diff options
author | Wen Heping <wen@FreeBSD.org> | 2017-10-30 02:27:23 +0000 |
---|---|---|
committer | Wen Heping <wen@FreeBSD.org> | 2017-10-30 02:27:23 +0000 |
commit | eaf75bad8db19247a962a42460aed3f5c5db613c (patch) | |
tree | 93c2c2f15f825030d7a4a4609111a70c7d5a3cf2 /biology/mummer | |
parent | d91015f8f4894e7f079987591313b3d4aab327a7 (diff) | |
download | ports-eaf75bad8db19247a962a42460aed3f5c5db613c.tar.gz ports-eaf75bad8db19247a962a42460aed3f5c5db613c.zip |
- Fix installing scripts and support binaries
- Add LICENSE
PR: 223098
Submitted by: mzaki@niid.go.jp
Notes
Notes:
svn path=/head/; revision=453152
Diffstat (limited to 'biology/mummer')
-rw-r--r-- | biology/mummer/Makefile | 26 | ||||
-rw-r--r-- | biology/mummer/distinfo | 1 | ||||
-rw-r--r-- | biology/mummer/files/patch-Makefile | 14 | ||||
-rw-r--r-- | biology/mummer/pkg-plist | 6 |
4 files changed, 39 insertions, 8 deletions
diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile index 9d3b56bc5d00..4a7311012156 100644 --- a/biology/mummer/Makefile +++ b/biology/mummer/Makefile @@ -3,7 +3,7 @@ PORTNAME= mummer PORTVERSION= 3.23 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= SF DISTNAME= MUMmer${PORTVERSION} @@ -11,20 +11,36 @@ DISTNAME= MUMmer${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Modular system for rapid whole genome alignment -USES= gmake perl5 +LICENSE= ART10 +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= gmake perl5 shebangfix + +SHEBANG_FILES= scripts/*.csh scripts/*.pl +SHEBANG_LANG= csh +perl_OLD_CMD= __PERL_PATH +csh_OLD_CMD= __CSH_PATH +csh_CMD= /bin/csh +_SHEBANG_REINPLACE_ARGS+= -e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g" PROGRAMS= annotate combineMUMs delta-filter gaps \ mgaps mummer repeat-match show-aligns \ show-coords show-diff show-snps show-tiling -SCRIPTS= dnadiff exact-tandems mapview mummerplot nucmer \ - nucmer2xfig promer run-mummer1 run-mummer3 +SCRIPTS= dnadiff.pl exact-tandems.csh mapview.pl mummerplot.pl nucmer.pl \ + nucmer2xfig.pl promer.pl run-mummer1.csh run-mummer3.csh +LIBEXEC= Foundation.pm tandem-repeat.awk DOCUMENTS= COPYRIGHT INSTALL LICENSE README OPTIONS_DEFINE= DOCS do-install: ${INSTALL_PROGRAM} ${PROGRAMS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin - ${INSTALL_SCRIPT} ${SCRIPTS:S|^|${WRKSRC}/|} ${STAGEDIR}${PREFIX}/bin +.for file in ${SCRIPTS} + ${INSTALL_SCRIPT} ${WRKSRC}/scripts/${file} ${STAGEDIR}${PREFIX}/bin/${file:R} +.endfor + @${MKDIR} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} + ${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/* ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} + ${INSTALL_DATA} ${LIBEXEC:S|^|${WRKSRC}/scripts/|} ${STAGEDIR}${PREFIX}/libexec/${PORTNAME} @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DOCUMENTS:S|^|${WRKSRC}/|} ${STAGEDIR}${DOCSDIR} diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo index 01b7da161860..f291784990f0 100644 --- a/biology/mummer/distinfo +++ b/biology/mummer/distinfo @@ -1,2 +1,3 @@ +TIMESTAMP = 1509357521 SHA256 (MUMmer3.23.tar.gz) = 1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f SIZE (MUMmer3.23.tar.gz) = 3160143 diff --git a/biology/mummer/files/patch-Makefile b/biology/mummer/files/patch-Makefile index 96948037b961..ff72cf75230c 100644 --- a/biology/mummer/files/patch-Makefile +++ b/biology/mummer/files/patch-Makefile @@ -1,4 +1,4 @@ ---- Makefile.orig 2015-08-05 01:03:53 UTC +--- Makefile.orig 2011-12-17 02:49:27 UTC +++ Makefile @@ -35,16 +35,11 @@ SCRIPT_DIR := $(TOP_DIR)/scripts TIGR_SRC_DIR := $(TOP_DIR)/src/tigr @@ -8,8 +8,7 @@ -CXX := $(filter /%,$(shell /bin/sh -c 'type g++')) SED := $(filter /%,$(shell /bin/sh -c 'type sed')) CSH := $(filter /%,$(shell /bin/sh -c 'type csh')) --PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) -+PERL := ${LOCALBASE}/bin/perl + PERL := $(filter /%,$(shell /bin/sh -c 'type perl')) AR := $(filter /%,$(shell /bin/sh -c 'type ar')) -CXXFLAGS = -O3 @@ -18,3 +17,12 @@ FLATS = ACKNOWLEDGEMENTS COPYRIGHT INSTALL LICENSE Makefile README ChangeLog +@@ -60,7 +55,7 @@ export BIN_DIR AUX_BIN_DIR CXX CC CFLAGS + .PHONY: all check clean dist scripts uninstall + + +-all: kurtz tigr scripts ++all: kurtz tigr + + + check: diff --git a/biology/mummer/pkg-plist b/biology/mummer/pkg-plist index ea64212aea4e..53b5159185a0 100644 --- a/biology/mummer/pkg-plist +++ b/biology/mummer/pkg-plist @@ -19,6 +19,12 @@ bin/show-coords bin/show-diff bin/show-snps bin/show-tiling +libexec/mummer/Foundation.pm +libexec/mummer/postnuc +libexec/mummer/postpro +libexec/mummer/prenuc +libexec/mummer/prepro +libexec/mummer/tandem-repeat.awk %%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT %%PORTDOCS%%%%DOCSDIR%%/INSTALL %%PORTDOCS%%%%DOCSDIR%%/LICENSE |