Attachment #227917 for bug #258478

Lines 2-8 Link Here

(-)/usr/ports/wip/emboss/Makefile (-1 / +5 lines)
2		2
3	PORTNAME= emboss	3	PORTNAME= emboss
4	PORTVERSION= 6.6.0	4	PORTVERSION= 6.6.0
5	PORTREVISION= 5	5	PORTREVISION= 6
6	CATEGORIES= biology	6	CATEGORIES= biology
7	MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/	7	MASTER_SITES= ftp://emboss.open-bio.org/pub/EMBOSS/
8	DISTNAME= ${PORTNAME:tu}-${PORTVERSION}	8	DISTNAME= ${PORTNAME:tu}-${PORTVERSION}
Lines 50-55 Link Here
50	post-patch:	50	post-patch:
51	@${REINPLACE_CMD} -e 's/-liconv/${ICONV_LIB}/' ${WRKSRC}/configure	51	@${REINPLACE_CMD} -e 's/-liconv/${ICONV_LIB}/' ${WRKSRC}/configure
52		52
		53	post-build:
		54	${CC} -DEMBOSS_PREFIX="\"${PREFIX}\"" ${FILESDIR}/emboss.c -o ${WRKDIR}/emboss
		55
53	pre-install:	56	pre-install:
54	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${PREFIX}/share/${PORTNAME:tu}#' ${CONFIG_FILE}	57	@ ${REINPLACE_CMD} -e 's#%%DATADIR%%#${PREFIX}/share/${PORTNAME:tu}#' ${CONFIG_FILE}
55		58
Lines 57-61 Link Here
57	@${MKDIR} ${STAGEDIR}${LOCALBASE}/bin	60	@${MKDIR} ${STAGEDIR}${LOCALBASE}/bin
58	${INSTALL_SCRIPT} ${WRKDIR}/emboss-shell ${STAGEDIR}${LOCALBASE}/bin	61	${INSTALL_SCRIPT} ${WRKDIR}/emboss-shell ${STAGEDIR}${LOCALBASE}/bin
59	${INSTALL_DATA} ${CONFIG_FILE} ${STAGEDIR}${DATADIR}	62	${INSTALL_DATA} ${CONFIG_FILE} ${STAGEDIR}${DATADIR}
		63	${INSTALL_PROGRAM} ${WRKDIR}/emboss ${STAGEDIR}${LOCALBASE}/bin
60		64
61	.include <bsd.port.mk>	65	.include <bsd.port.mk>

Lines 1-3 Link Here

(-)/usr/ports/wip/emboss/distinfo (-1 lines)
1	TIMESTAMP = 1630940920
2	SHA256 (emboss/EMBOSS-6.6.0.tar.gz) = 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e	1	SHA256 (emboss/EMBOSS-6.6.0.tar.gz) = 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e
3	SIZE (emboss/EMBOSS-6.6.0.tar.gz) = 117962028	2	SIZE (emboss/EMBOSS-6.6.0.tar.gz) = 117962028




/***************************************************************************
 *  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);
}

Lines 77-82 Link Here

(-)/usr/ports/wip/emboss/pkg-plist (+1 lines)
77	bin/edamname	77	bin/edamname
78	bin/edialign	78	bin/edialign
79	bin/einverted	79	bin/einverted
		80	%%LOCALBASE%%/bin/emboss
80	%%LOCALBASE%%/bin/emboss-shell	81	%%LOCALBASE%%/bin/emboss-shell
81	bin/embossdata	82	bin/embossdata
82	bin/embossupdate	83	bin/embossupdate

Return to bug 258478

Line 0 Link Here

(-)/usr/ports/wip/emboss/files/emboss.c (+59 lines)
	1	/***************************************************************************
	2	* Description:
	3	* Wrapper to turn emboss commands into subcommands. The emboss suite
	4	* contains executables that conflict with multiple other software
	5	* packages and therefore cannot be safely installed directly under a
	6	* standard prefix. This wrapper can be installed under the standard
	7	* PATH and used to to execute emboss commands installed under a
	8	* private prefix, without altering PATH, activating a special
	9	* environment, opening a container, etc. This sub-command paradigm
	10	* is already familiar to bioinformaticians thanks to other suites
	11	* like samtools, bedtools, etc.
	12	*
	13	* Example:
	14	*
	15	* emboss seqret args
	16	*
	17	* instead of one of the following:
	18	*
	19	* prefix/bin/seqret args
	20	*
	21	* env PATH=prefix/bin:$PATH seqret args
	22	*
	23	* conda activate emboss
	24	* seqret args
	25	*
	26	* Arguments:
	27	* The full emboss command you would use if it were in PATH.
	28	*
	29	* Compile with EMBOSS_PREFIX set to the parent of the bin directory
	30	* containing the emboss binaries.
	31	*
	32	* History:
	33	* Date Name Modification
	34	* 2021-09-13 Jason Bacon Begin
	35	***************************************************************************/
	36
	37	#include <stdio.h>
	38	#include <sysexits.h>
	39	#include <limits.h>
	40	#include <unistd.h>
	41
	42	#ifndef EMBOSS_PREFIX
	43	#define EMBOSS_PREFIX "/usr/local/emboss"
	44	#endif
	45
	46	int main(int argc,char *argv[])
	47
	48	{
	49	char cmd[PATH_MAX + 1];
	50
	51	if ( argc < 2 )
	52	{
	53	fprintf(stderr, "Usage: %s emboss-command [args]\n", argv[0]);
	54	return EX_USAGE;
	55	}
	56
	57	snprintf(cmd, PATH_MAX, "%s/bin/%s", EMBOSS_PREFIX, argv[1]);
	58	execv(cmd, argv + 1);
	59	}