gentoo resync : 16.11.2017

12 files changed, 346 insertions, 0 deletions

diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
new file mode 100644
index 000000000000..446bbef36efb
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+else
+	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="
+	${RDEPEND}
+	>=dev-lang/swig-3.0.8
+	dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
new file mode 100644
index 000000000000..446bbef36efb
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+else
+	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="
+	${RDEPEND}
+	>=dev-lang/swig-3.0.8
+	dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
new file mode 100644
index 000000000000..ea6d4df9fe10
--- /dev/null
+++ b/sci-biology/HTSeq/Manifest
@@ -0,0 +1,4 @@
+DIST HTSeq-0.9.1.tar.gz 596941 SHA256 af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344 WHIRLPOOL da3f1d867f9cfa05e34321f75fb34ef79e943476ee650d4689e320078821703721168bfdd9e46f10f1319cc1006771cd205a80569549d21719d38aea6b0be3a8
+EBUILD HTSeq-0.9.1.ebuild 715 SHA256 21b215f330c0df909001000b539028aadb79b5a25652d236e11d7f69e4674a1e SHA512 eee6989a6910b4022b94982f1c8f598215431c6e0674609d8f30b992a4b9036fde82156fbec0bb4fad1b6bfbd56aa33dcb05cff136cb90a7f5678f18218f3fd0 WHIRLPOOL 1729d114f931a0617e59f95943175b890e80cbc678fbae57e1903e8ff18bfdd47cc526bbde26594efb3558d20ce7789e8050e9f7c33df89632c553fd65ea1b47
+EBUILD HTSeq-9999.ebuild 715 SHA256 21b215f330c0df909001000b539028aadb79b5a25652d236e11d7f69e4674a1e SHA512 eee6989a6910b4022b94982f1c8f598215431c6e0674609d8f30b992a4b9036fde82156fbec0bb4fad1b6bfbd56aa33dcb05cff136cb90a7f5678f18218f3fd0 WHIRLPOOL 1729d114f931a0617e59f95943175b890e80cbc678fbae57e1903e8ff18bfdd47cc526bbde26594efb3558d20ce7789e8050e9f7c33df89632c553fd65ea1b47
+MISC metadata.xml 564 SHA256 102e5db302a66dded538eafc86b66661637591f72fcda8cffea62b12b5aa031e SHA512 16ec7f26466ba1bb2549ee5a0362a7aebb1b8b48de51bacd37bb67a20ca1ca41b0009ca5eae304c5f29e991a79a2fda7bbc93c7dd7e2c8491a0df69a97d9821f WHIRLPOOL 4824b6a5f524d4783b04a3b9cf8c83752309a1101ce4905cd49db5c474718bd88e04afe065d64d7e9276b795fe1a98c18192719acf85f99b46873134549d4782
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
new file mode 100644
index 000000000000..e9ba18c35b3c
--- /dev/null
+++ b/sci-biology/HTSeq/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>proxy-maint@gentoo.org</email>
+		<name>Proxy Maintainers</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">HTSeq</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest
new file mode 100644
index 000000000000..aa4c23836486
--- /dev/null
+++ b/sci-biology/STAR/Manifest
@@ -0,0 +1,4 @@
+AUX STAR-2.5.3a-fix-build-system.patch 5318 SHA256 2af4122153f1691e913d64578830c9e802ff61193a64525d724598d3fcdbcae9 SHA512 412bdf74c50869f470f3d7452d3799e92a45da198e50ecad63688e4c24444a25f044d464e462e19ba41c5abf590865e43542cd1b60a1f3948bf357be468e8441 WHIRLPOOL 14297e673a2ebfb0a68a857ace654d14edbf363de90e3ec3f21065273ecdec9648dfc90c7c356e4c6fe6b603da688b0c48177ee84ad11afbd55d21546e4d9f63
+DIST STAR-2.5.3a.tar.gz 9857460 SHA256 2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04 SHA512 8bd86ad384f2c0331fd701873b02641301f4205a5ff0fceeb800d425da42c53b6c61a74500d37fee7fc13a5bff10e1fb44b9142811883b8f5cd012f51f1f9fdf WHIRLPOOL 64bb7dc68e24ecd7d198d281e98042fd1463fc96af8ab8be9cab8e1588c2d08ab7cd1435187f2e0ebe870da11ab607c8f8a981d76360c55dd76e1fb4bb304006
+EBUILD STAR-2.5.3a.ebuild 881 SHA256 803807893287bccc74cc3d89a5ffa73f27d17c71b4598086af834ac5bb91a3df SHA512 9b8a80c19b0da8e697c913a8401c08a71a07511477c71b1dd20748e5487e8bb5ab870c37058d49abc27a5ac56722e98b2d784431c19f7173275b82f41f9a2663 WHIRLPOOL 6f9e95aacfe4d56047d630a05d64f7590e6d229c3051893792c0a4319e596bd1d5d93148bd2ee0153e9f9bcc616feaf356ea22d67d5fdca98556629e4408195f
+MISC metadata.xml 575 SHA256 c3631d72689ac1c5c560c1f8893cd29f5b9242dda5a14b99319bd966f630e1a8 SHA512 72c19651f868881808c0cad72c1db2a4a5d7f1b77d387dc0539e0e0624f404ea15380f64ccf48ddd0acc33c5e1369f3cdd53dc329e603a943b15205e647f53cf WHIRLPOOL e484372fcd947a84f05dbaf2f073380380e4abbba2b8f86183eb80ca4faacdadaece2f19a3094203aa488007f2e75d10444a1f35d9bc13ac78d735a8e89ae8f6
diff --git a/sci-biology/STAR/STAR-2.5.3a.ebuild b/sci-biology/STAR/STAR-2.5.3a.ebuild
new file mode 100644
index 000000000000..73743cbb4e59
--- /dev/null
+++ b/sci-biology/STAR/STAR-2.5.3a.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays"
+HOMEPAGE="https://github.com/alexdobin/STAR"
+SRC_URI="https://github.com/alexdobin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="sci-libs/htslib:="
+DEPEND="${RDEPEND}
+	virtual/pkgconfig"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.5.3a-fix-build-system.patch )
+DOCS=( README.md CHANGES.md RELEASEnotes.md doc/STARmanual.pdf )
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
+}
+
+src_configure() {
+	tc-export CC CXX PKG_CONFIG
+}
+
+src_compile() {
+	emake -C source STAR
+}
+
+src_install() {
+	dobin source/STAR
+	einstalldocs
+}
diff --git a/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
new file mode 100644
index 000000000000..8e504fa429e0
--- /dev/null
+++ b/sci-biology/STAR/files/STAR-2.5.3a-fix-build-system.patch
@@ -0,0 +1,123 @@
+* unbundle htslib
+* honour all user flags
+* use pkg-config for linking
+
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -8,24 +8,12 @@
+ LDFLAGSextra ?=
+ CXXFLAGSextra ?=
+ 
+-# user may define the compiler
+-CXX ?= g++
+-
+ # pre-defined flags
+-LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz -lrt
+-LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
+-LDFLAGS_Mac :=-pthread -lz htslib/libhts.a
+-LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
+-LDFLAGS_gdb := $(LDFLAGS_shared)
+-
+ COMPTIMEPLACE := -D'COMPILATION_TIME_PLACE="$(shell echo `date` $(HOSTNAME):`pwd`)"'
+ 
+-CXXFLAGS_common := -pipe -std=c++11 -Wall -Wextra -fopenmp $(COMPTIMEPLACE)
+-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+-CXXFLAGS_gdb :=  -O0 -g $(CXXFLAGS_common)
+-
+-CFLAGS := -O3 -pipe -Wall -Wextra $(CFLAGS)
+-
++CFLAGS_common = -Wall -Wextra -pthread `$(PKG_CONFIG) --cflags htslib` `$(PKG_CONFIG) --cflags zlib`
++CXXFLAGS_common = $(CFLAGS_common) -std=c++11 -fopenmp $(COMPTIMEPLACE)
++LIBS_common = -pthread `$(PKG_CONFIG) --libs htslib` `$(PKG_CONFIG) --libs zlib` -lrt
+ 
+ ##########################################################################################################
+ 
+@@ -54,10 +42,10 @@
+ 
+ 
+ %.o : %.cpp
+-	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $<
++	$(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $(CXXFLAGS_common) $<
+ 
+ %.o : %.c
+-	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $<
++	$(CXX) -c $(CPPFLAGS) $(CFLAGS) $(CFLAGS_common) $<
+ 
+ all: STAR
+ 
+@@ -84,7 +72,7 @@
+ ifneq ($(MAKECMDGOALS),CLEAN)
+ ifneq ($(MAKECMDGOALS),STARforMac)
+ ifneq ($(MAKECMDGOALS),STARforMacGDB)
+-Depend.list: $(SOURCES) parametersDefault.xxd htslib
++Depend.list: $(SOURCES) parametersDefault.xxd
+ 	echo $(SOURCES)
+ 	/bin/rm -f ./Depend.list
+ 	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
+@@ -95,57 +83,34 @@
+ endif
+ endif
+ 
+-htslib : htslib/libhts.a
+-
+-htslib/libhts.a :
+-	$(MAKE) -C htslib lib-static
+-
+ parametersDefault.xxd: parametersDefault
+ 	xxd -i parametersDefault > parametersDefault.xxd
+ 
+-STAR : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STAR : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STAR : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-POSIXSHARED : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -DPOSIX_SHARED_MEM $(CXXFLAGS)
+-POSIXSHARED : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ POSIXSHARED : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-STARstatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) $(CXXFLAGS)
+-STARstatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARstatic : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-STARlong : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlong : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_shared) $(LDFLAGS)
+ STARlong : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-STARlongStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-STARlongStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_static) $(LDFLAGS)
+ STARlongStatic : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-gdb : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) $(CXXFLAGS)
+-gdb : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
+ gdb : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-gdb-long : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_gdb) -D'COMPILE_FOR_LONG_READS' $(CXXFLAGS)
+-gdb-long : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_gdb) $(LDFLAGS)
+ gdb-long : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-STARforMacStatic : CXXFLAGS := $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
+-STARforMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
+ STARforMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STAR $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STAR $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+-STARlongForMacStatic : CXXFLAGS := -D'COMPILE_FOR_LONG_READS' $(CXXFLAGSextra) $(CXXFLAGS_main) -D'COMPILE_FOR_MAC' $(CXXFLAGS)
+-STARlongForMacStatic : LDFLAGS := $(LDFLAGSextra) $(LDFLAGS_Mac_static) $(LDFLAGS)
+ STARlongForMacStatic : Depend.list parametersDefault.xxd $(OBJECTS)
+-	$(CXX) -o STARlong $(CXXFLAGS) $(OBJECTS) $(LDFLAGS)
++	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) $(LDFLAGS) -o STARlong $(OBJECTS) $(LIBS) $(LIBS_common)
+ 
+ 
diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml
new file mode 100644
index 000000000000..22727da1cad8
--- /dev/null
+++ b/sci-biology/STAR/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>proxy-maint@gentoo.org</email>
+		<name>Proxy Maintainers</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">alexdobin/STAR</remote-id>
+	</upstream>
+</pkgmetadata>
diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest
new file mode 100644
index 000000000000..5ed38ff9ece7
--- /dev/null
+++ b/sci-biology/kallisto/Manifest
@@ -0,0 +1,4 @@
+DIST kallisto-0.43.1.tar.gz 1067076 SHA256 2164938c2c61c04e338c4c132cf749f56d39e6f0b4c517121bca1fbc218e430e SHA512 c7725a2d649cf96fcd24a20d542b409777cfd9fe97c09f0f459a5ec2981e0a4f5f0ea03d76d3ec3edf0e498c799fc7d074d442d5e35ddb4043d1f7634619dda8 WHIRLPOOL a0f8c2cab5afa3df7cf7f540319d32a99d698ac50e4574c941972fff789e9d8e258124153d16a777180595b201d91e240e5ffd17994cc2571e71f6fcb47fdeee
+EBUILD kallisto-0.43.1.ebuild 573 SHA256 06b09d70b72ee00819c1185d503d3b3e0a5c8f60afa22594554c618153ecf709 SHA512 bb8667422d4015ca7a3aad912385b5322b83c1122a99f79893f527c886cbc05049f2e37f7cc85d2c789994ebd477b9ff60019e4c91b7b95f65a51dd7343c4aff WHIRLPOOL 26e198e8a369eeff6da2da14366bac57c26ea248559afae434a63be3003178a611ce823d5fa695974c6dd6878fd0d8fb8564035243add21e9c7295ec6fd191f7
+EBUILD kallisto-9999.ebuild 573 SHA256 06b09d70b72ee00819c1185d503d3b3e0a5c8f60afa22594554c618153ecf709 SHA512 bb8667422d4015ca7a3aad912385b5322b83c1122a99f79893f527c886cbc05049f2e37f7cc85d2c789994ebd477b9ff60019e4c91b7b95f65a51dd7343c4aff WHIRLPOOL 26e198e8a369eeff6da2da14366bac57c26ea248559afae434a63be3003178a611ce823d5fa695974c6dd6878fd0d8fb8564035243add21e9c7295ec6fd191f7
+MISC metadata.xml 574 SHA256 ea8f0878ecc78b897b0dda2d342df7062ecff912790cb0c407929526e6313b3d SHA512 322d73b8e377ce74593d5c79a4e2f2041ab9313d8d5f59866e148ccda89892fd4fe56a7f0c8d12458f97de52efc4e933044788ad24fd99ffd4fb81dbbc2b2bcc WHIRLPOOL 93e91e065cfc28afe65738fb66928bbd938fcf168543cd75f0a724074e0c5e42afcbd51ab79f824344f7055caedc5bb4c43b0a29a6740056455f029752dd6af1
diff --git a/sci-biology/kallisto/kallisto-0.43.1.ebuild b/sci-biology/kallisto/kallisto-0.43.1.ebuild
new file mode 100644
index 000000000000..0020e891a032
--- /dev/null
+++ b/sci-biology/kallisto/kallisto-0.43.1.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+DESCRIPTION="Near-optimal RNA-Seq quantification"
+HOMEPAGE="http://pachterlab.github.io/kallisto/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
+else
+	SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	sci-libs/hdf5:=
+	sys-libs/zlib:="
+DEPEND="${RDEPEND}"
diff --git a/sci-biology/kallisto/kallisto-9999.ebuild b/sci-biology/kallisto/kallisto-9999.ebuild
new file mode 100644
index 000000000000..0020e891a032
--- /dev/null
+++ b/sci-biology/kallisto/kallisto-9999.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils
+
+DESCRIPTION="Near-optimal RNA-Seq quantification"
+HOMEPAGE="http://pachterlab.github.io/kallisto/"
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git"
+else
+	SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+
+RDEPEND="
+	sci-libs/hdf5:=
+	sys-libs/zlib:="
+DEPEND="${RDEPEND}"
diff --git a/sci-biology/kallisto/metadata.xml b/sci-biology/kallisto/metadata.xml
new file mode 100644
index 000000000000..aba0d0ebf330
--- /dev/null
+++ b/sci-biology/kallisto/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mschu.dev@gmail.com</email>
+		<name>Michael Schubert</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>proxy-maint@gentoo.org</email>
+		<name>Proxy Maintainers</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="github">pachterlab/kallisto</remote-id>
+	</upstream>
+</pkgmetadata>