Date: Fri, 24 Sep 2021 21:58:05 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: d94f19ab9ffc - main - biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin
Message-ID: <202109242158.18OLw5eB057628@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=d94f19ab9ffcd2fac7650802d6aea3f68156f5d7 commit d94f19ab9ffcd2fac7650802d6aea3f68156f5d7 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-09-24 21:53:30 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-09-24 21:53:30 +0000 biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin Standard kent userapps commands are installed under ${PREFIX}/userapps because of multiple conflicts. The kent command turns the standard commands into subcommands, so no special PATH is needed. /usr/local/ucsc-userapps/bin/bigWigToBedGraph [args] can be run as kent bigWigToBedGraph [args] --- biology/ucsc-userapps/Makefile | 3 ++ biology/ucsc-userapps/files/kent.c | 59 ++++++++++++++++++++++++++++++++++++++ biology/ucsc-userapps/pkg-plist | 1 + 3 files changed, 63 insertions(+) diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile index c7e44cc879ed..da61329ba20b 100644 --- a/biology/ucsc-userapps/Makefile +++ b/biology/ucsc-userapps/Makefile @@ -2,6 +2,7 @@ PORTNAME= ucsc-userapps DISTVERSION= 414 +PORTREVISION= 1 CATEGORIES= biology perl5 python MASTER_SITES= http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ DISTNAME= userApps.v${PORTVERSION}.src @@ -57,6 +58,7 @@ do-build: @(cd ${WRKSRC}/kent/src/jkOwnLib && ${DO_MAKE_BUILD}) @(cd ${WRKSRC}/kent/src/hg/lib && ${DO_MAKE_BUILD}) @(cd ${WRKSRC}/kent/src/utils && ${DO_MAKE_BUILD}) + ${CC} -DUCSC_PREFIX="\"${PREFIX}/userapps\"" ${FILESDIR}/kent.c -o ${WRKDIR}/kent do-install: @${MKDIR} ${WRKSRC}/scripts ${WRKSRC}/binaries @@ -71,5 +73,6 @@ do-install: ${STAGEDIR}${PREFIX}/userapps/bin ${INSTALL_SCRIPT} ${WRKDIR}/ucsc-shell \ ${STAGEDIR}${PREFIX}/bin + ${INSTALL_PROGRAM} ${WRKDIR}/kent ${STAGEDIR}${LOCALBASE}/bin .include <bsd.port.mk> diff --git a/biology/ucsc-userapps/files/kent.c b/biology/ucsc-userapps/files/kent.c new file mode 100644 index 000000000000..f1c8887068f5 --- /dev/null +++ b/biology/ucsc-userapps/files/kent.c @@ -0,0 +1,59 @@ +/*************************************************************************** + * Description: + * Wrapper to turn ucsc kent commands into subcommands. The kent 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 kent 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: + * + * kent bigWigToBedGraph args + * + * instead of one of the following: + * + * prefix/bin/bigWigToBedGraph args + * + * env PATH=prefix/bin:$PATH bigWigToBedGraph args + * + * conda activate kent + * bigWigToBedGraph args + * + * Arguments: + * The full kent utils command you would use if it were in PATH. + * + * Compile with UCSC_PREFIX set to the parent of the bin directory + * containing the kent binaries. + * + * History: + * Date Name Modification + * 2021-09-13 Jason Bacon Begin + ***************************************************************************/ + +#include <stdio.h> +#include <sysexits.h> +#include <limits.h> +#include <unistd.h> + +#ifndef UCSC_PREFIX +#define UCSC_PREFIX "/usr/local/userapps" +#endif + +int main(int argc,char *argv[]) + +{ + char cmd[PATH_MAX + 1]; + + if ( argc < 2 ) + { + fprintf(stderr, "Usage: %s UCSC-userapps-command [args]\n", argv[0]); + return EX_USAGE; + } + + snprintf(cmd, PATH_MAX, "%s/bin/%s", UCSC_PREFIX, argv[1]); + execv(cmd, argv + 1); +} diff --git a/biology/ucsc-userapps/pkg-plist b/biology/ucsc-userapps/pkg-plist index e8304be64af2..f8605fc771d0 100644 --- a/biology/ucsc-userapps/pkg-plist +++ b/biology/ucsc-userapps/pkg-plist @@ -1,3 +1,4 @@ +bin/kent bin/ucsc-shell userapps/bin/aNotB userapps/bin/addCols
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