Merge branch 'master' of git://git.overlays.gentoo.org/proj/sci

24 files changed, 339 insertions, 130 deletions

diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog
new file mode 100644
index 000000000..a5df6d9b6
--- /dev/null
+++ b/sci-biology/jellyfish/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/jellyfish
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*jellyfish-2.1.3 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +jellyfish-2.1.3.ebuild, +metadata.xml:
+  sci-biology/jellyfish: new package, works
diff --git a/sci-biology/jellyfish/Manifest b/sci-biology/jellyfish/Manifest
new file mode 100644
index 000000000..b5035d2e6
--- /dev/null
+++ b/sci-biology/jellyfish/Manifest
@@ -0,0 +1,2 @@
+DIST JellyfishUserGuide.pdf 142367 SHA256 6f4365f1839b0370fff50fcd25ffcf2dad4192c2ff5b8540fd929d73a8cf85c3 SHA512 a9d65be7591d4b9b275b9f76ab79806d31bf7ef36b297b67b1802a302687aa8d49d4c491c3bb9201aec58268bcfc8c703940c72991b9080bbd1bde95bbda5b8a WHIRLPOOL 1c57b1596ccfff2159bb86359f9dafac1f994b33ab38dc334827d74b8c7541728c6c8b400df54d756bfa0b98ae023fae020ccbebbb24e3eb51baccac5024a6e6
+DIST jellyfish-2.1.3.tar.gz 955773 SHA256 00530abd01c1253646f29fa4554e96fd31148ed92402940e6f357bd5cab38e9b SHA512 2b6fea6c2686de7b568988543d5a9466676eb17252ecce3243b0dc7e3c833aed02ae6570749df58c2921289db0167b39848ccd80eb3cc568cdbaa0045114b702 WHIRLPOOL 4a1e6568932db0cc4773e89e4b8f049e96ed929723ffd518ce7e0ed12bd29041d0774fba1069251a336e448dd75703a350917ffc3db5a35f2cfac828572da566
diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
new file mode 100644
index 000000000..4ac06b224
--- /dev/null
+++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="k-mer counter withing reads for assemblies"
+HOMEPAGE="http://www.genome.umd.edu/jellyfish.html"
+SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz
+	ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml
new file mode 100644
index 000000000..2bc893037
--- /dev/null
+++ b/sci-biology/jellyfish/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog
index d48473ae8..8b3878105 100644
--- a/sci-biology/tablet-bin/ChangeLog
+++ b/sci-biology/tablet-bin/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*tablet-bin-1.14.04.10 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +tablet-bin-1.14.04.10.ebuild:
+  sci-biology/tablet-bin: version bump; updated the license
+
 *tablet-bin-1.13.12.17 (20 Jan 2014)
 
   20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest
index ae1e4a6af..7c1877c79 100644
--- a/sci-biology/tablet-bin/Manifest
+++ b/sci-biology/tablet-bin/Manifest
@@ -1,2 +1,3 @@
 DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664
 DIST tablet-bin-1.13.12.17.sh 34395356 SHA256 fab481dd2a19e1c25142c41e75c483eeac36cc6793921a2643d9472f0aecbd2b SHA512 6fee28fd68ac4dde777dc7b873735e165d19bec47997a49185f21eecaaf2f38ca019b5af30ff18177ed69ad01eb8a797ef8b892631780ad548bf8fdf3ceb2f0b WHIRLPOOL 274e3849096179707af5ad36001ba060b5c5be068350454553997a120ec5c5f33b347ea26f3f9bd356bb7191b1c1e07199a6f6c0073e5b7edb7bf953d46c0974
+DIST tablet-bin-1.14.04.10.sh 36267340 SHA256 d716eab1c4f8f7de099bed6b10a7346fcc2340cf69e527e5af33f521fad00b97 SHA512 9ef7f3332171f66bee6cfceb46dae56170fc744709bc34ebcd6abf201b8d4dd9f6a3e21b61ec341297b66c1b2527970cd15715d1b87f9b864ac97aae4f994ac9 WHIRLPOOL 0369d8bd46ce3ce5bd4da66f23d21a47dcdb74bfa54ff7748fd1ae28180c3ec300eb1e02caeeb8f7090e908fe3984bd14845d9a4e5c099e76bd67ee562759124
diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
new file mode 100644
index 000000000..1a0fdf12d
--- /dev/null
+++ b/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 python-r1
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
+SRC_URI="
+	x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
+	amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
+	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
+
+# Upstream says regarding source code unavailability:
+# Tablet uses a modified version of the BSD License which has been edited to
+# remove references to distribution and use in source forms. This means that
+# we are happy for you to distribute and use Tablet however you please, but we
+# do not (yet) want to make the source code publicly available.
+
+# The licence file itself is in the installer, and ends up on disk after
+# installation at /opt/Tablet/docs/tablet.html
+# The original BSD licence was modified to remove references to distribution
+# and use in source forms, because we cannot make the source code available
+# for Tablet.
+
+LICENSE="Tablet"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}"
+RDEPEND="${DEPEND}
+		virtual/jre"
+
+S="${WORKDIR}"
+
+src_unpack() {
+	local file
+	for file in ${A}; do
+		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
+	done
+}
+
+src_install() {
+	# In theory it seems this binary package could be installed through ant
+	# instead of the install4j package which is not easy to be forced
+	# non-interactive. The below approach via install4j is not ideal but works.
+	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
+
+	# the intallation script somehow does not pickup
+	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
+	# we place the file rather directly into the place where it should reside.
+	# In the file you can read details how the variables were mangled. For
+	# example, the trick with sys.symlinkDir in the response.varfile is to
+	# disable the installation process to symlink from /usr/local/bin/table to
+	# /opt/Tablet/tablet. That was logged in that file with the following line:
+	#
+	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
+	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
+	#
+	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
+	dodir /opt/Tablet/.install4j
+	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
+
+	# make sure we force java to point a to $HOME which is inside our sanbox
+	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
+	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
+	sed \
+		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
+		-i "${WORKDIR}"/${P}.sh || die
+	sh \
+		"${WORKDIR}"/${P}.sh \
+		-q -overwrite \
+		-varfile="${DISTDIR}"/response.varfile \
+		--destination="${ED}"/opt/Tablet \
+		-dir "${ED}"/opt/Tablet || die
+
+	rm -rf "${ED}"/opt/Tablet/jre || die
+
+    # this dies with tablet-bin-1.14.04.10 with
+	#  * python2_7: running python_doscript /mnt/1TB/var/tmp/portage/sci-biology/tablet-bin-1.14.04.10/work/coveragestats.py
+	#  * The file has incompatible shebang:
+	#  *   file: /usr/lib/python-exec/python2.7/coveragestats.py
+	#  *   current shebang: #!/usr/bin/env python
+	#  *   requested impl: python2.7
+	#
+	# python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+
+	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+	doenvd 99Tablet || die
+}
diff --git a/sci-biology/tablet/ChangeLog b/sci-biology/tablet/ChangeLog
index 0080ef21c..0cca8d837 100644
--- a/sci-biology/tablet/ChangeLog
+++ b/sci-biology/tablet/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*tablet-1.14.04.10 (02 Jul 2014)
+
+  02 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +tablet-1.14.04.10.ebuild, -Manifest, tablet-1.13.12.17.ebuild,
+  tablet-9999.ebuild:
+  sci-biology/tablet: cleaned up the ebuilds, they compile and install but the
+  bundled samtools-*.jar is not found
+
 *tablet-1.13.12.17 (28 Mar 2014)
 *tablet-9999 (28 Mar 2014)
 
diff --git a/sci-biology/tablet/Manifest b/sci-biology/tablet/Manifest
deleted file mode 100644
index 05da7e849..000000000
--- a/sci-biology/tablet/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664
-DIST tablet-1.13.12.17.sh 34395356 SHA256 fab481dd2a19e1c25142c41e75c483eeac36cc6793921a2643d9472f0aecbd2b SHA512 6fee28fd68ac4dde777dc7b873735e165d19bec47997a49185f21eecaaf2f38ca019b5af30ff18177ed69ad01eb8a797ef8b892631780ad548bf8fdf3ceb2f0b WHIRLPOOL 274e3849096179707af5ad36001ba060b5c5be068350454553997a120ec5c5f33b347ea26f3f9bd356bb7191b1c1e07199a6f6c0073e5b7edb7bf953d46c0974
diff --git a/sci-biology/tablet/tablet-1.13.12.17.ebuild b/sci-biology/tablet/tablet-1.13.12.17.ebuild
index 112709b08..1940cb9c7 100644
--- a/sci-biology/tablet/tablet-1.13.12.17.ebuild
+++ b/sci-biology/tablet/tablet-1.13.12.17.ebuild
@@ -6,84 +6,45 @@ EAPI=5
 
 PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit java-pkg-2 python-r1
+inherit java-pkg-2 java-ant-2 python-r1
+
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
 HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
-SRC_URI="
-	x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
-	amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
-	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+	KEYWORDS=""
+else
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
+	KEYWORDS=""
+fi
 
 LICENSE="Tablet"
 SLOT="0"
-KEYWORDS=""
 IUSE=""
 
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
-DEPEND="${PYTHON_DEPS}"
+DEPEND="${PYTHON_DEPS}
+	>=virtual/jdk-1.7"
 RDEPEND="${DEPEND}
-		virtual/jre"
+	>=virtual/jre-1.7
+	sci-biology/samtools
+	sci-biology/picard
+	dev-db/sqlite"
 
 S="${WORKDIR}"
 
-src_unpack() {
-	local file
-	for file in ${A}; do
-		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
-	done
-}
-
 src_install() {
-	# In theory it seems this binary package could be installed through ant
-	# instead of the install4j package which is not easy to be forced
-	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
-
-	# the intallation script somehow does not pickup
-	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
-	# we place the file rather directly into the place where it should reside.
-	# In the file you can read details how the variables were mangled. For
-	# example, the trick with sys.symlinkDir in the response.varfile is to
-	# disable the installation process to symlink from /usr/local/bin/table to
-	# /opt/Tablet/tablet. That was logged in that file with the following line:
-	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
-	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
-	#
-	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	dodir /opt/Tablet/.install4j
-	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
-
-	# make sure we force java to point a to $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed \
-		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
-		-i "${WORKDIR}"/${P}.sh || die
-	sh \
-		"${WORKDIR}"/${P}.sh \
-		-q -overwrite \
-		-varfile="${DISTDIR}"/response.varfile \
-		--destination="${ED}"/opt/Tablet \
-		-dir "${ED}"/opt/Tablet || die
-
-	rm -rf "${ED}"/opt/Tablet/jre || die
+	java-pkg_dojar lib/tablet-resources.jar || die
+	java-pkg_dojar lib/tablet.jar || die
+	java-pkg_dojar lib/flamingo.jar || die
+	java-pkg_dojar lib/scri-commons.jar || die
+	java-pkg_dojar lib/samtools*.jar || die
 
-	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+	dobin www/additional/coveragestats.py
 
 	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
 	doenvd 99Tablet || die
diff --git a/sci-biology/tablet/tablet-1.14.04.10.ebuild b/sci-biology/tablet/tablet-1.14.04.10.ebuild
new file mode 100644
index 000000000..1940cb9c7
--- /dev/null
+++ b/sci-biology/tablet/tablet-1.14.04.10.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit java-pkg-2 java-ant-2 python-r1
+
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
+
+DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
+HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
+if [ "$PV" == "9999" ]; then
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/"
+	KEYWORDS=""
+else
+	ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}"
+	KEYWORDS=""
+fi
+
+LICENSE="Tablet"
+SLOT="0"
+IUSE=""
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="${PYTHON_DEPS}
+	>=virtual/jdk-1.7"
+RDEPEND="${DEPEND}
+	>=virtual/jre-1.7
+	sci-biology/samtools
+	sci-biology/picard
+	dev-db/sqlite"
+
+S="${WORKDIR}"
+
+src_install() {
+	java-pkg_dojar lib/tablet-resources.jar || die
+	java-pkg_dojar lib/tablet.jar || die
+	java-pkg_dojar lib/flamingo.jar || die
+	java-pkg_dojar lib/scri-commons.jar || die
+	java-pkg_dojar lib/samtools*.jar || die
+
+	dobin www/additional/coveragestats.py
+
+	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
+	doenvd 99Tablet || die
+}
diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild
index 40472c753..1940cb9c7 100644
--- a/sci-biology/tablet/tablet-9999.ebuild
+++ b/sci-biology/tablet/tablet-9999.ebuild
@@ -6,9 +6,10 @@ EAPI=5
 
 PYTHON_COMPAT=( python{2_6,2_7} )
 
-inherit java-pkg-2 java-ant-2 python-r1 eutils
+inherit java-pkg-2 java-ant-2 python-r1
 
-[ "$PV" == "9999" ] && inherit subversion
+# [ "$PV" == "9999" ] && inherit subversion
+inherit subversion
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments."
 HOMEPAGE="http://bioinf.scri.ac.uk/tablet/"
@@ -20,23 +21,6 @@ else
 	KEYWORDS=""
 fi
 
-#SRC_URI="
-#	x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh )
-#	amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh )
-#	http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py"
-
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
 LICENSE="Tablet"
 SLOT="0"
 IUSE=""
@@ -44,56 +28,23 @@ IUSE=""
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 DEPEND="${PYTHON_DEPS}
-	virtual/jdk"
+	>=virtual/jdk-1.7"
 RDEPEND="${DEPEND}
-		virtual/jre"
+	>=virtual/jre-1.7
+	sci-biology/samtools
+	sci-biology/picard
+	dev-db/sqlite"
 
 S="${WORKDIR}"
 
-src_unpack() {
-	local file
-	for file in ${A}; do
-		cp "${DISTDIR}"/${file} "${WORKDIR}" || die
-	done
-}
-
 src_install() {
-	# In theory it seems this binary package could be installed through ant
-	# instead of the install4j package which is not easy to be forced
-	# non-interactive. The below approach via install4j is not ideal but works.
-	sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed"
-
-	# the intallation script somehow does not pickup
-	# -varfile="${DISTDIR}"/response.varfile from the commandline and therefore
-	# we place the file rather directly into the place where it should reside.
-	# In the file you can read details how the variables were mangled. For
-	# example, the trick with sys.symlinkDir in the response.varfile is to
-	# disable the installation process to symlink from /usr/local/bin/table to
-	# /opt/Tablet/tablet. That was logged in that file with the following line:
-	#
-	# /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log:
-	#	Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String]
-	#
-	# The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile
-	dodir /opt/Tablet/.install4j
-	cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die
-
-	# make sure we force java to point a to $HOME which is inside our sanbox
-	# directory area. We force -Duser.home . It seems also -Dinstall4j.userHome
-	# could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/
-	sed \
-		-e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \
-		-i "${WORKDIR}"/${P}.sh || die
-	sh \
-		"${WORKDIR}"/${P}.sh \
-		-q -overwrite \
-		-varfile="${DISTDIR}"/response.varfile \
-		--destination="${ED}"/opt/Tablet \
-		-dir "${ED}"/opt/Tablet || die
-
-	rm -rf "${ED}"/opt/Tablet/jre || die
+	java-pkg_dojar lib/tablet-resources.jar || die
+	java-pkg_dojar lib/tablet.jar || die
+	java-pkg_dojar lib/flamingo.jar || die
+	java-pkg_dojar lib/scri-commons.jar || die
+	java-pkg_dojar lib/samtools*.jar || die
 
-	python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py
+	dobin www/additional/coveragestats.py
 
 	echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet
 	doenvd 99Tablet || die
diff --git a/sci-chemistry/cpmgfit/ChangeLog b/sci-chemistry/cpmgfit/ChangeLog
new file mode 100644
index 000000000..7eb5da667
--- /dev/null
+++ b/sci-chemistry/cpmgfit/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/cpmgfit
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cpmgfit-1.43 (03 Jul 2014)
+
+  03 Jul 2014; Justin Lecher <jlec@gentoo.org> +cpmgfit-1.43.ebuild,
+  +metadata.xml:
+  New package written by me
+
diff --git a/sci-chemistry/cpmgfit/Manifest b/sci-chemistry/cpmgfit/Manifest
new file mode 100644
index 000000000..ba3c56168
--- /dev/null
+++ b/sci-chemistry/cpmgfit/Manifest
@@ -0,0 +1 @@
+DIST cpmgfit-1.43.tar.gz 89002 SHA256 b96c356c9783d95ee1fe14f2fdc66fa80d2f1839d538f9417747829527befc2a SHA512 ad10ec8cde4eb13dd21f99ebca5552ec844b89785a0485df287e8fad7b63a2f99cd713d281904d2f83cc9485c5fc0a0b3f963d23af8785f0277cb1f7418051a3 WHIRLPOOL c8368f69ed2e3c17da84397f014a590cc83ce69ca33e8f798efc84e22538dab4b0c3917737cb4c497bac78847404afb02cba61cb7d3aa73a836cf5b51e66e624
diff --git a/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild b/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild
new file mode 100644
index 000000000..37c657edd
--- /dev/null
+++ b/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild
@@ -0,0 +1,49 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit fortran-2 multilib
+
+DESCRIPTION="non-linear least squares fitting of CPMG relaxation dispersion curves"
+HOMEPAGE="http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.html"
+SRC_URI="http://biochemistry.hs.columbia.edu/labs/palmer/software/cpmgfit.linux.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-libs/blas-reference
+	sys-devel/gcc:4.1"
+DEPEND="dev-util/patchelf"
+
+S="${WORKDIR}"/linux
+
+QA_PREBUILT="opt/bin/.*"
+
+src_install() {
+	local _exe
+
+	exeinto /opt/bin
+	if use x86; then
+		_exe=./linux_32/${PN}
+	elif use amd64; then
+		_exe=./linux_64/${PN}
+	fi
+
+	patchelf --set-rpath "${EPREFIX}/opt/${PN}:${EPREFIX}/usr/$(get_libdir)/gcc/x86_64-pc-linux-gnu/4.1.2/" ${_exe}
+
+	doexe ${_exe}
+
+	dosym ../../usr/$(get_libdir)/librefblas.so /opt/${PN}/libblas.so.3
+
+	dohtml ${PN}_manual.html
+
+	if use examples; then
+		insinto /usr/share/${PN}/examples/
+		doins sample*
+	fi
+}
diff --git a/sci-chemistry/cpmgfit/metadata.xml b/sci-chemistry/cpmgfit/metadata.xml
new file mode 100644
index 000000000..51fdedab1
--- /dev/null
+++ b/sci-chemistry/cpmgfit/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-chemistry</herd>
+</pkgmetadata>
diff --git a/sci-libs/cblas-reference/ChangeLog b/sci-libs/cblas-reference/ChangeLog
index a48b811ad..b998a4a77 100644
--- a/sci-libs/cblas-reference/ChangeLog
+++ b/sci-libs/cblas-reference/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-libs/cblas-reference/ChangeLog,v 1.33 2010/03/07 19:14:51 jlec Exp $
 
+  02 Jul 2014; François Bissey <francois.bissey@canterbury.ac.nz>
+  cblas-reference-20110218.ebuild:
+  More fix for macos. We need to create the link for both linux and macos.
+
   30 Jun 2014; François Bissey <francois.bissey@canterbury.ac.nz>
   cblas-reference-20110218.ebuild:
   Tweak src_install for OS X support. Added documentation in the ebuild itself.
diff --git a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
index 52fa8c817..cec9dae28 100644
--- a/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
+++ b/sci-libs/cblas-reference/cblas-reference-20110218.ebuild
@@ -46,8 +46,8 @@ static_to_shared() {
 		if [[ $(get_version_component_count) -gt 1 ]]; then
 			ln -s ${soname} ${libdir}/${libname}$(get_libname $(get_major_version)) || die
 		fi
-		ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
 	fi
+	ln -s ${soname} ${libdir}/${libname}$(get_libname) || die
 }
 
 src_prepare() {
diff --git a/sci-physics/espresso++/ChangeLog b/sci-physics/espresso++/ChangeLog
index ff742e1d5..ea6f0050e 100644
--- a/sci-physics/espresso++/ChangeLog
+++ b/sci-physics/espresso++/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Jul 2014; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild:
+  use ninja
+
   21 Jun 2014; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild:
   added missing deps (bug #514084)
 
diff --git a/sci-physics/espresso++/espresso++-9999.ebuild b/sci-physics/espresso++/espresso++-9999.ebuild
index 66425269b..43c4297a0 100644
--- a/sci-physics/espresso++/espresso++-9999.ebuild
+++ b/sci-physics/espresso++/espresso++-9999.ebuild
@@ -5,6 +5,7 @@
 EAPI=5
 
 PYTHON_COMPAT=( python{2_6,2_7} )
+CMAKE_MAKEFILE_GENERATOR="ninja"
 
 inherit cmake-utils multilib python-single-r1
 
diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog
index 9b12ba532..893e1ea58 100644
--- a/sci-physics/root/ChangeLog
+++ b/sci-physics/root/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.96 2012/03/29 18:21:49 bicatali Exp $
 
+  03 Jul 2014; Andrew Savchenko <bircoph@gmail.com> root-9999.ebuild:
+  Tutorial-dirs patch is accepted upstream.
+
+  02 Jul 2014; Andrew Savchenko <bircoph@gmail.com> root-6.00.01-r1.ebuild,
+  root-9999.ebuild, files/root-6.00.01-tutorials-path.patch:
+  Do not compress files required for .credits, .demo, .license
+  commands. Fix tutorials patch.
+
   02 Jul 2014; Andrew Savchenko <bircoph@gmail.com> root-6.00.01-r1.ebuild,
   +files/root-6.00.01-tutorials-path.patch:
   Honor --tutdir from .demos CLI command.
diff --git a/sci-physics/root/files/root-6.00.01-tutorials-path.patch b/sci-physics/root/files/root-6.00.01-tutorials-path.patch
index 2e496a494..cb6861554 100644
--- a/sci-physics/root/files/root-6.00.01-tutorials-path.patch
+++ b/sci-physics/root/files/root-6.00.01-tutorials-path.patch
@@ -10,6 +10,18 @@ index 5950401..e4fbfbf 100644
  #define ROOTSRCDIR    "@srcdir@"
  #define ROOTICONPATH  "@iconpath@"
  #define EXTRAICONPATH "@extraiconpath@"
+diff --git a/configure b/configure
+index 131df92..2c8ea95 100755
+--- a/configure
++++ b/configure
+@@ -7537,6 +7537,7 @@ sed \
+     -e "s|@prefix@|$prefix|"               \
+     -e "s|@srcdir@|$srcdir|"               \
+     -e "s|@ttffontdir@|$fontdir|"          \
++    -e "s|@tutdir@|$tutdir|"               \
+     -e "s|@setresuid@|$setresuid|"         \
+     -e "s|@hasmathmore@|$hasmathmore|"     \
+     -e "s|@haspthread@|$haspthread|"       \
 diff --git a/core/base/src/TApplication.cxx b/core/base/src/TApplication.cxx
 index 1c1809a..7d7ed37 100644
 --- a/core/base/src/TApplication.cxx
diff --git a/sci-physics/root/root-6.00.01-r1.ebuild b/sci-physics/root/root-6.00.01-r1.ebuild
index 74c7af805..d5993c073 100644
--- a/sci-physics/root/root-6.00.01-r1.ebuild
+++ b/sci-physics/root/root-6.00.01-r1.ebuild
@@ -426,9 +426,9 @@ src_install() {
 	cleanup_install
 
 	# do not copress files used by ROOT's CLI (.credit, .demo, .license)
-	docompress -x "${DOC_DIR}/{CREDITS,LICENSE,examples/tutorials}"
+	docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials}
 	# needed for .license command to work
-	dosym "${ED}"/usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE"
+	dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE"
 }
 
 pkg_postinst() {
diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild
index 26f1dd15c..66f8d8795 100644
--- a/sci-physics/root/root-9999.ebuild
+++ b/sci-physics/root/root-9999.ebuild
@@ -422,6 +422,11 @@ src_install() {
 	daemon_install
 	desktop_install
 	cleanup_install
+
+	# do not copress files used by ROOT's CLI (.credit, .demo, .license)
+	docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials}
+	# needed for .license command to work
+	dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE"
 }
 
 pkg_postinst() {