diff options
Diffstat (limited to 'sci-biology/prodigal')
| -rw-r--r-- | sci-biology/prodigal/Manifest | 6 | ||||
| -rw-r--r-- | sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch | 45 | ||||
| -rw-r--r-- | sci-biology/prodigal/metadata.xml | 12 | ||||
| -rw-r--r-- | sci-biology/prodigal/prodigal-2.6.3.ebuild | 26 |
4 files changed, 89 insertions, 0 deletions
diff --git a/sci-biology/prodigal/Manifest b/sci-biology/prodigal/Manifest new file mode 100644 index 000000000000..9b0a5204df82 --- /dev/null +++ b/sci-biology/prodigal/Manifest @@ -0,0 +1,6 @@ +AUX prodigal-2.6.3-fix-build-system.patch 1004 SHA256 a591b4457c5915767f4beb8e35dc24cad27c7465fc7187d2ef7c4cb3279d884a SHA512 c96e93cbe344bbab43b03b0046b1bca5030f4a731a0b43ea4d4ee87d303502d172fc93975a9d7b907d6ea6beeb865113122e0e2cbca7d660290994bb8214a17b WHIRLPOOL d30873d8195731fa6d3e064ab29ae955c7007c6768bece16b51964678cfa339097cea3fe013bd35550710963aab20b0e8475b469b3dd6f2743cf910027e0c793 +DIST prodigal-2.6.3.tar.gz 610934 SHA256 89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f SHA512 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541 WHIRLPOOL d218510194777a15699cde33641768b24844e2077a1f63274a9d02c0d494c0d854dbbcf638df92839acd89916af63267d8e50b307a325f2e8026023675050fec +EBUILD prodigal-2.6.3.ebuild 518 SHA256 efe4a785351a8be9cd3432dc15c41724ecf305d6fd04faa9e54ccd98773bafc8 SHA512 44048cc1a61e2e7decd5b4dda026e4b89ba54decfb1f63ad3d378c3b8ebef707b3e3c2338108186be9a3f9400bca165f3331a1f1dd668345716b15c01189a0e1 WHIRLPOOL a4a56de898c2d2808769b4d6c9483d792c5b7f62c4d9d093724bb667f82218993633274543562ebe32f5eacb77ce0e3abfa72524132382b61928245da89e1e46 +MISC ChangeLog 2849 SHA256 ef72db7ba5819079c8675ca2da4b53e194874a6ae35497bfabf03df3f1f97b17 SHA512 901c7cbff9425af0de5bda56919a98e38e453ec433772ad7848daa4a8e33ed9c2fdd73ee58c5648053a01e918c97158fc3d3180aac96b8dd907d0ae56e65cb50 WHIRLPOOL c40dc7b605ff2d672714524c65ec33b467beacfa9f7be3530a4e3aa3358ec89d0ab15ee85f2320953f7a204c2c72893de757bea68f801c482d981c72d1745690 +MISC ChangeLog-2015 489 SHA256 b2ce355b89ace8cf2e9a0feb96fe463dcc091efcc33d5dfb783b6d219394a5e8 SHA512 3c06823730bb20bf16b25bafcaf46d80dcc81c8bde872dc6d7062fc4e41407c765db070811fc87f0da92ae91f8abbd21c9794d225db020bf3686451639e74c78 WHIRLPOOL 3a1470d72ae3f1c9e0c48fbeffd108949a1b5bfc10ae11ff39a258c9c5044fbaad3e241304734ff9c50deef1bb9e4ab33a51936f9a524dd2931111d692741701 +MISC metadata.xml 395 SHA256 a2d34a89290a1b9bbe5f012a54abf168ee3ba251804c4bd1af93a0fbe20fa9a7 SHA512 d824206729a7012b67bc0dff475f08d769484c601165a72c159383cc23247726cc38d9dae85492f39cdae99dc83c2a4adbb44cc8abded5ee8cad8067bec7873a WHIRLPOOL 8c63f9d2150459cc5b406d808fc3aa322ab446b1ba9ec3700cf553ff9f3027e11467c5f134cb4ae1311ff742fbadaf506d8f592b0528b33214bbe4970729cec1 diff --git a/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch new file mode 100644 index 000000000000..b6d92392d179 --- /dev/null +++ b/sci-biology/prodigal/files/prodigal-2.6.3-fix-build-system.patch @@ -0,0 +1,45 @@ +Fix build system to honour user variables. + +--- a/Makefile ++++ b/Makefile +@@ -19,32 +19,31 @@ + ############################################################################## + + SHELL = /bin/sh +-CC = gcc ++CC ?= gcc + +-CFLAGS += -pedantic -Wall -O3 +-LFLAGS = -lm $(LDFLAGS) ++LIBS = -lm + + TARGET = prodigal + SOURCES = $(shell echo *.c) + HEADERS = $(shell echo *.h) + OBJECTS = $(SOURCES:.c=.o) + +-INSTALLDIR = /usr/local/bin ++BINDIR = $(EPREFIX)/usr/bin + + all: $(TARGET) + + $(TARGET): $(OBJECTS) +- $(CC) $(CFLAGS) -o $@ $^ $(LFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS) + + %.o: %.c $(HEADERS) +- $(CC) $(CFLAGS) -c -o $@ $< ++ $(CC) -Wall -pedantic $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + + install: $(TARGET) +- install -d -m 0755 $(INSTALLDIR) +- install -m 0755 $(TARGET) $(INSTALLDIR) ++ install -d -m 0755 $(DESTDIR)$(BINDIR) ++ install -m 0755 $(TARGET) $(DESTDIR)$(BINDIR) + + uninstall: +- -rm $(INSTALLDIR)/$(TARGET) ++ -rm $(DESTDIR)$(BINDIR)/$(TARGET) + + clean: + -rm -f $(OBJECTS) diff --git a/sci-biology/prodigal/metadata.xml b/sci-biology/prodigal/metadata.xml new file mode 100644 index 000000000000..e086d08df6f7 --- /dev/null +++ b/sci-biology/prodigal/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <upstream> + <remote-id type="google-code">prodigal</remote-id> + <remote-id type="github">hyattpd/Prodigal</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/prodigal/prodigal-2.6.3.ebuild b/sci-biology/prodigal/prodigal-2.6.3.ebuild new file mode 100644 index 000000000000..db8382982284 --- /dev/null +++ b/sci-biology/prodigal/prodigal-2.6.3.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +DESCRIPTION="Prokaryotic Dynamic Programming Genefinding Algorithm" +HOMEPAGE="http://prodigal.ornl.gov/" +SRC_URI="https://github.com/hyattpd/${PN^}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="" + +S=${WORKDIR}/${P^} + +PATCHES=( "${FILESDIR}"/${PN}-2.6.3-fix-build-system.patch ) + +src_configure() { + tc-export CC +} |