Merge remote-tracking branch 'github/master'

51 files changed, 1 insertions, 1406 deletions

diff --git a/dev-java/jhealpix/Manifest b/dev-java/jhealpix/Manifest
deleted file mode 100644
index 983581ad4..000000000
--- a/dev-java/jhealpix/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Healpix_3.11_2013Apr24.tar.gz 24256278 SHA256 f80aa3633601664afe99c8b7dc7253828f22e6d832187ab46ac90b2ad83e6831 SHA512 aae5592dda40103918a6c6520863e2aeddf40a34531e4ce2f38a1ce7411731218d7e20bd02107f92384a7b371c2415ed640ad27aa398f64857f5ed7d9dba32bb WHIRLPOOL 1e3f0588502b6b9e68c19de9763ae775d01031cd7a3120bb663a71bae1fa7e2baf6ac4997ff07598ca45e610ae919839ecf04c66a201256665f5e5f1727f7299
diff --git a/dev-java/jhealpix/jhealpix-3.11.ebuild b/dev-java/jhealpix/jhealpix-3.11.ebuild
deleted file mode 100644
index 0c4c2eccd..000000000
--- a/dev-java/jhealpix/jhealpix-3.11.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-JAVA_PKG_IUSE="doc"
-inherit java-pkg-2 java-ant-2
-
-MYP="Healpix_${PV}"
-MYPP="2013Apr24"
-
-DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - Java"
-HOMEPAGE="http://healpix.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}/${MYP}_${MYPP}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-IUSE="doc test"
-
-DEPEND=">=virtual/jdk-1.5
-	test? ( dev-java/junit:4 )"
-RDEPEND=">=virtual/jre-1.5"
-
-S="${WORKDIR}/${MYP}/src/java"
-
-EANT_BUILD_TARGET="distonly distsrc newcompile"
-EANT_DOC_TARGET="docs newdocs"
-
-src_test() {
-	EANT_TEST_TARGET="test newtest"
-	EANT_TEST_GENTOO_CLASSPATH="junit-4"
-	java-pkg-2_src_test
-}
-
-src_install() {
-	java-pkg_dojar dist/*.jar
-	dodoc README CHANGES SuggestedIdeas.txt
-	dodoc ../../READ_Copyrights_Licenses.txt
-	use doc && java-pkg_dojavadoc healpixdoc
-}
diff --git a/dev-java/jhealpix/metadata.xml b/dev-java/jhealpix/metadata.xml
deleted file mode 100644
index 00602ead0..000000000
--- a/dev-java/jhealpix/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-astronomy@gentoo.org</email>
-    <name>Gentoo Astronomy Project</name>
-  </maintainer>
-  <longdescription lang="en">
-  HEALPix is an acronym for Hierarchical Equal Area isoLatitude
-  Pixelization of a sphere. As suggested in the name, this pixelization produces a
-  subdivision of a spherical surface in which each pixel covers the same
-  surface area as every other pixel. This package contains the Java framework.
-</longdescription>
-  <upstream>
-    <remote-id type="sourceforge">jhealpix</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/dev-python/astroquery/Manifest b/dev-python/astroquery/Manifest
deleted file mode 100644
index a09ab9d97..000000000
--- a/dev-python/astroquery/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST astroquery-0.2.tar.gz 2212909 SHA256 30cdd66828dedf81795ab4e3d6d496d5e4a83c15a740981a1f34cbf4bc75cb01 SHA512 06549526b8fe7fafd7a5ac7d8a97a3d78ceec048a27f6a5c7a8274aca8ff666f300998347c2d8a3dd86e2f8706d8a2bfdfa07f684e7fa87016281851436225c0 WHIRLPOOL e53c61d1a3a0e590b19c3be77e5bf399f3ffb5db8e99c9c9a1064e2def4729431662488cb9d80b841c47e4e8a239dc4f6c1a16ef4ea05f0b0690ac8a9cbaf58a
diff --git a/dev-python/astroquery/astroquery-0.2.ebuild b/dev-python/astroquery/astroquery-0.2.ebuild
deleted file mode 100644
index 869250100..000000000
--- a/dev-python/astroquery/astroquery-0.2.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_3,3_4} )
-inherit distutils-r1
-
-MY_PV=${PV/_/-}
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="A collection of packages to access online astronomical resources"
-HOMEPAGE="https://github.com/astropy/astroquery"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.2[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/requests[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
-	dev-python/html5lib[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-
-S=${WORKDIR}/${PN}-${MY_PV}
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import astroquery, sys;r = astroquery.test();sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
-
-pkg_postinst() {
-	elog "To use the ESO archive web service, dev-python/keyring"
-	elog "must be installed."
-}
diff --git a/dev-python/ccdproc/Manifest b/dev-python/ccdproc/Manifest
deleted file mode 100644
index 942838314..000000000
--- a/dev-python/ccdproc/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST ccdproc-0.2.1.tar.gz 600743 SHA256 b4f23a5e6e1de6d88cd2b4a38398a922ae009896f807366d8625140320557f27 SHA512 50640b019c6d72d2c8e0a3dcb8d9021216fca606a5cdea90f65bb3241ebffe9d369c8d4697fd4ed1cdb158f4c1add514683d232ba8db5cb088580d64f8b4a57d WHIRLPOOL a5e12e25d242b9a2dc90facbcabb382c02683b166ed1f0090dbf38f8e9a9e22f89f5f11b14394f311392f942ae27438f451bc4d3eb51d5ba93093d96a796ef62
-DIST ccdproc-0.2.tar.gz 480410 SHA256 4be572f7fb6d87ff4ded744485fe76a699a132ed6777d3971eb88dcfe5c34d3a SHA512 36e8938ac29e317ce1d4055ed1ba8a985499904c5caea06bbd0b50b8abf31e9248d46754bf7c2f721e0174f51af27cc94870db0e48dee2a8adde620fe9c5f376 WHIRLPOOL 0bb93d0712d40641412a610231264315d50389c71c70482af73b56ff27d27b9af62e15bd683d12461700df25c374356de63e8f80d4fdf7fad9335642a387792b
diff --git a/dev-python/ccdproc/ccdproc-0.2.1.ebuild b/dev-python/ccdproc/ccdproc-0.2.1.ebuild
deleted file mode 100644
index 678a5379e..000000000
--- a/dev-python/ccdproc/ccdproc-0.2.1.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_3,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Astropy affiliated package for reducing optical/IR CCD data"
-HOMEPAGE="https://github.com/astropy/ccdproc"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/ccdproc/ccdproc-0.2.ebuild b/dev-python/ccdproc/ccdproc-0.2.ebuild
deleted file mode 100644
index 678a5379e..000000000
--- a/dev-python/ccdproc/ccdproc-0.2.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_3,3_4} )
-inherit distutils-r1
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/astropy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="Astropy affiliated package for reducing optical/IR CCD data"
-HOMEPAGE="https://github.com/astropy/ccdproc"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
diff --git a/dev-python/emcee/Manifest b/dev-python/emcee/Manifest
deleted file mode 100644
index 02b2f1c53..000000000
--- a/dev-python/emcee/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST emcee-1.2.0.tar.gz 22281 SHA256 97c0e342b093f00203aad4f99c0fcdd8a27a0f98d5f8e3b5f2f1f17a1adc1cb7 SHA512 774680b9f43c0b0ed8de73040246a63ddd36cd543b792cc6eb546b5ddcc826b45cc416c118619d5972daaac8bf707338cd05dc2ff9a09a36061cff9fd8f25dfd WHIRLPOOL 24ee8417e7c5d2deca73faa2517fd3304ef16ed7580ee8533cc5987d4d782677926493a761ef0fff061a6018270364f1ef55dd0277ab704404a9d740faaa9a5a
-DIST emcee-2.0.0.tar.gz 18774 SHA256 75edb32374afab669877846bd57fc1990a1f48958614b3d349362a2e7110b429 SHA512 5996e22c9ebb231be7e25c6b7f8f396f747bed5d5b64fa7f5c66e5d3c68cfaf6f450e48ccc0af9bc1245a1521afbfcf4da9096fd49a018d5a5d4fbb90a66344a WHIRLPOOL cc8f25808c93c9d95378a213243267f117d7e0c8728d7f8676059d9870acc9bd599d030fa5ce54dd991229e8d95084b7454665e413d9c3ca133834783ba73c01
diff --git a/dev-python/emcee/emcee-1.2.0.ebuild b/dev-python/emcee/emcee-1.2.0.ebuild
deleted file mode 100644
index 21ecbfad0..000000000
--- a/dev-python/emcee/emcee-1.2.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python ensemble sampling toolkit for affine-invariant MCMC"
-HOMEPAGE="http://danfm.ca/emcee/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${DEPEND}"
-
-python_test() {
-	distutils_install_for_testing
-	${EPYTHON} -c "import ${PN}; ${PN}.test()" 2>&1 | tee test.log || die
-	grep -Eq "^(ERROR|FAIL):" test.log && die
-}
diff --git a/dev-python/emcee/emcee-2.0.0.ebuild b/dev-python/emcee/emcee-2.0.0.ebuild
deleted file mode 100644
index 7bd6a5110..000000000
--- a/dev-python/emcee/emcee-2.0.0.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_3} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python ensemble sampling toolkit for affine-invariant MCMC"
-HOMEPAGE="http://danfm.ca/emcee/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${DEPEND}"
-
-python_test() {
-	distutils_install_for_testing
-	${EPYTHON} -c "import ${PN}; ${PN}.test()" 2>&1 | tee test.log || die
-	grep -Eq "^(ERROR|FAIL):" test.log && die
-}
diff --git a/dev-python/emcee/metadata.xml b/dev-python/emcee/metadata.xml
deleted file mode 100644
index 04a193100..000000000
--- a/dev-python/emcee/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci@gentoo.org</email>
-    <name>Gentoo Science Project</name>
-  </maintainer>
-  <longdescription lang="en">
-  This provides a set of sparse matrix types for Python, with modules
-  which implement:
-  - Iterative methods for solving linear systems of equations
-  - A set of standard preconditioners
-  - An interface to a direct solver for sparse linear systems of equations
-  - The JDSYM eigensolver.
-  All of these modules are implemented as C extension modules based on
-  standard sparse and dense matrix libraries (UMFPACK/AMD, SuperLU,
-  BLAS/LAPACK) for maximum performance and robustness.
-</longdescription>
-  <upstream>
-    <remote-id type="pypi">emcee</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/dev-python/gammapy/Manifest b/dev-python/gammapy/Manifest
deleted file mode 100644
index 94f9234bc..000000000
--- a/dev-python/gammapy/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gammapy-0.1.tar.gz 1014544 SHA256 f646d470506cb9b7a4b69d6d18043a7fa01b0a64b9948251b8df3976486b40a2 SHA512 ef6c5b12bc9d6929dff65cc9520d853f423aa22e13820cec378ce065bddaefd21dcd55ba2f7ed3ede7b33d7d7d118653e2884dc85d32d8621e4f832218004e6f WHIRLPOOL 7edc8864c5abeac980f11bad0f965da386aa20de28a56eece863d3eae350dc3b50726902d5242dee94340ed4e1c39b9d5d32a2cbd0f87d1f6f54c02cda7e8be7
diff --git a/dev-python/gammapy/gammapy-0.1.ebuild b/dev-python/gammapy/gammapy-0.1.ebuild
deleted file mode 100644
index e2a68b9dd..000000000
--- a/dev-python/gammapy/gammapy-0.1.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_7,3_3,3_4} )
-inherit distutils-r1 eutils
-
-if [ ${PV} == "9999" ] ; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/gammapy/${PN}.git"
-else
-	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-DESCRIPTION="A Python package for gamma-ray astronomy"
-HOMEPAGE="https://github.com/gammapy/gammapy"
-
-LICENSE="BSD"
-SLOT="0"
-IUSE="doc"
-DOCS=( README.rst )
-
-RDEPEND="
-	>=dev-python/astropy-0.4[${PYTHON_USEDEP}]
-	dev-python/astropy-helpers[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]"
-
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-	distutils-r1_python_prepare_all
-	sed -e '/import ah_bootstrap/d' -i setup.py || die "Removing ah_bootstrap failed"
-}
-
-python_compile_all() {
-	if use doc; then
-		python_export_best
-		VARTEXFONTS="${T}"/fonts \
-			MPLCONFIGDIR="${BUILD_DIR}" \
-			PYTHONPATH="${BUILD_DIR}"/lib \
-			esetup.py build_sphinx
-	fi
-}
-
-python_test() {
-	distutils_install_for_testing
-	cd "${TEST_DIR}" || die
-	"${EPYTHON}" -c "import ${PN}, sys;r = ${PN}.test(verbose=True);sys.exit(r)" \
-		|| die "tests fail with ${EPYTHON}"
-}
-
-python_install_all() {
-	use doc && local HTML_DOCS=( docs/_build/html/. )
-	distutils-r1_python_install_all
-}
-
-pkg_postinst() {
-	elog "To get additional features, a number of optional runtime"
-	elog "dependencies may be installed:"
-	elog ""
-	optfeature "Numerical Methods" sci-libs/scipy
-	optfeature "Plotting" dev-python/matplotlib
-	optfeature "Plotting Astronomical Images" dev-python/aplpy
-	optfeature "Read/write CVS files" dev-python/pandas
-	optfeature "Image Processing" sci-libs/scikits_image
-	optfeature "Conversion helper functions" dev-python/rootpy
-
-	# In science overlay:
-	optfeature "Image photometry" dev-python/photutils
-	optfeature "Image Utility Functions" dev-python/imageutils
-
-	# Not packaged: Gammalib, ctools, sherpa, imfun, uncertainties, reproject
-}
diff --git a/dev-python/healpy/Manifest b/dev-python/healpy/Manifest
deleted file mode 100644
index c1fd88083..000000000
--- a/dev-python/healpy/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST healpy-1.7.4.tar.gz 3990803 SHA256 3cca7ed7786ffcca70e2f39f58844667ffb8521180ac890d4da651b459f51442 SHA512 be54ff3445feea33cba2bbff79b2d5c98bbb3b9ecccebfe5b24655a935cadff5d1c270a1a12e338f5f40b5920654a9aac0efac8cff1d100acaaed904d8ceb030 WHIRLPOOL a8e746a0351129b09bd32194b73f38c0002dc6e73c72589cf8216c429d67008bd4aab9092d421c667584ff9d01a9b3141195176a518acc2bc2fb6ab68a244894
diff --git a/dev-python/healpy/healpy-1.7.4.ebuild b/dev-python/healpy/healpy-1.7.4.ebuild
deleted file mode 100644
index 01189494a..000000000
--- a/dev-python/healpy/healpy-1.7.4.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python wrapper for healpix"
-HOMEPAGE="https://github.com/healpy"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pyfits[${PYTHON_USEDEP}]
-	sci-astronomy/healpix_cxx
-	sci-libs/cfitsio"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-python_test() {
-	cd "${BUILD_DIR}"/lib || die
-	echo "backend: Agg" > matplotlibrc || die
-	MPLCONFIGDIR=. nosetests || die
-	rm matplotlibrc || die
-}
diff --git a/dev-python/healpy/metadata.xml b/dev-python/healpy/metadata.xml
deleted file mode 100644
index b279857a5..000000000
--- a/dev-python/healpy/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-astronomy@gentoo.org</email>
-    <name>Gentoo Astronomy Project</name>
-  </maintainer>
-  <longdescription lang="en">
-  Healpy provides a python package to manipulate healpix maps. It is
-  based on the standard numeric and visualisation tools for Python,
-  Numpy and matplotlib.
-</longdescription>
-  <upstream>
-    <remote-id type="pypi">healpy</remote-id>
-    <remote-id type="github">healpy</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-astronomy/chealpix/Manifest b/sci-astronomy/chealpix/Manifest
deleted file mode 100644
index 31b81ab19..000000000
--- a/sci-astronomy/chealpix/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST chealpix-3.11.2.tar.gz 309153 SHA256 fae83cbc353a18999f48397a14f8b41cf9f41f0f1e5927feac8e2acf2f6583e3 SHA512 205628e97b4b3c3776d0e276c81b00348764a98d31e56902f03db92c992c24b3f8b75222f84e68ecfd4da45579cf57458f8a29a22211327320e9cae1553d1cf4 WHIRLPOOL 6205b09564ebf1a8057d0cade551fc0dbb69f24ecabb0590941d3f2f3d91574825cfdd86c91382a066b37e54ee56978b1f0f940ce126251863896af522b1e450
diff --git a/sci-astronomy/chealpix/chealpix-3.11.2.ebuild b/sci-astronomy/chealpix/chealpix-3.11.2.ebuild
deleted file mode 100644
index fe4e8de38..000000000
--- a/sci-astronomy/chealpix/chealpix-3.11.2.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools-utils
-
-MYP="Healpix_3.11"
-
-DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - C Library"
-HOMEPAGE="http://healpix.sourceforge.net/"
-SRC_URI="mirror://sourceforge/healpix/${MYP}/autotools_packages/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-IUSE="static-libs"
-
-RDEPEND="
-	>=sci-libs/cfitsio-3"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
diff --git a/sci-astronomy/chealpix/metadata.xml b/sci-astronomy/chealpix/metadata.xml
deleted file mode 100644
index 49927d38d..000000000
--- a/sci-astronomy/chealpix/metadata.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-astronomy@gentoo.org</email>
-    <name>Gentoo Astronomy Project</name>
-  </maintainer>
-  <longdescription lang="en">
-  HEALPix is an acronym for Hierarchical Equal Area isoLatitude
-  Pixelization of a sphere. As suggested in the name, this pixelization produces a
-  subdivision of a spherical surface in which each pixel covers the same
-  surface area as every other pixel. This package contains the C library.
-</longdescription>
-  <upstream>
-    <remote-id type="sourceforge">healpix</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-astronomy/healpix_cxx/Manifest b/sci-astronomy/healpix_cxx/Manifest
deleted file mode 100644
index 270d908bb..000000000
--- a/sci-astronomy/healpix_cxx/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST healpix_cxx-3.11.2.tar.gz 474320 SHA256 0e36478d82be566e85524c3be15890e1374afb4d83c98eae35bc426b06d1db8d SHA512 61e3183373940386e52d272b53df91278cf8bfaad8c89c0c2246708c69f7154697437593ac6fca06c9c3f42068a1f2be47bff3ba18736527a8fd53215bbadd9a WHIRLPOOL 51ec31f92f8ac9bde061d54c9568e14c6c2ac7fc73db3939ac8800cebd112116cb20aa37c30885c5577e5adeec1092a448218d27c6c1a9c9ff06d546faca5f53
diff --git a/sci-astronomy/healpix_cxx/healpix_cxx-3.11.2.ebuild b/sci-astronomy/healpix_cxx/healpix_cxx-3.11.2.ebuild
deleted file mode 100644
index 399bbce9e..000000000
--- a/sci-astronomy/healpix_cxx/healpix_cxx-3.11.2.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=1
-inherit autotools-utils toolchain-funcs
-
-MYP="Healpix_3.11"
-
-DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - C++"
-HOMEPAGE="http://healpix.sourceforge.net/"
-SRC_URI="mirror://sourceforge/healpix/${MYP}/autotools_packages/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-IUSE="openmp static-libs"
-
-RDEPEND="
-	>=sci-libs/cfitsio-3"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-pkg_setup() {
-	if use openmp && [[ $(tc-getCXX)$ == *g++* ]]; then
-		if ! tc-has-openmp; then
-			ewarn "You are using a g++ without OpenMP capabilities"
-			die "Need an OpenMP capable compiler"
-		fi
-	fi
-}
-
-src_prepare() {
-	# why was static-libtool-libs forced?
-	# it screws up as-neeeded
-	use static-libs || sed -i -e '/-static-libtool-libs/d' Makefile.am
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		$(use_enable openmp)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-astronomy/healpix_cxx/metadata.xml b/sci-astronomy/healpix_cxx/metadata.xml
deleted file mode 100644
index 97134d3dc..000000000
--- a/sci-astronomy/healpix_cxx/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-astronomy@gentoo.org</email>
-    <name>Gentoo Astronomy Project</name>
-  </maintainer>
-  <longdescription lang="en">
-  HEALPix is an acronym for Hierarchical Equal Area isoLatitude
-  Pixelization of a sphere. As suggested in the name, this pixelization produces a
-  subdivision of a spherical surface in which each pixel covers the same
-  surface area as every other pixel. This package contains the C++
-  library and programs.
-</longdescription>
-  <upstream>
-    <remote-id type="sourceforge">healpix</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-astronomy/healpix_idl/Manifest b/sci-astronomy/healpix_idl/Manifest
deleted file mode 100644
index 983581ad4..000000000
--- a/sci-astronomy/healpix_idl/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Healpix_3.11_2013Apr24.tar.gz 24256278 SHA256 f80aa3633601664afe99c8b7dc7253828f22e6d832187ab46ac90b2ad83e6831 SHA512 aae5592dda40103918a6c6520863e2aeddf40a34531e4ce2f38a1ce7411731218d7e20bd02107f92384a7b371c2415ed640ad27aa398f64857f5ed7d9dba32bb WHIRLPOOL 1e3f0588502b6b9e68c19de9763ae775d01031cd7a3120bb663a71bae1fa7e2baf6ac4997ff07598ca45e610ae919839ecf04c66a201256665f5e5f1727f7299
diff --git a/sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild b/sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild
deleted file mode 100644
index 9aec068b3..000000000
--- a/sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-MYP="Healpix_${PV}"
-MYPP="2013Apr24"
-
-DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - IDL routines"
-HOMEPAGE="http://healpix.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${MYP}/${MYP}_${MYPP}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-IUSE="doc"
-
-RDEPEND="
-	dev-lang/gdl
-	sci-astronomy/idlastro"
-
-S="${WORKDIR}/${MYP}/src/idl"
-
-src_prepare() {
-	# duplocate of idlastro (in rdeps)
-	rm -r zzz_external/astron || die
-	mv zzz_external/README README.external || die
-}
-
-src_install() {
-	insinto /usr/share/gnudatalanguage/healpix
-	doins -r examples fits interfaces misc toolkit visu zzz_external
-	doins HEALPix_startup
-	dodoc README.*
-}
diff --git a/sci-astronomy/healpix_idl/metadata.xml b/sci-astronomy/healpix_idl/metadata.xml
deleted file mode 100644
index 09fbd9273..000000000
--- a/sci-astronomy/healpix_idl/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-astronomy@gentoo.org</email>
-    <name>Gentoo Astronomy Project</name>
-  </maintainer>
-  <longdescription lang="en">
-  HEALPix is an acronym for Hierarchical Equal Area isoLatitude
-  Pixelization of a sphere. As suggested in the name, this pixelization produces a
-  subdivision of a spherical surface in which each pixel covers the same
-  surface area as every other pixel. This package contains the IDL/GDL
-  routines and plots.
-</longdescription>
-  <upstream>
-    <remote-id type="sourceforge">healpix_idl</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest
deleted file mode 100644
index 77dfde1ec..000000000
--- a/sci-biology/abyss/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914
-DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01
-DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07
diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild
deleted file mode 100644
index 76f15b496..000000000
--- a/sci-biology/abyss/abyss-1.3.3-r1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit autotools eutils toolchain-funcs
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-cpp/sparsehash
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-src_prepare() {
-	tc-export AR
-	epatch \
-		"${FILESDIR}"/${P}-gcc-4.7.patch \
-		"${FILESDIR}"/${P}-ac_prog_ar.patch \
-		"${FILESDIR}"/${P}-samtoafg.patch
-
-	sed -i -e "s/-Werror//" configure.ac || die #365195
-	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--docdir="${EPREFIX}/usr/share/doc/${PF}" \
-		$(use_enable openmp)
-}
diff --git a/sci-biology/abyss/abyss-1.3.4-r1.ebuild b/sci-biology/abyss/abyss-1.3.4-r1.ebuild
deleted file mode 100644
index 762d49a79..000000000
--- a/sci-biology/abyss/abyss-1.3.4-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-cpp/sparsehash
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch
-	"${FILESDIR}"/${P}-samtoafg.patch
-	)
-
-src_prepare() {
-	tc-export AR
-	sed -i -e "s/-Werror//" configure.ac || die #365195
-	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--docdir="${EPREFIX}/usr/share/doc/${PF}"
-		$(use_enable openmp)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild
deleted file mode 100644
index f002a9578..000000000
--- a/sci-biology/abyss/abyss-1.3.6-r1.ebuild
+++ /dev/null
@@ -1,48 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils
-
-DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"
-HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/"
-SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz"
-
-LICENSE="abyss"
-SLOT="0"
-IUSE="+mpi openmp"
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="
-	dev-cpp/sparsehash
-	dev-libs/boost
-	mpi? ( virtual/mpi )"
-RDEPEND="${DEPEND}"
-
-# todo: --enable-maxk=N configure option
-# todo: fix automagic mpi toggling
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc-4.7.patch
-	"${FILESDIR}"/${P}-ac_prog_ar.patch
-	"${FILESDIR}"/${P}-samtoafg.patch
-	)
-
-src_prepare() {
-	tc-export AR
-	sed -i -e "s/-Werror//" configure.ac || die #365195
-	sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--docdir="${EPREFIX}/usr/share/doc/${PF}"
-		$(use_enable openmp)
-	)
-	autotools-utils_src_configure
-}
diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
deleted file mode 100644
index 300868f52..000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 5c6cb92..b99bedd 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- 
- # Checks for header files.
- AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
deleted file mode 100644
index 42066f7f2..000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 506ea0c..a0a403c 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -15,6 +15,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
deleted file mode 100644
index cb7dfb08a..000000000
--- a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Hello,
-
-I see Shaun Jackmans' (abyss-)sam2afg script is available within the 
-Amos source repository. I find this very useful for coercing output from 
-assemblers which which don't track read location into amos by remapping 
-reads against the assembly and converting to afg - not ideal but better 
-than nothing when you don't have the 'real' read locations to work with.
-
-This fails, however when reads are aligned with 'bwa mem', which can 
-output multi-part alignments. sam2afg checks for reuse of the same read 
-id (presumably to prevent the generation of non-unique eid values), 
-consequently encountering multiple alignments for a read causes it to die.
-
-The following one-line patch allows sam2afg to skip these secondary 
-alignments present in 'bwa mem' output, provided bwa mem has been run 
-with the '-M' argument which sets the SAM 'secondary alignment' flag on 
-the alignments in question.
-
-Hopefully this will also be of use to others...
-
-Best Regards,
-James
-
--- 
-Dr. James Abbott
-Lead Bioinformatician
-Bioinformatics Support Service
-Imperial College, London
-
-
---- abyss-1.3.6/bin/abyss-samtoafg.ori	2015-05-23 23:43:46.797747928 +0200
-+++ abyss-1.3.6/bin/abyss-samtoafg	2015-05-23 23:44:09.227747743 +0200
-@@ -105,6 +105,7 @@
- 	die unless defined $qqual;
- 
- 	$tstart--; # convert to zero-based coordinate
-+        next if $flag & 0x100; # secondary alignment
- 	$qid .= "/1" if $flag & 0x40; #FREAD1
- 	$qid .= "/2" if $flag & 0x80; #FREAD2
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
deleted file mode 100644
index c2cc35c31..000000000
--- a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 1a169cf..36cc05b 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -16,6 +16,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
deleted file mode 100644
index cb7dfb08a..000000000
--- a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Hello,
-
-I see Shaun Jackmans' (abyss-)sam2afg script is available within the 
-Amos source repository. I find this very useful for coercing output from 
-assemblers which which don't track read location into amos by remapping 
-reads against the assembly and converting to afg - not ideal but better 
-than nothing when you don't have the 'real' read locations to work with.
-
-This fails, however when reads are aligned with 'bwa mem', which can 
-output multi-part alignments. sam2afg checks for reuse of the same read 
-id (presumably to prevent the generation of non-unique eid values), 
-consequently encountering multiple alignments for a read causes it to die.
-
-The following one-line patch allows sam2afg to skip these secondary 
-alignments present in 'bwa mem' output, provided bwa mem has been run 
-with the '-M' argument which sets the SAM 'secondary alignment' flag on 
-the alignments in question.
-
-Hopefully this will also be of use to others...
-
-Best Regards,
-James
-
--- 
-Dr. James Abbott
-Lead Bioinformatician
-Bioinformatics Support Service
-Imperial College, London
-
-
---- abyss-1.3.6/bin/abyss-samtoafg.ori	2015-05-23 23:43:46.797747928 +0200
-+++ abyss-1.3.6/bin/abyss-samtoafg	2015-05-23 23:44:09.227747743 +0200
-@@ -105,6 +105,7 @@
- 	die unless defined $qqual;
- 
- 	$tstart--; # convert to zero-based coordinate
-+        next if $flag & 0x100; # secondary alignment
- 	$qid .= "/1" if $flag & 0x40; #FREAD1
- 	$qid .= "/2" if $flag & 0x80; #FREAD2
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
deleted file mode 100644
index 158e9b126..000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- configure.ac | 4 ++++
- 1 file changed, 4 insertions(+)
-
-diff --git a/configure.ac b/configure.ac
-index 9d4bb66..aa94364 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -12,6 +12,10 @@ AC_PROG_CPP
- AC_PROG_CXX
- AC_PROG_INSTALL
- AC_PROG_RANLIB
-+AN_MAKEVAR([AR], [AC_PROG_AR])
-+AN_PROGRAM([ar], [AC_PROG_AR])
-+AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
-+AC_PROG_AR
- AC_CHECK_TOOL(GHC, ghc)
- AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
deleted file mode 100644
index c2cc35c31..000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- ParseAligns/abyss-fixmate.cc |    1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
-index 1a169cf..36cc05b 100644
---- a/ParseAligns/abyss-fixmate.cc
-+++ b/ParseAligns/abyss-fixmate.cc
-@@ -16,6 +16,7 @@
- #include <iterator>
- #include <sstream>
- #include <string>
-+#include <unistd.h>
- 
- using namespace std;
- 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
deleted file mode 100644
index cb7dfb08a..000000000
--- a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Hello,
-
-I see Shaun Jackmans' (abyss-)sam2afg script is available within the 
-Amos source repository. I find this very useful for coercing output from 
-assemblers which which don't track read location into amos by remapping 
-reads against the assembly and converting to afg - not ideal but better 
-than nothing when you don't have the 'real' read locations to work with.
-
-This fails, however when reads are aligned with 'bwa mem', which can 
-output multi-part alignments. sam2afg checks for reuse of the same read 
-id (presumably to prevent the generation of non-unique eid values), 
-consequently encountering multiple alignments for a read causes it to die.
-
-The following one-line patch allows sam2afg to skip these secondary 
-alignments present in 'bwa mem' output, provided bwa mem has been run 
-with the '-M' argument which sets the SAM 'secondary alignment' flag on 
-the alignments in question.
-
-Hopefully this will also be of use to others...
-
-Best Regards,
-James
-
--- 
-Dr. James Abbott
-Lead Bioinformatician
-Bioinformatics Support Service
-Imperial College, London
-
-
---- abyss-1.3.6/bin/abyss-samtoafg.ori	2015-05-23 23:43:46.797747928 +0200
-+++ abyss-1.3.6/bin/abyss-samtoafg	2015-05-23 23:44:09.227747743 +0200
-@@ -105,6 +105,7 @@
- 	die unless defined $qqual;
- 
- 	$tstart--; # convert to zero-based coordinate
-+        next if $flag & 0x100; # secondary alignment
- 	$qid .= "/1" if $flag & 0x40; #FREAD1
- 	$qid .= "/2" if $flag & 0x80; #FREAD2
- 
diff --git a/sci-biology/abyss/metadata.xml b/sci-biology/abyss/metadata.xml
deleted file mode 100644
index 959160fe4..000000000
--- a/sci-biology/abyss/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild
index 4bcb6a0c5..3e9dc991c 100644
--- a/sci-biology/fsl/fsl-5.0.8.ebuild
+++ b/sci-biology/fsl/fsl-5.0.8.ebuild
@@ -128,7 +128,7 @@ src_install() {
 	#fi
 
 	doenvd "${FILESDIR}"/99fsl
-	rm "${ED}"/usr/bin/cluster || die
+	mv "${ED}"/usr/bin/{,fsl_}cluster || die
 }
 
 pkg_postinst() {
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index a95bf6f41..c633d383f 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,4 +1 @@
-DIST pysam-0.6.tar.gz 841790 SHA256 081c980481f31a81acb06f6fa5638b899321eddfd9eeb5075393e4dad84a1fc8 SHA512 b60df4551600f04e8ae67aec0f2745846d2411e2a1cc4c874ef296ee80ab075256190ebb0ec64eb78231d4d7b59670c5259818cd315f52c923774cc4c0b8b391 WHIRLPOOL eddeb19f3ebf0c6326f7c1b6b7224b2b8cb708e0bf7ceb66b1cac18909abafd1704b264452b70ee6721af4b3b360b51285dcffd7f137c6128920f91dc0dec7b2
 DIST pysam-0.7.5.tar.gz 1466667 SHA256 fa85900ead3d1c2c9ce24f28d2b1843c0a8ffb761cd21d440049e29eca2e2453 SHA512 ce609c65eef1188186c28cb8ea1bad73608d738c47089a5ef3a22a14e7bba5acd8f8b6a3fd67935cf1dc9fb57927205ad0f009dc0122b12c1866955ada01198c WHIRLPOOL c9a4488fb8f6fbd2aa74081f5b286befbab980e8544036956e83d82b3f4f9238c6f0138f094b090b30e18b3eb25c36ce4f6cadf65d6e80195091de6d7995f19d
-DIST pysam-0.8.4.tar.gz 2878207 SHA256 4acbfe4b15b1db2417094ea64836d416a66e368e6c0e3031b597509f21e8c021 SHA512 1b00fd08d3701988cb2bc01534a739d0cd479894a9b99be934ed476770558707758078714740df39e042c675164fbc7e8ed8e470e05b73682940247f165b29a2 WHIRLPOOL cb53c63cbacfecfad4782f77c5d7def76946595ce2914f657e2383943181df2fbc1b487792c6418d55732e30603e6c59f1cf551dfbfdbd632bac2f514837d995
-DIST v0.8.3.tar.gz 2828558 SHA256 ab6c78ec64f4ccf525728a26f676bcc1f37ad021d120fe210ed819dbe6dac992 SHA512 b36fbd0e0c9139f15ea9fdf07a0002219c6e502ca0c113be0de988b9171bf6c6c2e6fe372083949490fdec7eb4bf4d4f7b8114f756dd87ab2b951e3c8dfd8137 WHIRLPOOL b2cbd3a4a506a159cf60aaa7b0f478ce01f8b4c1c52f08dc7def9b72692cfab20b186e03c71fee4f6b7c76c9ad7512e14867d18dd692c4282eabb1e4f307c064
diff --git a/sci-biology/pysam/pysam-0.6-r2.ebuild b/sci-biology/pysam/pysam-0.6-r2.ebuild
deleted file mode 100644
index 01f86da85..000000000
--- a/sci-biology/pysam/pysam-0.6-r2.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam"
-SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-	<=sci-biology/samtools-0.1.18[${PYTHON_USEDEP}]"
-
-python_compile() {
-	python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}
diff --git a/sci-biology/pysam/pysam-0.8.3.ebuild b/sci-biology/pysam/pysam-0.8.3.ebuild
deleted file mode 100644
index a08855f80..000000000
--- a/sci-biology/pysam/pysam-0.8.3.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam"
-SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-	>=sci-biology/samtools-1.2[${PYTHON_USEDEP}]
-	>=sci-libs/htslib-1.2.1"
-
-PATCHES=( "${FILESDIR}/${P}-cython-0.23.patch" )
-
-python_compile() {
-	python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}
diff --git a/sci-biology/pysam/pysam-0.8.4.ebuild b/sci-biology/pysam/pysam-0.8.4.ebuild
deleted file mode 100644
index 2b4d3d997..000000000
--- a/sci-biology/pysam/pysam-0.8.4.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="https://github.com/pysam-developers/pysam http://pypi.python.org/pypi/pysam"
-SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-	>=sci-biology/samtools-1.2[${PYTHON_USEDEP}]
-	>=sci-libs/htslib-1.2.1"
-
-python_compile() {
-	python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}
diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
deleted file mode 100644
index fd00473d3..000000000
--- a/sci-biology/tophat/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST tophat-2.0.12.tar.gz 1767329 SHA256 ce97d9f3c6d6c0dd256744498b5209a9260ca3118a8e5210d9404fae890a4d74 SHA512 c2eae628cb1d0a19793708df710a10e04663e3dae12725f93faf17d1784360239a82a7fd9cee6e3d9b7156fe74b9612b71a97de540c9ba0ff9a61005a14c4b3b WHIRLPOOL a2582c7ec91fd589e0e8854b65250eaafe567241fad0023b788359e1d67b3cbf024ddf3a3543974bf43e13b13420ea37186a85d1b55059ea1cfd87915e4d39c0
-DIST tophat-2.0.13.tar.gz 1998819 SHA256 acbe8f1a47131053d4b766df117c9f83458fdc5df6a500d7488e4c6cef51e512 SHA512 1fd38f4e866997f82209892111c976d29dc9e1055ba8fc65ee3ea2436a4d9673a73985dcac73519c7f8abc719bda20366aa84a36e8dea4a9b7d135c1b94afb89 WHIRLPOOL bf4dc17c5d508194c85dc73c73d66a390e95484db14ca282c5be5ca6ab55e2c7edfd9861ff6f0daba4344089a25e47372ceaf2d4ea269d27dc6808f4e0b637b0
-DIST tophat-2.0.14.tar.gz 2013476 SHA256 547c5c9d127cbf7d61bc73c4251ff98a07d57e59b3718666a18b58acfb8fcfbf SHA512 fcdf7c8ad298284acabeac3bc96c7f08e74927d3c6e38fa93914a0bba470ba495cc5920ef0c22efcd652788e484162c0632c6d3574f3d90ba15fe8690feb0ec8 WHIRLPOOL ca2bcc89553160480b5594cfb755701d3b72ee8c8c7629b8b6091a9849bd910423a699dd7750f7ee654fa15c216538bfa0786ecdc14855eb73e39a30029ca00e
-DIST tophat-2.1.0.tar.gz 4300174 SHA256 eceb56527c23c970f51cb3ff4f4c2a2d28d110cfa8f2f0a333d1b58152c35274 SHA512 c1c9e3006ab7777811fdfe61611143117af0819ba8eaa0ca359e76352a6d2c03c8616195bc7aca79fedbc1cd1a15e6d242ef5f006500bdee7e35b11787afcea6 WHIRLPOOL 8c0336d0b3b2675df1c6e2f9d8da6ed08f30626e957e41655042eb8c7dae8d892c233f17fd235da327a3bfba45ba1a8715558f6a65d9d4adeaa870049cc01940
diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch
deleted file mode 100644
index af89e7208..000000000
--- a/sci-biology/tophat/files/tophat-2.0.9-flags.patch
+++ /dev/null
@@ -1,109 +0,0 @@
- configure.ac    |  3 ++-
- src/Makefile.am | 50 +++++++++++++++++++++++++-------------------------
- 2 files changed, 27 insertions(+), 26 deletions(-)
-
-diff --git a/configure.ac b/configure.ac
-index 75e9218..98b05d2 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -68,7 +68,8 @@ AC_CANONICAL_HOST
- # set CFLAGS and CXXFLAGS
- #user_CFLAGS="${CXXFLAGS}"
- user_CFLAGS=${CFLAGS}
--generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
-+generic_CFLAGS=""
- ext_CFLAGS=""
- debug_CFLAGS=""
- user_LDFLAGS="$LDFLAGS"
-diff --git a/src/Makefile.am b/src/Makefile.am
-index dde692e..ebb9fcd 100644
---- a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -545,10 +545,10 @@ CLEANFILES = \
- 	tophat2
- 
- tophat2: tophat2.in
--	sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2
-+	sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2
- 
- tophat: tophat.py
--	sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat
-+	sed -e 's|__VERSION__|$(VERSION)|' $(top_srcdir)/src/tophat.py > tophat
- 
- #SUFFIXES = .py
- #.py:
-@@ -617,49 +617,49 @@ libgc_a_SOURCES = \
- #-- program sources
- 
- prep_reads_SOURCES = prep_reads.cpp
--prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) 
-+prep_reads_LDADD = libtophat.a $(BAM_LIB)
-+prep_reads_LDFLAGS = $(BAM_LDFLAGS) 
- 
- segment_juncs_SOURCES = segment_juncs.cpp
--segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- long_spanning_reads_SOURCES = long_spanning_reads.cpp
--long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- gtf_juncs_SOURCES = gtf_juncs.cpp
--gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+gtf_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- juncs_db_SOURCES = juncs_db.cpp
--juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+juncs_db_LDADD = libtophat.a $(BAM_LIB)
-+juncs_db_LDFLAGS = $(BAM_LDFLAGS)
- 
- tophat_reports_SOURCES = tophat_reports.cpp
--tophat_reports_LDADD = $(top_builddir)/src/libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
--tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
-+tophat_reports_LDADD = libtophat.a  $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
-+tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS)
- 
- fix_map_ordering_SOURCES = fix_map_ordering.cpp
--fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+fix_map_ordering_LDADD = libtophat.a $(BAM_LIB)
-+fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam2fastx_SOURCES = bam2fastx.cpp
--bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB)
--bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+bam2fastx_LDADD = libgc.a $(BAM_LIB)
-+bam2fastx_LDFLAGS = $(BAM_LDFLAGS)
- 
- bam_merge_SOURCES = bam_merge.cpp
--bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB)
--bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+bam_merge_LDFLAGS = $(BAM_LDFLAGS)
- 
- sam_juncs_SOURCES = sam_juncs.cpp
--sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB)
--sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+sam_juncs_LDADD = libtophat.a $(BAM_LIB)
-+sam_juncs_LDFLAGS = $(BAM_LDFLAGS)
- 
- map2gtf_SOURCES = map2gtf.cpp
--map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+map2gtf_LDFLAGS = $(BAM_LDFLAGS)
- 
- gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp
--gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
--gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS)
-+gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB)
-+gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS)
diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml
deleted file mode 100644
index dce054e1c..000000000
--- a/sci-biology/tophat/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">infphilo/tophat</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-biology/tophat/tophat-2.0.12.ebuild b/sci-biology/tophat/tophat-2.0.12.ebuild
deleted file mode 100644
index 7c9cf0777..000000000
--- a/sci-biology/tophat/tophat-2.0.12.ebuild
+++ /dev/null
@@ -1,58 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils python-single-r1
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
-HOMEPAGE="http://ccb.jhu.edu/software/tophat"
-# https://github.com/infphilo/tophat
-# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
-SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-#	samtools_0.1.18 view -h -
-#	samtools_0.1.18 sort
-#	samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
-	>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
-
-# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
-
-src_prepare() {
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* src/Makefile* || die
-	sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die
-	#rm -rf src/SeqAn* || die
-	eautoreconf
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-optim
-		$(use_enable debug)
-	)
-	autotools-utils_src_configure
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* src/Makefile* || die
-}
-
-src_install() {
-	# introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
-	sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
-	autotools-utils_src_install
-	python_fix_shebang "${ED}"/usr/bin/tophat
-}
diff --git a/sci-biology/tophat/tophat-2.0.13.ebuild b/sci-biology/tophat/tophat-2.0.13.ebuild
deleted file mode 100644
index 6625162e2..000000000
--- a/sci-biology/tophat/tophat-2.0.13.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils python-single-r1
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
-HOMEPAGE="http://ccb.jhu.edu/software/tophat"
-# https://github.com/infphilo/tophat
-# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
-SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-#   samtools_0.1.18 view -h -
-#   samtools_0.1.18 sort
-#   samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
-	>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
-
-# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
-
-src_prepare() {
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die
-	sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die
-	# rm -rf src/SeqAn* || die
-	eautoreconf
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-optim
-		$(use_enable debug)
-	)
-	autotools-utils_src_configure
-	cd ../"${P}"_build/src || die
-	ln -s ../"${P}"/src/SeqAn-1.3 . || die
-	ln -s ../../"${P}"/src/samtools-0.1.18 . || die
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die
-}
-
-src_install() {
-	# introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
-	sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
-	autotools-utils_src_install
-	python_fix_shebang "${ED}"/usr/bin/tophat
-}
diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild b/sci-biology/tophat/tophat-2.0.14.ebuild
deleted file mode 100644
index 0b8f1e80e..000000000
--- a/sci-biology/tophat/tophat-2.0.14.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils python-single-r1
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
-HOMEPAGE="http://ccb.jhu.edu/software/tophat"
-# https://github.com/infphilo/tophat
-# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz
-SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-#   samtools_0.1.18 view -h -
-#   samtools_0.1.18 sort
-#   samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
-	>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
-
-# see https://aur.archlinux.org/packages/tophat/ about linking issues
-
-# PATCHES=( "${FILESDIR}"/${P}-flags.patch )
-
-src_prepare() {
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die
-	sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die
-	eautoreconf
-	autotools-utils_src_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--disable-optim
-		$(use_enable debug)
-	)
-	autotools-utils_src_configure
-	cd ../"${P}"_build/src || die
-	ln -s ../../"${P}"/src/SeqAn-1.3 . || die
-	ln -s ../../"${P}"/src/samtools-0.1.18 . || die
-	sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die
-}
-
-src_install() {
-	# introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?)
-	sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die
-	autotools-utils_src_install
-	python_fix_shebang "${ED}"/usr/bin/tophat
-}
diff --git a/sci-biology/tophat/tophat-2.1.0.ebuild b/sci-biology/tophat/tophat-2.1.0.ebuild
deleted file mode 100644
index 05a7bfa5b..000000000
--- a/sci-biology/tophat/tophat-2.1.0.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=yes
-AUTOTOOLS_IN_SOURCE_BUILD=yes
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils python-single-r1
-
-DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2"
-HOMEPAGE="http://ccb.jhu.edu/software/tophat"
-SRC_URI="https://github.com/infphilo/tophat/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="debug"
-
-DEPEND="dev-libs/boost"
-# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency
-# boost and seqan is needed for tophat_reporter
-
-# tophat.py calls
-#   samtools_0.1.18 view -h -
-#   samtools_0.1.18 sort
-#   samtools_0.1.18 merge -f -h -u -Q --sam-header
-RDEPEND="${DEPEND}
-	>=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )"
-
-src_configure() {
-	local myeconfargs=(
-		$(use_enable debug)
-	)
-	autotools-utils_src_configure
-
-	echo "../src/libtophat.a: libtophat.a" >> src/Makefile
-	echo "../src/libgc.a: libgc.a" >> src/Makefile
-	echo "samtools_0.1.18:" >> src/Makefile
-	echo -e "\tcp samtools-0.1.18/\$@ \$@" >> src/Makefile
-}