[gentoo-commits] proj/sci:master commit in: sci-biology/sgp2/, profiles/, sci-biology/sgp2/files/

[gentoo-commits] proj/sci:master commit in: sci-biology/sgp2/, profiles/, sci-biology/sgp2/files/

[Andrew Ammerlaan]

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>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</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
-}