Date: Fri, 24 Sep 2021 21:38:55 GMT
From: "Jason W. Bacon" <jwb@FreeBSD.org>
To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org
Subject: git: c68b6dc6448c - main - biology/emboss: Add "emboss" command in ${LOCALBASE}/bin
Message-ID: <202109242138.18OLctS6031614@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=c68b6dc6448c618b79c8d1800d25b789b1b01a90 commit c68b6dc6448c618b79c8d1800d25b789b1b01a90 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-09-24 21:34:20 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-09-24 21:34:20 +0000 biology/emboss: Add "emboss" command in ${LOCALBASE}/bin Standard emboss commands are installed under a special prefix because of multiple conflicts. The emboss command turns the standard commands into subcommands, so no special PATH is needed. /usr/local/emboss/bin/needle [args] can be run as emboss needle [args] --- biology/emboss/Makefile | 6 ++++- biology/emboss/distinfo | 2 +- biology/emboss/files/emboss.c | 59 +++++++++++++++++++++++++++++++++++++++++++ biology/emboss/pkg-plist | 1 + 4 files changed, 66 insertions(+), 2 deletions(-) diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index 24862d3e1732..fed3bdc4df4e 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -2,7 +2,7 @@ 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} @@ -50,6 +50,9 @@ 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}#' ${CONFIG_FILE} @@ -57,5 +60,6 @@ post-install: @${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 <bsd.port.mk> 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 <stdio.h> +#include <sysexits.h> +#include <limits.h> +#include <unistd.h> + +#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 @@ -77,6 +77,7 @@ bin/edamisid bin/edamname bin/edialign bin/einverted +%%LOCALBASE%%/bin/emboss %%LOCALBASE%%/bin/emboss-shell bin/embossdata bin/embossupdate
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