In tree

Signed-off-by: Justin Lecher <jlec@gentoo.org>

10 files changed, 0 insertions, 379 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
deleted file mode 100644
index b5f200eea..000000000
--- a/sci-biology/mira/ChangeLog
+++ /dev/null
@@ -1,57 +0,0 @@
-# ChangeLog for sci-biology/mira
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-*mira-4.0.1 (12 Apr 2014)
-
-  12 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +mira-4.0.1.ebuild:
-  sci-biology/mira-4.0.1: bump to current recommended bugfix release
-
-  06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.4.0.1.ebuild,
-  -mira-3.4.1.1.ebuild, -mira-3.9.9.ebuild, -mira-3.9.15.ebuild,
-  -mira-4.0_rc2.ebuild, mira-4.0_rc4.ebuild:
-  Drop old; punt base.eclass
-
-  12 Nov 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  mira-3.4.0.1.ebuild, mira-3.4.1.1.ebuild, mira-3.9.9.ebuild,
-  mira-3.9.15.ebuild, mira-4.0_rc2.ebuild, +mira-4.0_rc4.ebuild:
-  Added 4.0_rc4 release candidate. Removing the sed hack redirecting autoconf
-  to config/m4/ instead of m4/ because upstream accepted that source tree
-  layout change in _rc3 already.
-
-
-  01 Oct 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  mira-4.0_rc2.ebuild:
-  Improve ebuild to use MY_PV.
-
-  25 Sep 2013; Justin Lecher <jlec@gentoo.org> mira-4.0_rc2.ebuild,
-  metadata.xml:
-  Fix m4 macrodir location
-
-*mira-3.9.15 (30 Apr 2013)
-
-  30 Apr 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  +mira-3.9.15.ebuild:
-  sci-biology/mira-3.9.15: bump to current besta version mira-3.9.15.ebuild
-
-*mira-3.4.1.1 (22 Feb 2013)
-*mira-3.9.9 (22 Feb 2013)
-
-  22 Feb 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  +files/mira-3.4.0.2-boost-1.50.patch, +mira-3.4.1.1.ebuild,
-  +mira-3.9.9.ebuild:
-  sci-biology/mira: current stable and development version bumps
-
-  22 May 2012; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r2.ebuild,
-  -mira-3.2.1.17-r1.ebuild, -mira-3.2.1.20.ebuild, mira-3.4.0.1.ebuild:
-  Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop
-  old
-
-*mira-3.4.0.1 (08 Dec 2011)
-
-  08 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-  +mira-3.4.0.1.ebuild, +files/mira-3.4.0.1-asneeded.patch:
-  version bump and dropped the expat patch for --as-needed CFLAGS as upstream
-  fixed that in a different way, the still applicable part of the patch is
-  however provided under files/ but is just a cosmetic change (hence not really
-  needed)
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
deleted file mode 100644
index 98cb65231..000000000
--- a/sci-biology/mira/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST mira-4.0.2.tar.bz2 10368046 SHA256 a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80 SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e WHIRLPOOL d038472f9b129e97883f59c471df51f07315ee38eda5a9e804cdd2d33988306162b1bb1dde2cb7fd510c82be5734240dfd69364d39865a47af439762c7154747
-DIST mira-4.0rc4.tar.bz2 10418692 SHA256 5149e25462625be98a18945921e17bb3c9bef110d820af295c7473a44acf09b4 SHA512 9ada6abaf36993e8738cd8fbe7ec710e0672335afc83902fd962fe9c0c430dae80df64f272bfbb1b4d132cb080e93ed791eaf8a7652b22e5e6e816466fe3eb5b WHIRLPOOL f2d605f2ad7985f60038ed93d4c1d45b6b60c97552588ac1daae449f8ee503691c0ef79d52df75bd9241cdc888a107df2801d31c9e6c9b8e3c6f3c561910c09f
-DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
diff --git a/sci-biology/mira/files/libtool.m4.patch b/sci-biology/mira/files/libtool.m4.patch
deleted file mode 100644
index 9cfaeef09..000000000
--- a/sci-biology/mira/files/libtool.m4.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- config/m4/libtool.m4.ori	2011-06-22 12:28:14.000000000 +0200
-+++ config/m4/libtool.m4	2011-06-22 12:28:39.000000000 +0200
-@@ -88,10 +88,6 @@
- # This can be used to rebuild libtool when needed
- LIBTOOL_DEPS="$ltmain"
- 
--# Always use our own libtool.
--LIBTOOL='$(SHELL) $(top_builddir)/libtool'
--AC_SUBST(LIBTOOL)dnl
--
- _LT_SETUP
- 
- # Only expand once:
diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch
deleted file mode 100644
index 9bbd267cf..000000000
--- a/sci-biology/mira/files/mira-3.0.0-asneeded.patch
+++ /dev/null
@@ -1,56 +0,0 @@
-http://bugs.gentoo.org/show_bug.cgi?id=305547
-
---- config/m4/ax_lib_expat.m4
-+++ config/m4/ax_lib_expat.m4
-@@ -96,6 +99,7 @@
- 
-     EXPAT_CFLAGS=""
-     EXPAT_LDFLAGS=""
-+    EXPAT_LIBS=""
-     EXPAT_VERSION=""
- 
-     dnl
-@@ -105,7 +109,8 @@
- 
-     if test -n "$expat_prefix"; then
-         expat_include_dir="$expat_prefix/include"
--        expat_lib_flags="-L$expat_prefix/lib -lexpat"
-+        expat_lib_flags="-L$expat_prefix/lib"
-+        expat_libs="-lexpat"
-         run_expat_test="yes"
-     elif test "$expat_requested" = "yes"; then
-         if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then
-@@ -126,6 +131,8 @@
-         saved_LDFLAGS="$LDFLAGS"
-         LDFLAGS="$LDFLAGS $expat_lib_flags"
- 
-+        saved_LIBS="$LIBS"
-+        LIBS="$LIBS $expat_libs"
-         dnl
-         dnl Check Expat headers
-         dnl
-@@ -171,7 +178,8 @@
-                     ]]
-                 )],
-                 [
-                 EXPAT_LDFLAGS="$expat_lib_flags"
-+                EXPAT_LIBS="$expat_libs"
-                 expat_lib_found="yes"
-                 AC_MSG_RESULT([found])
-                 ],
-@@ -185,6 +193,7 @@
- 
-         CPPFLAGS="$saved_CPPFLAGS"
-         LDFLAGS="$saved_LDFLAGS"
-+        LIBS="$saved_LIBS"
-     fi
- 
-     AC_MSG_CHECKING([for Expat XML Parser])
-@@ -194,6 +203,7 @@
- 
-             AC_SUBST([EXPAT_CFLAGS])
-             AC_SUBST([EXPAT_LDFLAGS])
-+            AC_SUBST([EXPAT_LIBS])
- 
-             HAVE_EXPAT="yes"
-         else
diff --git a/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch b/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch
deleted file mode 100644
index 418432376..000000000
--- a/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch
+++ /dev/null
@@ -1,29 +0,0 @@
---- config/m4/ax_lib_expat.m4.ori	2011-12-08 01:59:42.000000000 +0100
-+++ config/m4/ax_lib_expat.m4	2011-12-08 02:00:08.000000000 +0100
-@@ -108,7 +108,8 @@
- 
-     if test -n "$expat_prefix"; then
-         expat_include_dir="$expat_prefix/include"
--        expat_lib_flags="-L$expat_prefix/lib -lexpat"
-+        expat_lib_flags="-L$expat_prefix/lib"
-+        expat_libs="-lexpat"
-         run_expat_test="yes"
-     elif test "$expat_requested" = "yes"; then
-         if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then
-@@ -129,6 +130,8 @@
-         saved_LDFLAGS="$LDFLAGS"
-         LIBS="$LDFLAGS $expat_lib_flags"
- 
-+        saved_LIBS="$LIBS"
-+        LIBS="$LIBS $expat_libs"
-         dnl
-         dnl Check Expat headers
-         dnl
-@@ -188,6 +191,7 @@
- 
-         CPPFLAGS="$saved_CPPFLAGS"
-         LDFLAGS="$saved_LDFLAGS"
-+        LIBS="$saved_LIBS"
-     fi
- 
-     AC_MSG_CHECKING([for Expat XML Parser])
diff --git a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch b/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
deleted file mode 100644
index 427192294..000000000
--- a/sci-biology/mira/files/mira-3.4.0.2-boost-1.50.patch
+++ /dev/null
@@ -1,24 +0,0 @@
- config/m4/ax_boost_regex.m4 | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/config/m4/ax_boost_regex.m4 b/config/m4/ax_boost_regex.m4
-index 1ac06af..5b7be93 100644
---- a/config/m4/ax_boost_regex.m4
-+++ b/config/m4/ax_boost_regex.m4
-@@ -78,14 +78,14 @@ AC_DEFUN([AX_BOOST_REGEX],
-                 for libextension in `ls $BOOSTLIBDIR/libboost_regex*.so* $BOOSTLIBDIR/libboost_regex*.a* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^lib\(boost_regex.*\)\.so.*$;\1;' -e 's;^lib\(boost_regex.*\)\.a*$;\1;'` ; do
-                      ax_lib=${libextension}
- 				    AC_CHECK_LIB($ax_lib, exit,
--                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-+                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-                                  [link_regex="no"])
- 				done
-                 if test "x$link_regex" != "xyes"; then
-                 for libextension in `ls $BOOSTLIBDIR/boost_regex*.{dll,a}* 2>/dev/null | sed 's,.*/,,' | sed -e 's;^\(boost_regex.*\)\.dll.*$;\1;' -e 's;^\(boost_regex.*\)\.a*$;\1;'` ; do
-                      ax_lib=${libextension}
- 				    AC_CHECK_LIB($ax_lib, exit,
--                                 [BOOST_REGEX_LIB="-l$ax_lib"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-+                                 [BOOST_REGEX_LIB="-l$ax_lib -lboost_system"; AC_SUBST(BOOST_REGEX_LIB) link_regex="yes"; break],
-                                  [link_regex="no"])
- 				done
-                 fi
diff --git a/sci-biology/mira/files/mira_left_clip.readpool.C.patch b/sci-biology/mira/files/mira_left_clip.readpool.C.patch
deleted file mode 100644
index 12977dd7c..000000000
--- a/sci-biology/mira/files/mira_left_clip.readpool.C.patch
+++ /dev/null
@@ -1,36 +0,0 @@
-*** src/mira/readpool.C.ori	2010-11-21 11:42:29.000000000 -0600
---- src/mira/readpool.C	2011-01-13 10:20:38.000000000 -0600
-***************
-*** 1751,1757 ****
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT  : {
-! 	  REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str()));
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT  : {
---- 1751,1757 ----
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT  : {
-! 	  REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str())-1);
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT  : {
-***************
-*** 1759,1765 ****
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT  : {
-! 	  REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str()));
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT  : {
---- 1759,1765 ----
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT  : {
-! 	  REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str())-1);
-  	  break;
-  	}
-  	case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT  : {
diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml
deleted file mode 100644
index 2bc893037..000000000
--- a/sci-biology/mira/metadata.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-  <maintainer>
-    <email>mmokrejs@fold.natur.cuni.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.0.2.ebuild
deleted file mode 100644
index f9c38faeb..000000000
--- a/sci-biology/mira/mira-4.0.2.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-MIRA_3RDPARTY_PV="06-07-2012"
-MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
-
-inherit autotools eutils multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="
-	http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-#	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
-#	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-S="${WORKDIR}"/"${PN}"-"${MY_PV}"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="doc"
-
-CDEPEND="
-	dev-libs/boost
-	dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	app-editors/vim-core
-	dev-libs/expat"
-RDEPEND="${CDEPEND}"
-
-#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
-#	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
-DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
-
-src_prepare() {
-	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
-	epatch \
-		"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch
-
-	sed \
-		-e "s:-O[23]::g" \
-		-e "s:-funroll-loops::g" \
-		-i configure.ac || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-thread=boost_thread-mt
-}
-
-#src_compile() {
-#	base_src_compile
-#	# TODO: resolve docbook incompatibility for building docs
-#	if use doc; then emake -C doc clean docs || die; fi
-#}
-
-src_install() {
-	default
-	dodoc ${DOCS[@]}
-
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
-}
-
-pkg_postinst() {
-	einfo "Documentation is no longer built, you can find it at:"
-	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}
diff --git a/sci-biology/mira/mira-4.0_rc4.ebuild b/sci-biology/mira/mira-4.0_rc4.ebuild
deleted file mode 100644
index f9c38faeb..000000000
--- a/sci-biology/mira/mira-4.0_rc4.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-MIRA_3RDPARTY_PV="06-07-2012"
-MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
-
-inherit autotools eutils multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="
-	http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-#	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
-#	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-S="${WORKDIR}"/"${PN}"-"${MY_PV}"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="doc"
-
-CDEPEND="
-	dev-libs/boost
-	dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	app-editors/vim-core
-	dev-libs/expat"
-RDEPEND="${CDEPEND}"
-
-#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
-#	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
-DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
-
-src_prepare() {
-	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
-	epatch \
-		"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch
-
-	sed \
-		-e "s:-O[23]::g" \
-		-e "s:-funroll-loops::g" \
-		-i configure.ac || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-thread=boost_thread-mt
-}
-
-#src_compile() {
-#	base_src_compile
-#	# TODO: resolve docbook incompatibility for building docs
-#	if use doc; then emake -C doc clean docs || die; fi
-#}
-
-src_install() {
-	default
-	dodoc ${DOCS[@]}
-
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
-}
-
-pkg_postinst() {
-	einfo "Documentation is no longer built, you can find it at:"
-	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}