superseeded by sci-biology/allpathslg

Upstream wants anybody to move over

11 files changed, 0 insertions, 960 deletions

diff --git a/sci-biology/allpaths/ChangeLog b/sci-biology/allpaths/ChangeLog
deleted file mode 100644
index 5ae5d3da4f41..000000000000
--- a/sci-biology/allpaths/ChangeLog
+++ /dev/null
@@ -1,54 +0,0 @@
-# ChangeLog for sci-biology/allpaths
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/ChangeLog,v 1.12 2013/07/17 06:17:01 jlec Exp $
-
-  17 Jul 2013; Justin Lecher <jlec@gentoo.org> allpaths-3.1-r1.ebuild:
-  Bump to EAPI=5
-
-  11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
-  Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
-
-  19 Nov 2012; Justin Lecher <jlec@gentoo.org> allpaths-2.0.ebuild,
-  allpaths-3.1.ebuild, allpaths-3.1-r1.ebuild:
-  Block sci-biology/allpathslg due to file collision, #443740
-
-*allpaths-3.1-r1 (08 Nov 2012)
-
-  08 Nov 2012; Justin Lecher <jlec@gentoo.org> +allpaths-3.1-r1.ebuild,
-  +files/allpaths-3.1-boost-1.50-2.patch, +files/allpaths-3.1-boost-1.50.patch,
-  files/allpaths-3.1-gcc4.7.patch, +files/allpaths-3.1-linking.patch:
-  Fix for latest boost, #421727; fix for additional problem with gcc-4.7;
-  enable openmp support; Respect LDFALGS and CFLAGS everywhere; make it gold
-  resistant
-
-  30 Aug 2012; Justin Lecher <jlec@gentoo.org> allpaths-3.1.ebuild:
-  Respect CXXFLAGS
-
-  30 Aug 2012; Justin Lecher <jlec@gentoo.org> allpaths-3.1.ebuild,
-  +files/allpaths-3.1-gcc4.7.patch:
-  Fix for gcc-4.7
-
-*allpaths-3.1 (26 Jan 2010)
-
-  26 Jan 2010; Andrey Kislyuk <weaver@gentoo.org> +allpaths-3.1.ebuild:
-  Version bump
-
-  03 Jan 2010; Pacho Ramos <pacho@gentoo.org> allpaths-2.0.ebuild:
-  amd64 stable, bug 290927
-
-  24 Nov 2009; Christian Faulhammer <fauli@gentoo.org> allpaths-2.0.ebuild:
-  stable x86, bug 290927
-
-  20 Aug 2009; Andrey Kislyuk <weaver@gentoo.org>
-  +files/allpaths-2.0-gcc-x86-no-autocast.patch, allpaths-2.0.ebuild:
-  Fix compile issue on x86, bug 279711
-
-  07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> allpaths-2.0.ebuild:
-  Typo and collision fixes
-
-*allpaths-2.0 (07 Jul 2009)
-
-  07 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml,
-  +allpaths-2.0.ebuild:
-  New package, ebuild written by me
-
diff --git a/sci-biology/allpaths/Manifest b/sci-biology/allpaths/Manifest
deleted file mode 100644
index b5588a49af77..000000000000
--- a/sci-biology/allpaths/Manifest
+++ /dev/null
@@ -1,34 +0,0 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA512
-
-AUX allpaths-2.0-gcc-x86-no-autocast.patch 1481 SHA256 933377d2066d6dd3c8015ad005a12fd60cb1b8e90e7a966d9ff52b8fa30c2338 SHA512 4fd9788fd1283cac2453a357e0af6c243afaba457cf840ceb873b5504367eacb1b41fd74889374a06d088d7de88307e84999632766409a1713d42737b7704c73 WHIRLPOOL 629c9e6921eab98c09ca7ae29a373954a0bbdfc476d8a7119b3f07fb9995a86fb349db0dbee05a20184c050b380f305990421ff8ca407992e44ef75ab63a0a87
-AUX allpaths-3.1-boost-1.50-2.patch 6547 SHA256 37f3a778d41d77139014fc4bfedc6b0bea46aaf6cdcb377cf9b5c2b89f751d51 SHA512 79f8e478b02402d8ed774f2b4d1be3cb54342786f545b9a798ec5fb57a5e2a9be1cd33a655ffe11b8d5f068b57693334a15f1831dc25fb5b4849476b5a106e09 WHIRLPOOL 49d3370227765669669a960fbbbfd83f8ec0ac65c5fedfea5cc75f4e246de21b0e1befd81909d16660fbc45be671dfe68feb06f92512a35e81668b2dcf95b6e6
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-AUX allpaths-3.1-gcc4.7.patch 10074 SHA256 97b7073cde2e079fe60686bd441f4365be850d1d637437c7e447fdaf9b37a814 SHA512 42e5004b825fa09c3c2f10f8ef49ab238e9356bb3bdd00ec06f9ae06a146cc66647308ad15b7f582d40aedf7ccc930409d301df5533335107e55ca03f9626f2c WHIRLPOOL a11bb43440064ec93fbdc8c7f02628b852dcc7a6a5f7b9c502511555b19dc87c1c2c25d197f79cd956837320dd5f67f7cd040a1b8c8e5e316392eb560796d02d
-AUX allpaths-3.1-linking.patch 6323 SHA256 c83df085ab0c4a1418136b9fd1fb8487b802408f2a564ff4c1ff649adc0b7af4 SHA512 ccdb8ed9ac125e7d1d4269d34dd57f848c62dec62ce7491e445fa91155209d9e3c2ce040f42c4be12dce167346aff353cc03fa425fa8a619efd433916084294a WHIRLPOOL 872106247b8b9deff225627aeabc79e3b6b1afad2ccf72932202fad9fdab321c2b08c8c93104bcf7737a466a6d18f2755a87d6102a9586547ccb5e37a3c73166
-DIST AllPathsV3_Manual_r1.0.docx 287870 SHA256 497ce1649e627c542ac676cca2a6ab054347534b8521583795ae11d995b7680e SHA512 60646b79bcc94e47c04039b9778b637c0ae565dd7193caa90d2300197de996272397792bcc43fb9b58dd1a29941a04e3e498e395242c862f31e51105e6aceb34 WHIRLPOOL 3220858d2fc44acfe1d5667e5247b0af7dd5eaafba0fb936e8ecfe70d21df4b7eba4cf509c6db546945b9466bf6c57c2f0de8c25ca9866d0c1a02fc999b48702
-DIST allpaths-2.0.manual.docx 287123 SHA256 f89d15f31d511d6bad587562fa2539c1d5a37a097e4c3f33bb5a00d47fba7e69 SHA512 2883fb43dc51e81555b25def36470b196448a5198c4a543324cba116c956a6245dee1eb76162c08f2f1cf47a202ff73df77161ef9deb649cb044a783ebcaae78 WHIRLPOOL 6c3eec836c3c9a15da43566e22fdcd2bc703a22d49f4d3c04d9cd4e1f4769dc09da2fddba2e51488682f3f09b92995de6487572cfa75ffb1ef4d18296f90174f
-DIST allpaths-2.0.tar.gz 11211652 SHA256 16dce075e7b4ebd8924a79c765a7a7b87c01a68502e256ec200680ba42d95f02 SHA512 c1820623ac8e5bfdc6e27481d2c5f6a3774944a0a19ddca33fb2f7bfd5dd0c90ff20b86b2f85ac8614cb9f40f66d7cca080aafe7da815eecc1fd4ce941b4ab3c WHIRLPOOL 38201e9a52dc34131225378cc84253aaedb27ab31020139cc7c4883d988ad20caaf58fd0e5c967fa1a5ea59dca30be2a39aaaf7709b60a43d16e478efc724033
-DIST allpaths-3.1.tgz 1482541 SHA256 bbdc43f82586fc0b67d3a2584e245c452c377f8b532c81e9fe4e2c309ac1a46b SHA512 c82fb89a9d2f9d6cf21082f54999546c8e5d9ce470e0ae4b6c57ad0f95c4e35ab8b5965b098f4444c38e40d1ee434ed22adf70dff4fe8320d9c154e2b904f4e2 WHIRLPOOL c3ceaaaec9ce40668796d72a864c9d903dd795825c2f2a6dcf9b4dff10e4b9b9d278b10c2b15982a8afd75f256f11e48a09fbd934e814b092666d14216678ab5
-EBUILD allpaths-2.0.ebuild 1130 SHA256 1b8fcd636cabe68b5e6208f6a6fc34b95b237c79dee26404a951d175b1447e6e SHA512 2ff78cc969ecb0ed0dff7d0f9bdd2e8444c13e1a1acccffebe7556254d923e8aa743718815ebd25e4989b26b45fa5b889898e9b749286405395282e8915c0c03 WHIRLPOOL 223dc09ff6b810e5aaa8cdf48027f25ac389afb33b30507fbe07483ac9d09481b08f3cb351fe63dbf454186da2cbb760cc20d0978b07c860106c394c1687429d
-EBUILD allpaths-3.1-r1.ebuild 1728 SHA256 02bf047e0b4bd45fe08839556559c15b143e92117c685aeb47eb0670cbddf6f2 SHA512 0bf76e9a827ae60d418f926f49b7006cce187dcca3acadccb5163f4e6e37947b0c3b06d5da0c3cd3ecbf87f499f266ebef353cea6ea47877b3cb63fdebe4e1e8 WHIRLPOOL 3c16649036d63a7c204afca7720a29670f9c1ad8eb419fae4315710a697b61125e5ea1d8bc2b580bf658a4786df5397cff45a13f4e0b1cb47a3128869af44a4e
-EBUILD allpaths-3.1.ebuild 1209 SHA256 78ecca1f1187d27fa1d9c272983bcc3cff4819ea84eae2e0df054ac37c600d38 SHA512 7f6d901d656ab328d48526edc88004213f92bb5e54cc2f6264ac97744d10a0259616a79e56e2fcf57222d8081d6960fbd306b1f08be901af2fa6185bccd19fd7 WHIRLPOOL b5d99a065498b1743e57e26a74ceaf3b58aacc31583f3d536a6b0e23e50a153c58134427f71028ab6d1d43e80a95285d4d27cf87c32e5e0f1df94b58ac54cb9b
-MISC ChangeLog 1976 SHA256 2d7bf5ab611e23368090a64de58635eee41af9e04019e36995fcc98cbc58c265 SHA512 e82494b1133f7d01e071e0d2ae5b04b63993d3a551b2b570e4fdea7943def93f77ea58912c0ead10d3d8ea26f81abeef85fc983e57d61dd255112c379a09a1d1 WHIRLPOOL db02c9cb36adbc618ee298c585852125f960aaf6350a87c4912f67a859967d296f5f3440a4ba1f2c7aad2f56e9296b962796baa314dde3387cae843c8bf5c5b7
-MISC metadata.xml 166 SHA256 29b228f683c71345323d841414e410c929a320f34536eb30910498728260c8ac SHA512 51c5345bb1c4466b73e2feac8895c64fc119365e7f2c156702f4c93664d3aba028b3da9daaabf24f61a88220345fca7806771a252e8ae906cac5dec97862c7e0 WHIRLPOOL 211bf955d94fc1d93b12388a2c597a8d440fb5d78f84d59b2549569537098c3525b1fbab707441d62fabe20edcac2fd9ebe09c5d9870f1c9558d7ee90d5db5b3
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diff --git a/sci-biology/allpaths/allpaths-2.0.ebuild b/sci-biology/allpaths/allpaths-2.0.ebuild
deleted file mode 100644
index 62a85a9c56d4..000000000000
--- a/sci-biology/allpaths/allpaths-2.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-2.0.ebuild,v 1.6 2012/11/19 10:27:46 jlec Exp $
-
-EAPI="2"
-
-inherit base
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-2-0/allpaths-2.0.tar.gz
-	ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-2-0/allpaths-2.0.manual.docx"
-
-LICENSE="Whitehead-MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND="!sci-biology/allpathslg"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc-x86-no-autocast.patch
-)
-
-S="${WORKDIR}"
-
-src_prepare() {
-	base_src_prepare
-	rm -rf libxerces* xerces_include || die
-}
-
-src_install() {
-	rm -rf bin/auxfiles
-	exeinto /usr/share/${PN}/bin
-	doexe bin/* || die
-	echo "PATH=\"/usr/share/${PN}/bin\"" > "${S}/99${PN}"
-	doenvd "${S}/99${PN}" || die
-	dosym /usr/share/${PN}/bin/RunAllPaths /usr/bin/RunAllPaths || die
-	insinto /usr/share/doc/${PF}
-	doins "${DISTDIR}/${P}.manual.docx"
-}
diff --git a/sci-biology/allpaths/allpaths-3.1-r1.ebuild b/sci-biology/allpaths/allpaths-3.1-r1.ebuild
deleted file mode 100644
index e7e1aeef6b79..000000000000
--- a/sci-biology/allpaths/allpaths-3.1-r1.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1-r1.ebuild,v 1.3 2013/07/17 06:17:01 jlec Exp $
-
-EAPI=5
-
-inherit base multilib
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="
-	ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
-	ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
-
-LICENSE="Whitehead-MIT"
-SLOT="3"
-KEYWORDS="~amd64 ~x86"
-IUSE="openmp"
-
-DEPEND="!sci-biology/allpathslg"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/AllPaths"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc4.7.patch
-	"${FILESDIR}"/${P}-boost-1.50.patch
-	"${FILESDIR}"/${P}-linking.patch
-	)
-
-pkg_setup() {
-	if use openmp; then
-		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
-			ewarn "OpenMP is not available in your current selected gcc"
-			die "need openmp capable gcc"
-		fi
-	fi
-}
-
-src_prepare() {
-	sed \
-		-e "s:-O3:${CXXFLAGS}:g" \
-		-e 's:-ggdb3::g' \
-		-i Makefile* || die
-
-	if use openmp; then
-		sed \
-			-e '/OPEN_MP/s:no:yes:g' \
-			-i Makefile.in || die
-	fi
-	base_src_prepare
-	export L_FLAGS="${LDFLAGS}"
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}/usr" \
-		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)"
-}
-
-src_compile() {
-	base_src_compile
-	emake install_scripts
-}
-
-src_install() {
-	exeinto /usr/libexec/${P}/
-	find bin -type f -executable | xargs doexe
-
-	echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
-	doenvd "${S}/50${P}" || die
-
-	dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
-
-	dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
-}
diff --git a/sci-biology/allpaths/allpaths-3.1.ebuild b/sci-biology/allpaths/allpaths-3.1.ebuild
deleted file mode 100644
index aea383b85949..000000000000
--- a/sci-biology/allpaths/allpaths-3.1.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/allpaths/allpaths-3.1.ebuild,v 1.4 2012/11/19 10:27:46 jlec Exp $
-
-EAPI=4
-
-inherit base
-
-DESCRIPTION="De novo assembly of whole-genome shotgun microreads"
-HOMEPAGE="http://www.broadinstitute.org/science/programs/genome-biology/crd"
-SRC_URI="
-	ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/allpaths-${PV}.tgz
-	ftp://ftp.broad.mit.edu/pub/crd/ALLPATHS/Release-3-0/AllPathsV3_Manual_r1.0.docx"
-
-LICENSE="Whitehead-MIT"
-SLOT="3"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/AllPaths"
-
-DEPEND="!sci-biology/allpathslg"
-RDEPEND="${DEPEND}"
-
-PATCHES=( "${FILESDIR}"/${P}-gcc4.7.patch )
-
-src_prepare() {
-	sed \
-		-e "s:-O3:${CXXFLAGS}:g" \
-		-e 's:-ggdb3::g' \
-		-i Makefile* || die
-	base_src_prepare
-}
-
-src_compile() {
-	base_src_compile
-	emake install_scripts
-}
-
-src_install() {
-	exeinto /usr/libexec/${P}/
-	find bin -type f -executable | xargs doexe || die
-
-	echo "PATH=\"/usr/libexec/${P}/\"" > "${S}/50${P}"
-	doenvd "${S}/50${P}" || die
-
-	dosym /usr/libexec/${P}/RunAllPaths3G /usr/bin/RunAllPaths3G
-
-	dodoc "${DISTDIR}/AllPathsV3_Manual_r1.0.docx"
-}
diff --git a/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch b/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch
deleted file mode 100644
index d4fe428efa26..000000000000
--- a/sci-biology/allpaths/files/allpaths-2.0-gcc-x86-no-autocast.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -durr work.orig/SortKmersImpl.h work/SortKmersImpl.h
---- work.orig/SortKmersImpl.h	2009-08-20 11:25:39.336695499 +0000
-+++ work/SortKmersImpl.h	2009-08-20 11:25:51.431932630 +0000
-@@ -98,7 +98,7 @@
-     {    if ( reads[l].size( ) < KSPAN ) continue;
-     unsigned int N = reads[l].size( ) - KSPAN + 1;
-     if ( S + 2*N >= R.size( ) ) {
--      unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
-+      unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
-       if ( nn < R.size( ) ) FatalErr( "SortKmers<1>: Unsigned-int overflow (R=" << R.size( ) << ")" );
-       R.resize(nn);
-     }
-@@ -180,7 +180,7 @@
- 	}
- 	if ( q == N ) break;
- 	if ( S + 2*N >= R.size( ) ) {
--	  unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
-+	  unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
- 	  if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
- 	  R.resize(nn);
- 	}
-@@ -207,7 +207,7 @@
-       top += Min( N - top, (unsigned int) 10000 );
-       
-       if ( S + 20000 >= R.size( ) || S + 2*N >= R.size( ) ) {
--	unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (R.size( ) + 2*N) );
-+	unsigned nn = Max( (long unsigned) ( 1.2 * R.size( ) ), (long unsigned) (R.size( ) + 2*N) );
- 	if ( nn < R.size( ) ) FatalErr( "SortKmers<10>: Unsigned-int overflow (R=" << R.size( ) << ")" );
- 	R.resize(nn);
-       }
diff --git a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch b/sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch
deleted file mode 100644
index 9a90410fe95c..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50-2.patch
+++ /dev/null
@@ -1,185 +0,0 @@
- MakeDepend.cc                |  9 +++++----
- Makefile.in                  | 12 ++++++------
- Makefile_g++                 |  3 ++-
- TestProgram.cc               |  1 +
- lookup/CreateLookupTab.cc    |  3 +++
- paths/AlignPairsToHyper3G.cc |  2 ++
- paths/ErrorCorrectJump.cc    |  2 ++
- reporting/FastbStats.cc      |  1 +
- util/FastaParser.cc          |  3 +++
- 9 files changed, 25 insertions(+), 11 deletions(-)
-
-diff --git a/MakeDepend.cc b/MakeDepend.cc
-index 619e6f7..b8d9c72 100644
---- a/MakeDepend.cc
-+++ b/MakeDepend.cc
-@@ -1032,7 +1032,7 @@ void makefile_builder::GenerateMakefileForSharedLibs( ostream &mf )
-       mf << " " << dep_iter->Provider();
-     mf << "\n";
-     mf << "\t" << "mkdir -p $(LIB)" << endl;
--    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) -o $(LIB)/" << *lib_iter;
-+    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) $(L_FLAGS) -o $(LIB)/" << *lib_iter;
-     for ( vector<dependency>::iterator dep_iter = link_deps.first;
-           dep_iter != link_deps.second; ++dep_iter )
-       mf << " $(OBJ)/" << dep_iter->Provider();
-@@ -1182,7 +1182,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       mf << " $(OBJ)/" << *dep_iter;     
-     }
-     mf << "\n\t$(BIN)/checkLock $(BIN)/$@";
--    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ ";
-+    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) $(L_FLAGS) -o $(BIN)/$@ ";
-     for ( set<string>::iterator dep_iter = obj_deps.begin();
-           dep_iter != obj_deps.end(); ++dep_iter )
-     {
-@@ -1195,7 +1195,8 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-         mf << " $(OBJ)/" << *dep_iter;
-       }
-     }
--    mf << " $(OBJ)/LinkTimestamp.o -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; 
-+    mf << " $(OBJ)/LinkTimestamp.o $(PTHREAD_OBJ) -L. -L$(LIB) -L$(OBJ)"; 
-+    mf << " -l" << libname;
-     for ( set<string>::iterator dep_iter = lib_deps.begin(); 
- 	  dep_iter != lib_deps.end(); ++dep_iter )
-       mf << " " << "$(" << *dep_iter << "_LFLAGS)";
-@@ -1208,7 +1209,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       sharedlib_name.erase( sharedlib_name.size() - 3, 3 );
-       mf << " -l" << sharedlib_name;
-     }
--    mf << " -l" << libname;
-+    mf << " $(LINK_LIBS)"; 
-     mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
-   }
- }    
-diff --git a/Makefile.in b/Makefile.in
-index f20db27..fe45b4c 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -106,9 +106,9 @@ vpath % $(BIN)
- ##############################################################################
- 
- # our boost dependancies
--BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- BOOST_IOSTREAMS_LFLAGS 	= -lboost_iostreams-@BOOST_TAG@
--BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- 
- # PUT OUR GMP FLAGS HERE
- GMP_LFLAGS	= @GMP_LIB@
-@@ -340,10 +340,10 @@ LINK_OPTIONS	= \
- 		$(PTHREAD_LINK)
- 
- LINK_LIBS	= \
-+		@LIBRARIES@ \
- 		@LIBS@ \
- 		$(OMP_LIBS) \
--		$(PTHREAD_LIBS) \
--		@LIBRARIES@
-+		$(PTHREAD_LIBS)
- 
- CPPO		= $(LINK_OPTIONS)
- CPPC		= $(CPP_OPTIONS) $(SYS_MEMTRACK)
-@@ -420,10 +420,10 @@ execs_size:
- MakeDepend: MakeDepend.cc
- 	@ mkdir -p $(BIN)
- 	echo $(PATH)
--	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) $(L_FLAGS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
- 
- checkLock: $(SRC)/util/checkLock.cc
--	$(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock 
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SRC)/util/checkLock.cc $(L_FLAGS) -o $(BIN)/checkLock 
- 
- MemTracker.o: MemTracker.cc
- 	@ mkdir -p $(OBJ)
-diff --git a/Makefile_g++ b/Makefile_g++
-index 8dc8572..2a29ecc 100644
---- a/Makefile_g++
-+++ b/Makefile_g++
-@@ -29,7 +29,8 @@ PIC		= -fPIC
- #############################################################
- 
- # pThread library
--PTHREAD_LFLAGS  = $(OBJ)/system/Threads.o -lpthread
-+PTHREAD_LFLAGS  = -lpthread
-+PTHREAD_OBJ	= $(OBJ)/system/Threads.o
- PTHREAD_LIB	= system/Threads.o
- 
- #### Zlib library setup ####
-diff --git a/TestProgram.cc b/TestProgram.cc
-index e779fab..b480add 100644
---- a/TestProgram.cc
-+++ b/TestProgram.cc
-@@ -1,5 +1,6 @@
- // MakeDepend: library BOOST_FILESYSTEM
- // MakeDepend: library GMPXX
-+// MakeDepend: library GMP
- #include <gmpxx.h>
- #include <iostream>
- #include <boost/filesystem/path.hpp>
-diff --git a/lookup/CreateLookupTab.cc b/lookup/CreateLookupTab.cc
-index 44f2579..ac5c3bb 100644
---- a/lookup/CreateLookupTab.cc
-+++ b/lookup/CreateLookupTab.cc
-@@ -18,6 +18,9 @@
-  * This program just builds a singly-linked list of Locations for each kmer, and then walks each
-  * list to write them out to a feudal file.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/AlignPairsToHyper3G.cc b/paths/AlignPairsToHyper3G.cc
-index 5a0fda6..7b284a8 100644
---- a/paths/AlignPairsToHyper3G.cc
-+++ b/paths/AlignPairsToHyper3G.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/ErrorCorrectJump.cc b/paths/ErrorCorrectJump.cc
-index 40c8536..bb4d779 100644
---- a/paths/ErrorCorrectJump.cc
-+++ b/paths/ErrorCorrectJump.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/reporting/FastbStats.cc b/reporting/FastbStats.cc
-index f87f295..ba7dbe3 100644
---- a/reporting/FastbStats.cc
-+++ b/reporting/FastbStats.cc
-@@ -8,6 +8,7 @@
- /////////////////////////////////////////////////////////////////////////////
- 
- // Basic stats for a fastb file.
-+// MakeDepend: library BOOST_SYSTEM
- 
- #include "Basevector.h"
- #include "math/Functions.h"
-diff --git a/util/FastaParser.cc b/util/FastaParser.cc
-index 8b3dbc8..dc1d2cf 100644
---- a/util/FastaParser.cc
-+++ b/util/FastaParser.cc
-@@ -13,6 +13,9 @@
-  *
-  * \brief Several utility classes for reading FASTA files.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
diff --git a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50.patch b/sci-biology/allpaths/files/allpaths-3.1-boost-1.50.patch
deleted file mode 100644
index 23c031041e14..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-boost-1.50.patch
+++ /dev/null
@@ -1,47 +0,0 @@
- configure          | 4 ++--
- system/file/File.h | 6 +++---
- 2 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/configure b/configure
-index 37b9812..b966fd7 100755
---- a/configure
-+++ b/configure
-@@ -9872,8 +9872,8 @@ $as_echo "found boost version $_version" >&6; }
-   # using system specifics
- 
-   # lets use the system library
--  BOOST_WITH_COMP="libboost_filesystem-$CC$GCC_MAJOR_MINOR-mt.a"
--  BOOST_WITHOUT="libboost_filesystem-mt.a"
-+  BOOST_WITH_COMP="libboost_filesystem-$CC$GCC_MAJOR_MINOR-mt.so"
-+  BOOST_WITHOUT="libboost_filesystem-mt.so"
- 
-   # lets say that we're checking that
-   { $as_echo "$as_me:$LINENO: checking for boost library name" >&5
-diff --git a/system/file/File.h b/system/file/File.h
-index da78272..14c9c62 100644
---- a/system/file/File.h
-+++ b/system/file/File.h
-@@ -149,7 +149,7 @@ public:
-     /// return the filename portion of the file path
-     /// e.g., /home/user/boat/file.txt would return file.txt
-     std::string Filename() const
--    { return mPath.filename(); }
-+    { return mPath.filename().string(); }
- 
-     /// return the path portion of the filename
-     /// e.g., /home/user/boat/file.txt would return /home/user/boat
-@@ -163,12 +163,12 @@ public:
-     /// return the filename with its final extension (if any) removed
-     /// e.g., /home/user/boat/file.txt would return /home/user/boat/file
-     std::string Stem() const
--    { return mPath.stem(); }
-+    { return mPath.stem().string(); }
- 
-     /// return the final extension (empty string, if there is none)
-     /// e.g., /home/user/boat/file.txt would return .txt
-     std::string Extension() const
--    { return mPath.extension(); }
-+    { return mPath.extension().string(); }
- 
-     /// make a new File with a path obtained by removing this File's final extension, if any,
-     /// and gluing on the newExtension (preceded by a '.' if it doesn't already start with one).
diff --git a/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch b/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch
deleted file mode 100644
index a2f4b4d37c75..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-gcc4.7.patch
+++ /dev/null
@@ -1,264 +0,0 @@
- MakeDepend.cc                |  1 +
- Vec.h                        | 12 ++++++------
- feudal/BinaryStream.h        |  4 ++++
- feudal/FeudalControlBlock.cc |  1 +
- feudal/FeudalFileReader.h    |  1 +
- feudal/MasterVec.h           | 14 +++++++-------
- feudal/SerfVec.h             |  4 ++--
- reporting/ScaffoldLayout.cc  | 10 +++++-----
- system/ProcBuf.cc            | 12 ++++++------
- 9 files changed, 33 insertions(+), 26 deletions(-)
-
-diff --git a/MakeDepend.cc b/MakeDepend.cc
-index 93032e8..619e6f7 100644
---- a/MakeDepend.cc
-+++ b/MakeDepend.cc
-@@ -25,6 +25,7 @@
- #include <iterator>
- #include <iostream>
- #include <ctype.h>
-+#include <unistd.h>
- 
- using namespace std;
- 
-diff --git a/Vec.h b/Vec.h
-index f26f3f4..e2d26a4 100644
---- a/Vec.h
-+++ b/Vec.h
-@@ -259,11 +259,11 @@ template <class T> class vec : public vector<T> {
- 
-   template <class U>
-   void append( const vec<U>& y ) 
--  {    insert( this->end( ), y.begin( ), y.end( ) );    }
-+  {    this->insert( this->end( ), y.begin( ), y.end( ) );    }
-   
-   void append( const vec<T>& y, size_type i, size_type j ) {
--    if ( j == y.size( ) ) insert( this->end( ), y.begin( ) + i, y.end( ) );
--    else insert( this->end( ), y.begin( ) + i, y.begin( ) + j );   
-+    if ( j == y.size( ) ) this->insert( this->end( ), y.begin( ) + i, y.end( ) );
-+    else this->insert( this->end( ), y.begin( ) + i, y.begin( ) + j );   
-   }
- 
-   // appends values in y, but only those whose indices are in entries
-@@ -339,7 +339,7 @@ template <class T> class vec : public vector<T> {
-     
-   void SetToRangeOf( const vec<T>& v, size_type i, size_type j ) {
-     AssertLe( i, j );
--    assign(v.begin() + i, v.begin() + j);
-+    this->assign(v.begin() + i, v.begin() + j);
-   }
- 
-   inline friend vec<T> RangeOf( const vec<T>& v, size_type i, size_type j ) {
-@@ -397,12 +397,12 @@ template <class T> class vec : public vector<T> {
-   /// Erase: erase range of elements, where range is given by half-open interval.
- 
-   void Erase( size_type start, size_type stop ) {
--    erase( this->begin( ) + start, this->begin( ) + stop );
-+    this->erase( this->begin( ) + start, this->begin( ) + stop );
-   }
- 
-   /// EraseValue: erase all entries having the given value.
-   void EraseValue( const T& x ) {
--    erase(remove(this->begin(), this->end(), x), this->end());
-+    this->erase(remove(this->begin(), this->end(), x), this->end());
-   }
- 
-   /// print values to ostream, separated by sep.
-diff --git a/feudal/BinaryStream.h b/feudal/BinaryStream.h
-index f54d8a9..c61469b 100644
---- a/feudal/BinaryStream.h
-+++ b/feudal/BinaryStream.h
-@@ -144,6 +144,10 @@ private:
-     std::ostream& mOS;
- };
- 
-+template <typename T1, typename T2>
-+inline size_t serializedSizeof( std::pair<T1,T2>* );
-+
-+
- /// Reader of binary streams.
- class BinaryReader
- {
-diff --git a/feudal/FeudalControlBlock.cc b/feudal/FeudalControlBlock.cc
-index bc64ecd..a709320 100644
---- a/feudal/FeudalControlBlock.cc
-+++ b/feudal/FeudalControlBlock.cc
-@@ -24,6 +24,7 @@
- #include <string.h>
- #include <errno.h>
- #include <iostream>
-+#include <unistd.h>
- 
- using std::cout;
- using std::endl;
-diff --git a/feudal/FeudalFileReader.h b/feudal/FeudalFileReader.h
-index b71bf6d..073a1a1 100644
---- a/feudal/FeudalFileReader.h
-+++ b/feudal/FeudalFileReader.h
-@@ -13,6 +13,7 @@
- #include <string>
- #include <cassert>
- #include <sstream>
-+#include <unistd.h>
- #include "feudal/BinaryStream.h"
- 
- /**
-diff --git a/feudal/MasterVec.h b/feudal/MasterVec.h
-index e6477d9..b88e9fe 100644
---- a/feudal/MasterVec.h
-+++ b/feudal/MasterVec.h
-@@ -60,20 +60,20 @@ public:
-     /// This function is deprecated: Use reserve() instead.
-     /// The pool size argument is ignored, anyway.
-     MasterVec& Reserve( unsigned long raw_mem_size_ignored, size_type capacity )
--    { reserve(capacity); return *this; }
-+    { this->reserve(capacity); return *this; }
- 
-     /// This function is deprecated:  Use clear().shrink_to_fit().
-     MasterVec& destroy() { BaseT::clear(); BaseT::shrink_to_fit(); return *this; }
- 
-     /// This function is deprecated:  Use push_back().
-     MasterVec& push_back_external( T const& val )
--    { push_back(val); return *this; }
-+    { this->push_back(val); return *this; }
- 
-     /// This function is deprecated:  Use push_back().
-     MasterVec& push_back_reserve( T const& val,
-                                   size_type growthIncr = 0,
-                                   float growthFact = 1.3f )
--    { push_back(val,growthFact,growthIncr); return *this; }
-+    { this->push_back(val,growthFact,growthIncr); return *this; }
- 
-     /// This function is deprecated:  Use append().
-     MasterVec& Append( MasterVec const& that )
-@@ -81,7 +81,7 @@ public:
- 
-     /// This function is deprecated:  Use append().
-     MasterVec& Append( MasterVec const& that, size_type from, size_type to )
--    { append(that.begin(from),that.begin(to)); return *this; }
-+    { this->append(that.begin(from),that.begin(to)); return *this; }
- 
-     MasterVec const& WriteAll( String const& fileName ) const
-     { return WriteRange(fileName,0UL,BaseT::size()); return *this; }
-@@ -99,7 +99,7 @@ public:
-     { if ( !append ) BaseT::clear();
-       FeudalFileReader rdr(fileName.c_str(),T::fixedDataLen());
-       size_type siz = rdr.getNElements();
--      reserve(BaseT::size()+siz);
-+      this->reserve(BaseT::size()+siz);
-       for ( size_type iii = 0; iii < siz; ++iii )
-         appendFromReader(rdr,iii);
-       return *this; }
-@@ -148,7 +148,7 @@ public:
-                            vec<int> const& entries,
-                            int /*extra*/ = 0, Bool /*pre_reserved*/ = False )
-     { VirtualMasterVec<T> vVec(fileName.c_str());
--      if ( BaseT::size() < vVec.size() ) resize(vVec.size());
-+      if ( BaseT::size() < vVec.size() ) this->resize(vVec.size());
-       vec<int>::const_iterator end(entries.end());
-       for ( vec<int>::const_iterator itr(entries.begin()); itr != end; ++itr )
-       { BaseT::operator[](*itr) = vVec[*itr]; }
-@@ -158,7 +158,7 @@ public:
-                                 size_t from, size_t to,
-                                 int /* extra */ = 0 )
-     { VirtualMasterVec<T> vVec(fileName.c_str());
--      if ( BaseT::size() < vVec.size() ) resize(vVec.size());
-+      if ( BaseT::size() < vVec.size() ) this->resize(vVec.size());
-       for ( ; from < to; ++from ) (*this)[from] = vVec[from];
-       return *this; }
- 
-diff --git a/feudal/SerfVec.h b/feudal/SerfVec.h
-index e91847c..d5f053d 100644
---- a/feudal/SerfVec.h
-+++ b/feudal/SerfVec.h
-@@ -79,10 +79,10 @@ public:
-     /// Deprecated:  Use assign().
-     SerfVec& SetToSubOf( SerfVec const& that, size_type pos, size_type len )
-     { if ( this != &that )
--      { assign(that.begin(pos),that.begin(pos+len)); }
-+      { this->assign(that.begin(pos),that.begin(pos+len)); }
-       else
-       { assert(that.size()>=pos+len);
--        erase(BaseT::begin(),BaseT::begin(pos));
-+        this->erase(BaseT::begin(),BaseT::begin(pos));
-         BaseT::resize(len); }
-       return *this; }
- 
-diff --git a/reporting/ScaffoldLayout.cc b/reporting/ScaffoldLayout.cc
-index 7c39718..646b106 100644
---- a/reporting/ScaffoldLayout.cc
-+++ b/reporting/ScaffoldLayout.cc
-@@ -66,13 +66,13 @@ int main(int argc, char **argv)
-        // This version finds the first and last non-ambiguous sequences of
-        // END_SIZE_MIN <= length <= end_size_max
-        // --bruce
--       int j, k;
-+       int l, k;
-        int end_size_max = min(END_SIZE_MAX, scaffold_size/2);
--       for (j = k = 0; k < scaffold_size; k++) {
-+       for (l = k = 0; k < scaffold_size; k++) {
- 	 if (assembly_amb[i][k]) {
--	   if (k-j >= END_SIZE_MIN) break;
--	   else j = k+1;
--	 } else if (k-j >= end_size_max) break;
-+	   if (k-l >= END_SIZE_MIN) break;
-+	   else l = k+1;
-+	 } else if (k-l >= end_size_max) break;
-        }
-        e.SetToSubOf( assembly[i], j, k-j );
-        ENDS.push_back_reserve(e);
-diff --git a/system/ProcBuf.cc b/system/ProcBuf.cc
-index 748cc6b..5b91ed3 100644
---- a/system/ProcBuf.cc
-+++ b/system/ProcBuf.cc
-@@ -189,12 +189,12 @@ basic_procbuf<charT,traits>::overflow( int_type c )
- 	    Assert(M_internal_put_buffer == NULL);
- 	    M_internal_put_buffer = new char_type [DEFAULT_PUT_BUFFER_SIZE];
- 	    M_internal_put_buffer_end = M_internal_put_buffer+DEFAULT_PUT_BUFFER_SIZE;
--	    setp(M_internal_put_buffer,
-+	    this->setp(M_internal_put_buffer,
- 		 M_internal_put_buffer_end);
- 	} else if (!flush())
- 	    return traits_type::eof();
- 	if (!traits_type::eq_int_type(c, traits_type::eof()))
--	    return sputc(c);
-+	    return this->sputc(c);
- 	else
- 	    return traits_type::not_eof(c);
-     }
-@@ -234,7 +234,7 @@ basic_procbuf<charT,traits>::pbackfail( int_type c )
- 	// (which is start of buffer)
- 	std::copy_backward(this->eback(), this->egptr(), this->egptr()+1);
- 	*(this->gptr()) = traits_type::to_char_type(c);
--	setg(this->eback(), this->gptr(), this->egptr()+1);
-+	this->setg(this->eback(), this->gptr(), this->egptr()+1);
-         return traits_type::not_eof(c);
-     } else
- 	return traits_type::eof();
-@@ -263,7 +263,7 @@ basic_procbuf<charT,traits>::flush( )
- 	// doing wchars and we write an odd # of bytes?
- 	return false;
-     } else {
--	setp(this->pbase(), this->epptr());
-+	this->setp(this->pbase(), this->epptr());
- 	return true;
-     }
- }
-@@ -277,7 +277,7 @@ basic_procbuf<charT,traits>::fill( )
- 	Assert(M_internal_get_buffer == NULL);
- 	M_internal_get_buffer = new char_type[DEFAULT_GET_BUFFER_SIZE];
- 	M_internal_get_buffer_end = M_internal_get_buffer + DEFAULT_GET_BUFFER_SIZE;
--	setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
-+	this->setg(M_internal_get_buffer, M_internal_get_buffer_end, M_internal_get_buffer_end);
-     }
-     // The "get" pointer should be at the end of the buffer - that's
-     // why we need to fill it.
-@@ -312,7 +312,7 @@ basic_procbuf<charT,traits>::fill( )
-     //
-     // reset the get pointers
-     //
--    setg(M_internal_get_buffer, 
-+    this->setg(M_internal_get_buffer, 
- 	 M_internal_get_buffer, 
- 	 M_internal_get_buffer+numusable/sizeof(char_type));
-     return true;
diff --git a/sci-biology/allpaths/files/allpaths-3.1-linking.patch b/sci-biology/allpaths/files/allpaths-3.1-linking.patch
deleted file mode 100644
index ccb54ea24530..000000000000
--- a/sci-biology/allpaths/files/allpaths-3.1-linking.patch
+++ /dev/null
@@ -1,173 +0,0 @@
- MakeDepend.cc                | 9 +++++----
- Makefile.in                  | 9 +++++----
- Makefile_g++                 | 3 ++-
- TestProgram.cc               | 1 +
- lookup/CreateLookupTab.cc    | 3 +++
- paths/AlignPairsToHyper3G.cc | 2 ++
- paths/ErrorCorrectJump.cc    | 2 ++
- reporting/FastbStats.cc      | 1 +
- util/FastaParser.cc          | 3 +++
- 9 files changed, 24 insertions(+), 9 deletions(-)
-
-diff --git a/MakeDepend.cc b/MakeDepend.cc
-index 619e6f7..b8d9c72 100644
---- a/MakeDepend.cc
-+++ b/MakeDepend.cc
-@@ -1032,7 +1032,7 @@ void makefile_builder::GenerateMakefileForSharedLibs( ostream &mf )
-       mf << " " << dep_iter->Provider();
-     mf << "\n";
-     mf << "\t" << "mkdir -p $(LIB)" << endl;
--    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) -o $(LIB)/" << *lib_iter;
-+    mf << "\t" << "$(CPLUSPLUS) $(CPPO) $(PIC) $(SYS_SHARED) $(L_FLAGS) -o $(LIB)/" << *lib_iter;
-     for ( vector<dependency>::iterator dep_iter = link_deps.first;
-           dep_iter != link_deps.second; ++dep_iter )
-       mf << " $(OBJ)/" << dep_iter->Provider();
-@@ -1182,7 +1182,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       mf << " $(OBJ)/" << *dep_iter;     
-     }
-     mf << "\n\t$(BIN)/checkLock $(BIN)/$@";
--    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) -o $(BIN)/$@ ";
-+    mf << "\n\t$(CPLUSPLUS) $(LINK_OPTIONS) $(L_FLAGS) -o $(BIN)/$@ ";
-     for ( set<string>::iterator dep_iter = obj_deps.begin();
-           dep_iter != obj_deps.end(); ++dep_iter )
-     {
-@@ -1195,7 +1195,8 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-         mf << " $(OBJ)/" << *dep_iter;
-       }
-     }
--    mf << " $(OBJ)/LinkTimestamp.o -L. -L$(LIB) -L$(OBJ) $(LINK_LIBS)"; 
-+    mf << " $(OBJ)/LinkTimestamp.o $(PTHREAD_OBJ) -L. -L$(LIB) -L$(OBJ)"; 
-+    mf << " -l" << libname;
-     for ( set<string>::iterator dep_iter = lib_deps.begin(); 
- 	  dep_iter != lib_deps.end(); ++dep_iter )
-       mf << " " << "$(" << *dep_iter << "_LFLAGS)";
-@@ -1208,7 +1209,7 @@ void makefile_builder::GenerateMakefileForExecutables( ostream &mf )
-       sharedlib_name.erase( sharedlib_name.size() - 3, 3 );
-       mf << " -l" << sharedlib_name;
-     }
--    mf << " -l" << libname;
-+    mf << " $(LINK_LIBS)"; 
-     mf << "\n\t" << "/bin/rm $(OBJ)/lib" << libname << ".a\n";
-   }
- }    
-diff --git a/Makefile.in b/Makefile.in
-index f20db27..289af1c 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -106,9 +106,10 @@ vpath % $(BIN)
- ##############################################################################
- 
- # our boost dependancies
--BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_SYSTEM = -lboost_system
-+BOOST_FILESYSTEM_LFLAGS	= -lboost_filesystem-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- BOOST_IOSTREAMS_LFLAGS 	= -lboost_iostreams-@BOOST_TAG@
--BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@
-+BOOST_SERIALIZATION_LFLAGS = -lboost_serialization-@BOOST_TAG@ -lboost_system-@BOOST_TAG@ -lboost_system
- 
- # PUT OUR GMP FLAGS HERE
- GMP_LFLAGS	= @GMP_LIB@
-@@ -420,10 +421,10 @@ execs_size:
- MakeDepend: MakeDepend.cc
- 	@ mkdir -p $(BIN)
- 	echo $(PATH)
--	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SYS_LANG) $(MAKEDEPEND_OPTS) $(L_FLAGS) -o $(BIN)/MakeDepend $(SRC)/MakeDepend.cc
- 
- checkLock: $(SRC)/util/checkLock.cc
--	$(CPLUSPLUS) $(SRC)/util/checkLock.cc -o $(BIN)/checkLock 
-+	$(CPLUSPLUS) $(CPPO) $(CPPC) $(SRC)/util/checkLock.cc $(L_FLAGS) -o $(BIN)/checkLock 
- 
- MemTracker.o: MemTracker.cc
- 	@ mkdir -p $(OBJ)
-diff --git a/Makefile_g++ b/Makefile_g++
-index 8dc8572..2a29ecc 100644
---- a/Makefile_g++
-+++ b/Makefile_g++
-@@ -29,7 +29,8 @@ PIC		= -fPIC
- #############################################################
- 
- # pThread library
--PTHREAD_LFLAGS  = $(OBJ)/system/Threads.o -lpthread
-+PTHREAD_LFLAGS  = -lpthread
-+PTHREAD_OBJ	= $(OBJ)/system/Threads.o
- PTHREAD_LIB	= system/Threads.o
- 
- #### Zlib library setup ####
-diff --git a/TestProgram.cc b/TestProgram.cc
-index e779fab..b480add 100644
---- a/TestProgram.cc
-+++ b/TestProgram.cc
-@@ -1,5 +1,6 @@
- // MakeDepend: library BOOST_FILESYSTEM
- // MakeDepend: library GMPXX
-+// MakeDepend: library GMP
- #include <gmpxx.h>
- #include <iostream>
- #include <boost/filesystem/path.hpp>
-diff --git a/lookup/CreateLookupTab.cc b/lookup/CreateLookupTab.cc
-index 44f2579..ac5c3bb 100644
---- a/lookup/CreateLookupTab.cc
-+++ b/lookup/CreateLookupTab.cc
-@@ -18,6 +18,9 @@
-  * This program just builds a singly-linked list of Locations for each kmer, and then walks each
-  * list to write them out to a feudal file.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/AlignPairsToHyper3G.cc b/paths/AlignPairsToHyper3G.cc
-index 5a0fda6..7b284a8 100644
---- a/paths/AlignPairsToHyper3G.cc
-+++ b/paths/AlignPairsToHyper3G.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/paths/ErrorCorrectJump.cc b/paths/ErrorCorrectJump.cc
-index 40c8536..bb4d779 100644
---- a/paths/ErrorCorrectJump.cc
-+++ b/paths/ErrorCorrectJump.cc
-@@ -7,6 +7,8 @@
- //   can be responsible for its use, misuse, or functionality.             //
- /////////////////////////////////////////////////////////////////////////////
- 
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
-diff --git a/reporting/FastbStats.cc b/reporting/FastbStats.cc
-index f87f295..ba7dbe3 100644
---- a/reporting/FastbStats.cc
-+++ b/reporting/FastbStats.cc
-@@ -8,6 +8,7 @@
- /////////////////////////////////////////////////////////////////////////////
- 
- // Basic stats for a fastb file.
-+// MakeDepend: library BOOST_SYSTEM
- 
- #include "Basevector.h"
- #include "math/Functions.h"
-diff --git a/util/FastaParser.cc b/util/FastaParser.cc
-index 8b3dbc8..dc1d2cf 100644
---- a/util/FastaParser.cc
-+++ b/util/FastaParser.cc
-@@ -13,6 +13,9 @@
-  *
-  * \brief Several utility classes for reading FASTA files.
-  */
-+
-+// MakeDepend: library BOOST_SYSTEM
-+
- #ifndef FORCE_DEBUG
- #define NDEBUG
- #endif
diff --git a/sci-biology/allpaths/metadata.xml b/sci-biology/allpaths/metadata.xml
deleted file mode 100644
index f17a827e3101..000000000000
--- a/sci-biology/allpaths/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <herd>sci-biology</herd>
-</pkgmetadata>