git: d94f19ab9ffc - main - biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin

[Jason W. Bacon]

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=d94f19ab9ffcd2fac7650802d6aea3f68156f5d7

commit d94f19ab9ffcd2fac7650802d6aea3f68156f5d7
Author:     Jason W. Bacon <jwb at FreeBSD.org>
AuthorDate: 2021-09-24 21:53:30 +0000
Commit:     Jason W. Bacon <jwb at 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