commit: 7be32ed8459070a16342335000525780151daeeb
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 09:41:21 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 09:41:21 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7be32ed8
sci-biology/sgp2: remove pack, upstream gone
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
sci-biology/sgp2/files/Makefile.patch | 88 -----------------------------------
sci-biology/sgp2/metadata.xml | 12 -----
sci-biology/sgp2/sgp2-1.1.ebuild | 34 --------------
4 files changed, 135 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 41a1db3ba..a4258e152 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -99,4 +99,3 @@ sci-biology/prokka
sci-biology/reptile
sci-biology/RSeQC
sci-biology/scaffold_builder
-sci-biology/sgp2
diff --git a/sci-biology/sgp2/files/Makefile.patch
b/sci-biology/sgp2/files/Makefile.patch
deleted file mode 100644
index c1d64bdc8..000000000
--- a/sci-biology/sgp2/files/Makefile.patch
+++ /dev/null
@@ -1,88 +0,0 @@
---- 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/, $(HSP2SR)) \
diff --git a/sci-biology/sgp2/metadata.xml b/sci-biology/sgp2/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/sgp2/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";>
-<pkgmetadata>
- <maintainer type="person">
- <email>[email protected]</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>[email protected]</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/sgp2/sgp2-1.1.ebuild b/sci-biology/sgp2/sgp2-1.1.ebuild
deleted file mode 100644
index 58620bbdb..000000000
--- a/sci-biology/sgp2/sgp2-1.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Find ORFs by comparing two genomic/EST sequences"
-HOMEPAGE="http://genome.crg.es/software/sgp2/";
-SRC_URI="ftp://genome.crg.es/pub/software/sgp2/sgp2_v1.1.May_8_2012.tar.gz";
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
- sci-biology/geneid"
-
-S="${WORKDIR}"/"${PN}"
-
-src_prepare() {
- # disable bundled geneid sources
- epatch "${FILESDIR}"/Makefile.patch
- # do not look for renamed geneid-sgp binary
- sed -i -e 's#geneid-sgp#geneid#g' src/sgp2.pl
-}
-
-src_install() {
- dobin bin/sgp2 bin/parseblast
- insinto /usr/share/"${PN}"
- doins -r param samples
-}
