretsplit bin/seqxref bin/seqxrefget bin/servertell bin/showalign bin/showdb bin/showfeat bin/showorf bin/showpep bin/showserver bin/showseq bin/shuffleseq bin/sigcleave bin/silent bin/sirna bin/sixpack bin/sizeseq bin/skipredundant bin/skipseq bin/splitsource bin/splitter bin/stretcher bin/stssearch bin/supermatcher bin/syco bin/taxget bin/taxgetdown bin/taxgetrank bin/taxgetspecies bin/taxgetup bin/tcode bin/textget bin/textsearch bin/tfextract bin/tfm bin/tfscan bin/tmap bin/tranalign bin/transeq bin/trimest bin/trimseq bin/trimspace bin/twofeat bin/union bin/urlget bin/variationget bin/vectorstrip bin/water bin/whichdb bin/wobble bin/wordcount bin/wordfinder bin/wordmatch bin/wossdata bin/wossinput bin/wossname bin/wossoperation bin/wossoutput 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