diff options
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/edena/ChangeLog | 9 | ||||
-rw-r--r-- | sci-biology/edena/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/edena/edena-3.131028.ebuild | 35 | ||||
-rw-r--r-- | sci-biology/edena/metadata.xml | 9 | ||||
-rw-r--r-- | sci-biology/epga/ChangeLog | 10 | ||||
-rw-r--r-- | sci-biology/epga/epga-9999.ebuild | 36 | ||||
-rw-r--r-- | sci-biology/epga/metadata.xml | 9 | ||||
-rw-r--r-- | sci-biology/mosaik/ChangeLog | 11 | ||||
-rw-r--r-- | sci-biology/mosaik/Manifest | 2 | ||||
-rw-r--r-- | sci-biology/mosaik/mosaik-2.2.3.ebuild (renamed from sci-biology/mosaik/mosaik-2.1.33.ebuild) | 10 | ||||
-rw-r--r-- | sci-biology/quast/ChangeLog | 11 | ||||
-rw-r--r-- | sci-biology/quast/Manifest | 2 | ||||
-rw-r--r-- | sci-biology/quast/quast-2.3.ebuild (renamed from sci-biology/quast/quast-2.2.ebuild) | 4 | ||||
-rw-r--r-- | sci-biology/sabre/ChangeLog | 9 | ||||
-rw-r--r-- | sci-biology/sabre/metadata.xml | 9 | ||||
-rw-r--r-- | sci-biology/sabre/sabre-9999.ebuild | 39 | ||||
-rw-r--r-- | sci-biology/sickle/ChangeLog | 6 | ||||
-rw-r--r-- | sci-biology/sickle/sickle-9999.ebuild | 4 |
18 files changed, 203 insertions, 13 deletions
diff --git a/sci-biology/edena/ChangeLog b/sci-biology/edena/ChangeLog new file mode 100644 index 000000000..a3f0909cc --- /dev/null +++ b/sci-biology/edena/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/edena +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*edena-3.131028 (15 Jan 2015) + + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +edena-3.131028.ebuild, +metadata.xml: + sci-biology/edena: new package diff --git a/sci-biology/edena/Manifest b/sci-biology/edena/Manifest new file mode 100644 index 000000000..cbe128f7c --- /dev/null +++ b/sci-biology/edena/Manifest @@ -0,0 +1 @@ +DIST EdenaV3.131028.tar.gz 497784 SHA256 4037fce486c9725107b1690fbc67731713eef54e3fa53081865904c783533230 SHA512 853a5eb0afe507ba7b967075795593df147ad87c7d45be30eac6b24054ec365d7db39c9cd20bb414478a629c98c82bf0621c007c22a447949ee3f749907cae58 WHIRLPOOL 409bdb1e2f4f344198bff0af50e78afd75fffa10b4c252316a61f0c55e49bb4bdb514ed2414343056d31783e27d8ae800f7e33495cbc8f6c61ec57c5c5d974d8 diff --git a/sci-biology/edena/edena-3.131028.ebuild b/sci-biology/edena/edena-3.131028.ebuild new file mode 100644 index 000000000..0c4fe10b3 --- /dev/null +++ b/sci-biology/edena/edena-3.131028.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="De novo short read assembler" +HOMEPAGE="http://www.genomic.ch/edena.php" +SRC_URI="http://www.genomic.ch/edena/EdenaV"${PV}".tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/EdenaV"${PV}" + +src_prepare(){ + sed -e "s@^CCC.*@CCC = $(tc-getCXX)@" -e "s@^CFLAGS.*@CFLAGS = ${CFLAGS} -pthread@" -i src/Makefile || die +} + +src_compile(){ + cd src + emake +} + +src_install(){ + dobin src/edena + dodoc referenceManual.pdf +} diff --git a/sci-biology/edena/metadata.xml b/sci-biology/edena/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/edena/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/epga/ChangeLog b/sci-biology/epga/ChangeLog new file mode 100644 index 000000000..5d20948a1 --- /dev/null +++ b/sci-biology/epga/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/epga +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*epga-9999 (15 Jan 2015) + + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +epga-9999.ebuild, + +metadata.xml: + new package; no LICENSE file + diff --git a/sci-biology/epga/epga-9999.ebuild b/sci-biology/epga/epga-9999.ebuild new file mode 100644 index 000000000..63a50e614 --- /dev/null +++ b/sci-biology/epga/epga-9999.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit git-2 + +inherit toolchain-funcs + +DESCRIPTION="De novo assembler using distribution of reads and insert size" +HOMEPAGE="https://github.com/bioinfomaticsCSU/EPGA" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/bioinfomaticsCSU/EPGA.git" + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="" +fi + +LICENSE="" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_compile(){ + $(tc-getCXX) ${CFLAGS} main.cpp -o epga -lpthread +} + +src_install(){ + dobin epga + dodoc README.md +} diff --git a/sci-biology/epga/metadata.xml b/sci-biology/epga/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/epga/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/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog index 87f4c4bbb..51160219f 100644 --- a/sci-biology/mosaik/ChangeLog +++ b/sci-biology/mosaik/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-biology/mosaik -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*mosaik-2.2.3 (15 Jan 2015) + + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +mosaik-2.2.3.ebuild, -mosaik-2.1.33.ebuild: + version bump, masking a crappy package until at least the Makefile's + propagate an error code back to upstream caller, https://code.google.com/p + /mosaik-aligner/issues/detail?id=135 + 07 Jan 2014; Justin Lecher <jlec@gentoo.org> mosaik-2.1.33.ebuild, mosaik-9999.ebuild, metadata.xml: Readd ebuild @@ -33,4 +41,3 @@ Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266, Fasta.cpp:268, but the package itself installs and executes at least mosaik-1.1.0021.ebuild - diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest index e7f7074d3..c378492e7 100644 --- a/sci-biology/mosaik/Manifest +++ b/sci-biology/mosaik/Manifest @@ -1,2 +1,2 @@ -DIST MOSAIK-2.1.33-source.tar 3911680 SHA256 210764cddbd8a3866976f065b912eb30fcd94d681901be93b42724708b86e2aa SHA512 9eeda8698bc929f95ff16b4e611174f631a5affb8712d582eda7e02a45f27ea8a50ffc56c6595f837af342f266a5bfe44ca1eb006d301caef671e01ed794ba20 WHIRLPOOL 89b65f5ff47dbce615f37e4ae2d3d207cde1482f3e9d4cb280cca55c399784eeb272d3af490327b3c1ac348f7d6bdc1305df67a726acea7b9e2502df02848136 +DIST MOSAIK-2.2.3-source.tar 3819520 SHA256 b2b291603949f179d5f0686045aaf48ab34ea47001bc1e0c573adf517e8b3b28 SHA512 d60a0559dced935f736ca105569593165474134985b1d32405c8f4537dc5da7a05d89ce3a10e4536e2b4f62f622055c327abddb3783c9331465061c5f866129f WHIRLPOOL a66221037900f64c15dc6f444ff19be5bb3496625d426515b5fb33c8b181d35ab69d6f383ce92912d4354c8b9acc1d23d68c544e38db056c0ef1314875dfadcf DIST Mosaik-1.0-Documentation.pdf 10589 SHA256 470e2a534668a2a8744df7b00b9b8af5a6966d2df70f0ab1a4b271bdddadae9c SHA512 b2febce1e85eea89e5ff5d9f1aae351c59574314f361b66503ec473da7641adc083e52ee739c04abfe5b074fd57271f2ca20bea215982ee3ecfce073bbfd7b38 WHIRLPOOL 764a984408590417345daf624cda3dfb5df4255f18efc8f8cfbfc61885ed14be9863eef886dacfe90562469cd6af50220c0a776653a429b888eedac86270dc06 diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.2.3.ebuild index bc26a056b..6bd994ba8 100644 --- a/sci-biology/mosaik/mosaik-2.1.33.ebuild +++ b/sci-biology/mosaik/mosaik-2.2.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -13,10 +13,16 @@ SRC_URI=" LICENSE="GPL-2 || ( MIT )" SLOT="0" IUSE="" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" + +# https://code.google.com/p/mosaik-aligner/issues/detail?id=135 S="${WORKDIR}"/MOSAIK-${PV}-source +src_prepare(){ + sed -e "s@export LDFLAGS = -Wl@#export LDFLAGS = -Wl@" -i Makefile +} + src_install() { dobin "${WORKDIR}"/bin/* diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog index ccf3a0e68..e29320d4a 100644 --- a/sci-biology/quast/ChangeLog +++ b/sci-biology/quast/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-biology/quast -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> quast-2.3.ebuild: + added a note about additional bundled package licenses + +*quast-2.3 (15 Jan 2015) + + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +quast-2.3.ebuild, + -quast-2.2.ebuild: + version bump + 13 Nov 2014; Justin Lecher <jlec@gentoo.org> quast-2.2.ebuild, metadata.xml: Bump to new python eclasses diff --git a/sci-biology/quast/Manifest b/sci-biology/quast/Manifest index 9ddb43cb2..f89b3dc4e 100644 --- a/sci-biology/quast/Manifest +++ b/sci-biology/quast/Manifest @@ -1 +1 @@ -DIST quast-2.2.tar.gz 19814517 SHA256 c66cb9b063d82962bceb11762794fb2e5a57846c8a3aa93ca5f83951cf669d85 SHA512 e979b63f53c3909f804d733ae2cbfd0963fca3dc9194b2a04c8d7be53d253d087853520198a8261a5eba186369486f6e2f4d469814a2d8632072bd73d0e5b8bb WHIRLPOOL 76078a45e24a961acd6fafadf26d08daa79d0b65f224d1bfb87fd404532161c4b667a2873fcf1023e7156bc1c5273de48adb7bfcc5eee68bd3218d03db3aaaa2 +DIST quast-2.3.tar.gz 17631110 SHA256 efad099097e4d148b02e98892c5e93a2407c4debecb12860629142192be62b0d SHA512 eddece31d2ba51548f3e395f77a382d019ef282fb97c5ecfa18cf124c6a619bee760f238b046517a67b7ccbc5354ff36666d0f01cc75b098e9baee2dd3652f40 WHIRLPOOL 82520b21ba791918f05d75e7cc098e54628af1f73bb3735efcd86c2eb669029a28ef40756b7c4aa23e0cd6a547032428cfcb718bbcd9aa970e43e1aa89d4667c diff --git a/sci-biology/quast/quast-2.2.ebuild b/sci-biology/quast/quast-2.3.ebuild index 383914717..701f274f4 100644 --- a/sci-biology/quast/quast-2.2.ebuild +++ b/sci-biology/quast/quast-2.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -12,7 +12,7 @@ DESCRIPTION="Compare quality of multiple genome assemblies to each other" HOMEPAGE="http://bioinf.spbau.ru/QUAST" SRC_URI="http://sourceforge.net/projects/quast/files/${P}.tar.gz" -LICENSE="GPL-2" +LICENSE="GPL-2" # and some other for the bundled copies, see http://quast.bioinf.spbau.ru/LICENSE SLOT="0" KEYWORDS="" IUSE="" diff --git a/sci-biology/sabre/ChangeLog b/sci-biology/sabre/ChangeLog new file mode 100644 index 000000000..f7f747fa1 --- /dev/null +++ b/sci-biology/sabre/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/sabre +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*sabre-9999 (15 Jan 2015) + + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +sabre-9999.ebuild: + sci-biology/sabre: new package diff --git a/sci-biology/sabre/metadata.xml b/sci-biology/sabre/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/sabre/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/sabre/sabre-9999.ebuild b/sci-biology/sabre/sabre-9999.ebuild new file mode 100644 index 000000000..2aee70121 --- /dev/null +++ b/sci-biology/sabre/sabre-9999.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit git-2 + +inherit toolchain-funcs + +DESCRIPTION="Barcode demultiplexing and trimming tool for Illumina FastQ files" +HOMEPAGE="https://github.com/najoshi/sabre" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/najoshi/sabre.git" + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="" +fi + + +LICENSE="MIT" # almost verbatim +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sys-libs/zlib" +RDEPEND="${DEPEND}" + +S="${S}"/src + +src_prepare(){ + sed -e "s#OPT = -O3#OPT = ${CFLAGS}#" \ + -e "s#CC = gcc#CC = $(tc-getCC)#" -i Makefile || die +} + +src_install(){ + dobin sabre +} diff --git a/sci-biology/sickle/ChangeLog b/sci-biology/sickle/ChangeLog index bdbc7e730..443ff95fa 100644 --- a/sci-biology/sickle/ChangeLog +++ b/sci-biology/sickle/ChangeLog @@ -1,11 +1,13 @@ # ChangeLog for sci-biology/sickle -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> sickle-9999.ebuild: + correct package description + *sickle-9999 (24 Mar 2014) 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sickle-9999.ebuild, +metadata.xml: simple ebuild, bundled Makefile forces compile flags, program version, but works - diff --git a/sci-biology/sickle/sickle-9999.ebuild b/sci-biology/sickle/sickle-9999.ebuild index d256d7313..022474e57 100644 --- a/sci-biology/sickle/sickle-9999.ebuild +++ b/sci-biology/sickle/sickle-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,7 +6,7 @@ EAPI=5 inherit eutils git-r3 -DESCRIPTION="Windowed adaptive adaptor trimming tool for FASTQ data from Illumina/Solexa" +DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data from Illumina/Solexa" HOMEPAGE="https://github.com/najoshi/sickle" EGIT_REPO_URI="https://github.com/najoshi/sickle" |