commit: 12a997ad3dcdf83f8bb23f4d6c0cc87708ebb784 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jun 17 10:42:01 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jun 17 10:42:01 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=12a997ad
sci-biology/sgp2: new package, works Package-Manager: portage-2.2.7 --- sci-biology/sgp2/ChangeLog | 9 ++++ sci-biology/sgp2/files/Makefile.patch | 88 +++++++++++++++++++++++++++++++++++ sci-biology/sgp2/metadata.xml | 9 ++++ sci-biology/sgp2/sgp2-1.1.ebuild | 34 ++++++++++++++ 4 files changed, 140 insertions(+) diff --git a/sci-biology/sgp2/ChangeLog b/sci-biology/sgp2/ChangeLog new file mode 100644 index 0000000..4175f83 --- /dev/null +++ b/sci-biology/sgp2/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/sgp2 +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*sgp2-1.1 (17 Jun 2014) + + 17 Jun 2014; Martin Mokrejs <[email protected]> + +files/Makefile.patch, +metadata.xml, +sgp2-1.1.ebuild: + sci-biology/sgp2: new package, works diff --git a/sci-biology/sgp2/files/Makefile.patch b/sci-biology/sgp2/files/Makefile.patch new file mode 100644 index 0000000..c1d64bd --- /dev/null +++ b/sci-biology/sgp2/files/Makefile.patch @@ -0,0 +1,88 @@ +--- Makefile.ori 2014-06-17 12:24:40.000000000 +0200 ++++ Makefile 2014-06-17 12:26:47.000000000 +0200 +@@ -39,12 +39,12 @@ + # + ### PATHS + +- BBIN = /bin +- UBIN = /usr/bin +- LBIN = /usr/local/bin ++ BBIN = $(DESTDIR)/bin ++ UBIN = $(DESTDIR)/usr/bin ++ LBIN = $(DESTDIR)/usr/local/bin + #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + # REMEMBER: INSTALLDIR is the only variable that should be modified +- INSTALLDIR = $(LBIN) ++ INSTALLDIR = $(UBIN) + #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + # +@@ -97,19 +97,19 @@ + + SGP2 = sgp2 + PARSEBLAST = parseblast +- GENEID = geneid ++# GENEID = geneid + # HSP2SR = blast2gff + + +- GENEIDD = $(SRC)/geneid ++# GENEIDD = $(SRC)/geneid + # HSP2SRD = $(SRC)/blast2gff + +- GENEIDSRC = $(wildcard $(addprefix $(GENEIDD)/src/, *.c)) \ +- $(wildcard $(addprefix $(GENEIDD)/include/, *.h)) ++# GENEIDSRC = $(wildcard $(addprefix $(GENEIDD)/src/, *.c)) \ ++# $(wildcard $(addprefix $(GENEIDD)/include/, *.h)) + # HSP2SRSRC = $(wildcard $(addprefix $(HSP2SRD)/src/, *.c)) \ + # $(wildcard $(addprefix $(HSP2SRD)/include/, *.h)) + +- SRCCODE = $(GENEID)-sgp $(PARSEBLAST) \ ++ SRCCODE = $(PARSEBLAST) \ + $(SGP2) + # SRCCODE = $(GENEID)-sgp $(PARSEBLAST) \ + # $(HSP2SR) $(SGP2) +@@ -134,9 +134,9 @@ + cleanbin : + -@$(RM) -f $(wildcard $(BIN)/*); + rmdir $(BIN); +- @echo "### Cleaning GENEID..." +- @cd $(GENEIDD); \ +- $(MAKE) clean; ++# @echo "### Cleaning GENEID..." ++# @cd $(GENEIDD); \ ++# $(MAKE) clean; + # @echo "### Cleaning HSP2SR..." + # @cd $(HSP2SRD); \ + # $(MAKE) clean; +@@ -147,6 +147,7 @@ + + installbin : $(BINCODE) + @echo "### COPYING BIN FILES TO $(INSTALLDIR)..."; ++ mkdir -p $(INSTALLDIR); + @$(CP) -p $^ $(INSTALLDIR)/; + + # +@@ -155,14 +156,14 @@ + $(BIN) : + mkdir $(BIN); + +-$(addprefix $(BIN)/, $(GENEID)-sgp) : $(addprefix $(GENEIDD)/bin/, $(GENEID)) +- @${CP} $(addprefix $(GENEIDD)/bin/, $(GENEID)) \ +- $(addprefix $(BIN)/, $(GENEID)-sgp) +- +-$(addprefix $(GENEIDD)/bin/, $(GENEID)) : $(GENEIDSRC) +- @echo "### Making GENEID..." +- @cd $(GENEIDD); \ +- $(MAKE) -f ./Makefile; ++#$(addprefix $(BIN)/, $(GENEID)-sgp) : $(addprefix $(GENEIDD)/bin/, $(GENEID)) ++# @${CP} $(addprefix $(GENEIDD)/bin/, $(GENEID)) \ ++# $(addprefix $(BIN)/, $(GENEID)-sgp) ++ ++#$(addprefix $(GENEIDD)/bin/, $(GENEID)) : $(GENEIDSRC) ++# @echo "### Making GENEID..." ++# @cd $(GENEIDD); \ ++# $(MAKE) -f ./Makefile; + + #$(addprefix $(BIN)/, $(HSP2SR)) : $(addprefix $(HSP2SRD)/bin/, $(HSP2SR)) + # @${CP} $(addprefix $(HSP2SRD)/bin/, $(HSP2SR)) \ diff --git a/sci-biology/sgp2/metadata.xml b/sci-biology/sgp2/metadata.xml new file mode 100644 index 0000000..2bc8930 --- /dev/null +++ b/sci-biology/sgp2/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>[email protected]</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/sgp2/sgp2-1.1.ebuild b/sci-biology/sgp2/sgp2-1.1.ebuild new file mode 100644 index 0000000..cd6becf --- /dev/null +++ b/sci-biology/sgp2/sgp2-1.1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Find ORFs by comparing two genomic/EST sequences using tblastx and geneid ab initio predictions" +HOMEPAGE="http://genome.crg.es/software/sgp2/"; +SRC_URI="ftp://genome.crg.es/pub/software/sgp2/sgp2_v1.1.May_8_2012.tar.gz"; + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="dev-lang/perl" +RDEPEND="${DEPEND} + sci-biology/geneid" + +S="${WORKDIR}"/"${PN}" + +src_prepare() { + # disable bundled geneid sources + epatch "${FILESDIR}"/Makefile.patch + # do not look for renamed geneid-sgp binary + sed -i -e 's#geneid-sgp#geneid#g' src/sgp2.pl +} + +src_install() { + insinto /usr/share/"${PN}" + doins -r param samples +}
