sci-biology/bedops: new package

The patch does not expand properly CXXFLAGS for some reason.
The package conatains bundled zlib. bzip2 and other 3rd-party stuff.
It compile statically at least some binaries.

Package-Manager: Portage-2.3.5, Repoman-2.3.2

4 files changed, 176 insertions, 0 deletions

diff --git a/sci-biology/bedops/Manifest b/sci-biology/bedops/Manifest
new file mode 100644
index 000000000..54a156cc2
--- /dev/null
+++ b/sci-biology/bedops/Manifest
@@ -0,0 +1 @@
+DIST bedops-2.4.26.tar.gz 27057360 SHA256 9b8ff43beec7b6e327179477b800a9c7ce98a010bbf59ba41fc2d7da9869586d SHA512 6c43ff4f42168da8e181e5d50e8d41a1c0a8c24bde3ca6ab81f9b2324d47b4f7d265e3031adf39ea7ad0e65773462d13ed59580774f5a0906b205b27648a8eaa WHIRLPOOL ad25d562dee5a51f10ee66d5a74984071b6aaddb1cde139b8fa2b420a2b6b10860c389eaf59f74c5fabc09851629f366747e7330432c0aa9c9d174606a3ffbfb
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild b/sci-biology/bedops/bedops-2.4.26.ebuild
new file mode 100644
index 000000000..d281fbede
--- /dev/null
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs eutils
+
+DESCRIPTION="Manipulate BED file (alternative to bedtools)"
+HOMEPAGE="http://bedops.readthedocs.io
+	https://github.com/bedops/bedops"
+SRC_URI="https://github.com/bedops/bedops/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+	default
+	local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
+	epatch ${PATCHES[@]}
+}
diff --git a/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
new file mode 100644
index 000000000..16ac4e2b0
--- /dev/null
+++ b/sci-biology/bedops/files/bedops-2.4.26-respect-cxxflags.patch
@@ -0,0 +1,138 @@
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile.darwin	2017-04-28 21:53:55.811777276 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS             = -O3 ${STDFLAGS}
++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
+ 
+ 
+ FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+--- bedops-2.4.26/applications/bed/bedextract/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedextract/src/Makefile	2017-04-28 21:54:05.952048644 +0200
+@@ -24,7 +24,7 @@
+ INCLUDES                = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION             = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES               = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS                = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS                = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS                  = -static
+ 
+ dependency_names        = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+@@ -64,4 +64,4 @@
+ 	rm -rf $(OBJDIR)
+ 	rm -f $(BINDIR)/$(PROG)
+ 	rm -f $(BINDIR)/*.$(PROG)
+-	rm -rf $(BINDIR)
+\ No newline at end of file
++	rm -rf $(BINDIR)
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile.darwin	2017-04-28 21:54:12.162214836 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBLIBDIR}
+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS             = -O3 ${STDFLAGS}
++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
+ 
+ FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+ 
+--- bedops-2.4.26/applications/bed/bedmap/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedmap/src/Makefile	2017-04-28 21:54:19.472410465 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES            = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11 
++BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11 
+ SFLAGS              = -static
+ 
+ dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile.darwin	2017-04-28 21:54:25.422569698 +0200
+@@ -1,7 +1,7 @@
+ MIN_OSX_VERSION           = 10.7
+ BLDFLAGS                  = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS               = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS                    = -O3
++CFLAGS                    = ${CXXFLAGS:--O3}
+ CDFLAGS                   = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS                   = -pg
+ LIBS                      = -lpthread
+--- bedops-2.4.26/applications/bed/conversion/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/conversion/src/Makefile	2017-04-28 21:54:30.832714482 +0200
+@@ -1,6 +1,6 @@
+ BLDFLAGS                  = -Wall -Wextra -pedantic -std=c99
+ COMMONFLAGS               = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1
+-CFLAGS                    = -O3
++CFLAGS                    = ${CXXFLAGS:--O3}
+ CDFLAGS                   = -DDEBUG=1 -g -O0 -fno-inline
+ CPFLAGS                   = -pg
+ LIBS                      = -lpthread
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile.darwin	2017-04-28 21:54:37.312887898 +0200
+@@ -27,7 +27,7 @@
+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS             = -O3 ${STDFLAGS}
++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
+ 
+ FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+ 
+--- bedops-2.4.26/applications/bed/bedops/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/bedops/src/Makefile	2017-04-28 21:54:43.513053823 +0200
+@@ -25,7 +25,7 @@
+ INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS              = -static
+ 
+ dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile.darwin	2017-04-28 21:54:49.093203153 +0200
+@@ -28,7 +28,7 @@
+ LIBLOCATION          = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES            = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+ STDFLAGS             = -Wall -pedantic -std=c++11 -stdlib=libc++
+-BLDFLAGS             = -O3 ${STDFLAGS}
++BLDFLAGS             = ${CXXFLAGS:--O3} ${STDFLAGS}
+ 
+ FLAGS                = $(BLDFLAGS) $(OBJDIR)/NaN.o $(OBJDIR)/starchConstants.o $(OBJDIR)/starchFileHelpers.o $(OBJDIR)/starchHelpers.o $(OBJDIR)/starchMetadataHelpers.o $(OBJDIR)/unstarchHelpers.o $(OBJDIR)/starchSha1Digest.o $(OBJDIR)/starchBase64Coding.o ${LIBLOCATION} ${INCLUDES}
+ 
+--- bedops-2.4.26/applications/bed/closestfeats/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/closestfeats/src/Makefile	2017-04-28 21:54:54.283342049 +0200
+@@ -23,7 +23,7 @@
+ INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+ LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
+ LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+-BLDFLAGS            = -Wall -pedantic -O3 -std=c++11
++BLDFLAGS            = -Wall -pedantic ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS              = -static
+ 
+ dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile.darwin	2017-04-28 21:55:00.023495662 +0200
+@@ -7,7 +7,7 @@
+ PROG                 = sort-bed
+ DIST_DIR             = ../bin
+ OBJ_DIR              = objects_${ARCH}
+-OPTIMIZE             = -O3 -std=c++11 -stdlib=libc++
++OPTIMIZE             = ${CXXFLAGS:--O3} -std=c++11 -stdlib=libc++
+ WARNINGS             = -Wall
+ MAIN                 = ../../../..
+ HEAD                 = ${MAIN}/interfaces/general-headers
+--- bedops-2.4.26/applications/bed/sort-bed/src/Makefile.ori	2017-03-14 08:43:22.000000000 +0100
++++ bedops-2.4.26/applications/bed/sort-bed/src/Makefile	2017-04-28 21:55:05.663646597 +0200
+@@ -29,7 +29,7 @@
+ BINDIR              = ../bin
+ OBJDIR             = objects
+ WARNINGS            = -Wall -Wextra -pedantic
+-BLDFLAGS            = ${WARNINGS} -O3 -std=c++11
++BLDFLAGS            = ${WARNINGS} ${CXXFLAGS:--O3} -std=c++11
+ SFLAGS              = -static
+ 
+ dependency_names    = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
diff --git a/sci-biology/bedops/metadata.xml b/sci-biology/bedops/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/bedops/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="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>