[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2024-03-26 Thread David Seifert 
commit: ca013469c4692182f51264a980af7b5688d34d15
Author: David Seifert  gentoo  org>
AuthorDate: Tue Mar 26 11:06:20 2024 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Mar 26 11:06:20 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ca013469

sci-libs/htslib: add 1.19.1

Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest |  1 +
 sci-libs/htslib/htslib-1.19.1.ebuild | 52 
 2 files changed, 53 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 38e157095820..23cea03c57b1 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1 +1,2 @@
 DIST htslib-1.17.tar.bz2 4619884 BLAKE2B 
c45591b3f1da4f6ddfdf5e1a20864583d57de2a460d42049715335fce7dafe1f5cd14403e6033fee4f9d0bfc75f8777b5835d2d01bf2cadff0155d9fc92b97d9
 SHA512 
624ab449d57713dab2d34399926c065f8cff8a45e6fbe68e0bb518c601421f587b613caeb095f8639b1d67cdb4a65d658c85f942173bcaa48da026fe15def5d3
+DIST htslib-1.19.1.tar.bz2 4775086 BLAKE2B 
3af6770ade9505a3c71f6d522c0971eb77ea2549670043a539a2a4681e583554dc154b9b9fb33f1faa94be336a09945a28c57aa4bcfe0f39b03dd7585c49269a
 SHA512 
a40de47ecae68756c158c1c7b578fa2a5c13bf6f98626e863af31a20d7880ffd415d966280c00bfe726f496d913eb0fcf014dd4beb8c1dbe36ed9735a48bd01e

diff --git a/sci-libs/htslib/htslib-1.19.1.ebuild 
b/sci-libs/htslib/htslib-1.19.1.ebuild
new file mode 100644
index ..2a38fa8634c8
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.19.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+   sys-libs/zlib
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+   -i htslib.pc.in || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   # doesn't use libtool, can't disable static libraries
+   find "${ED}" -name '*.a' -delete || die
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2023-04-06 Thread David Seifert 
commit: 29808b44599626d44da9202e86f99c5c6fc5edfd
Author: David Seifert  gentoo  org>
AuthorDate: Thu Apr  6 19:29:09 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Apr  6 19:29:09 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=29808b44

sci-libs/htslib: drop 1.16

Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest   |  1 -
 sci-libs/htslib/htslib-1.16.ebuild | 52 --
 2 files changed, 53 deletions(-)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 6f53bfe1e726..38e157095820 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,2 +1 @@
-DIST htslib-1.16.tar.bz2 4466776 BLAKE2B 
4957dd7a25b3d0b939d4e924db018916a5f8a13a81e55ebd1ce1acc548986e581d017ead9a08245a4af1ebdcd15536f082425ebe05f16eb4faad27d332e48482
 SHA512 
9fa0b1f9bba50f889d4542825c9543fb3b34c13b4cc0e18940a66fafd130749574bfa2c2663d8b39f0b4ed2b298bf130367cda1b17b2929093d64b386730cbc5
 DIST htslib-1.17.tar.bz2 4619884 BLAKE2B 
c45591b3f1da4f6ddfdf5e1a20864583d57de2a460d42049715335fce7dafe1f5cd14403e6033fee4f9d0bfc75f8777b5835d2d01bf2cadff0155d9fc92b97d9
 SHA512 
624ab449d57713dab2d34399926c065f8cff8a45e6fbe68e0bb518c601421f587b613caeb095f8639b1d67cdb4a65d658c85f942173bcaa48da026fe15def5d3

diff --git a/sci-libs/htslib/htslib-1.16.ebuild 
b/sci-libs/htslib/htslib-1.16.ebuild
deleted file mode 100644
index c4bd910685de..
--- a/sci-libs/htslib/htslib-1.16.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0/3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma"
-
-RDEPEND="
-   sys-libs/zlib
-   bzip2? ( app-arch/bzip2 )
-   curl? ( net-misc/curl )
-   lzma? ( app-arch/xz-utils )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-   default
-
-   # upstream injects LDFLAGS into the .pc file,
-   # which is a big nono for QA
-   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
-   -i htslib.pc.in || die
-}
-
-src_configure() {
-   econf \
-   --disable-gcs \
-   --disable-plugins \
-   --disable-s3 \
-   $(use_enable bzip2 bz2) \
-   $(use_enable curl libcurl) \
-   $(use_enable lzma)
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   # doesn't use libtool, can't disable static libraries
-   find "${ED}" -name '*.a' -delete || die
-}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2023-03-30 Thread David Seifert 
commit: 30fc69a81e71a3c6d6a72af3b9b24e5b742c2832
Author: David Seifert  gentoo  org>
AuthorDate: Thu Mar 30 11:10:58 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Mar 30 11:10:58 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=30fc69a8

sci-libs/htslib: add 1.17

Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest   |  1 +
 sci-libs/htslib/htslib-1.17.ebuild | 52 ++
 2 files changed, 53 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 5634c4532cc9..6f53bfe1e726 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1 +1,2 @@
 DIST htslib-1.16.tar.bz2 4466776 BLAKE2B 
4957dd7a25b3d0b939d4e924db018916a5f8a13a81e55ebd1ce1acc548986e581d017ead9a08245a4af1ebdcd15536f082425ebe05f16eb4faad27d332e48482
 SHA512 
9fa0b1f9bba50f889d4542825c9543fb3b34c13b4cc0e18940a66fafd130749574bfa2c2663d8b39f0b4ed2b298bf130367cda1b17b2929093d64b386730cbc5
+DIST htslib-1.17.tar.bz2 4619884 BLAKE2B 
c45591b3f1da4f6ddfdf5e1a20864583d57de2a460d42049715335fce7dafe1f5cd14403e6033fee4f9d0bfc75f8777b5835d2d01bf2cadff0155d9fc92b97d9
 SHA512 
624ab449d57713dab2d34399926c065f8cff8a45e6fbe68e0bb518c601421f587b613caeb095f8639b1d67cdb4a65d658c85f942173bcaa48da026fe15def5d3

diff --git a/sci-libs/htslib/htslib-1.17.ebuild 
b/sci-libs/htslib/htslib-1.17.ebuild
new file mode 100644
index ..6f690363326b
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.17.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+   sys-libs/zlib
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+   -i htslib.pc.in || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   # doesn't use libtool, can't disable static libraries
+   find "${ED}" -name '*.a' -delete || die
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2023-02-19 Thread David Seifert 
commit: d16051f7223082375cc255d34da4a12737092748
Author: David Seifert  gentoo  org>
AuthorDate: Sun Feb 19 15:44:21 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Feb 19 15:44:21 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d16051f7

sci-libs/htslib: drop 1.15.1

Closes: https://github.com/gentoo/gentoo/pull/29661
Closes: https://bugs.gentoo.org/873310
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest |  1 -
 sci-libs/htslib/htslib-1.15.1.ebuild | 52 
 2 files changed, 53 deletions(-)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index b8eaa4248e7d..5634c4532cc9 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,2 +1 @@
-DIST htslib-1.15.1.tar.bz2 4141140 BLAKE2B 
312f67c8916586199b32b7703b43a9fd365b8af22802bf4d63fc40960c62b956915e7c60bbd777a8b179066608cd3a281929a10b60eef21d6eedb4caf8c147c1
 SHA512 
69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620
 DIST htslib-1.16.tar.bz2 4466776 BLAKE2B 
4957dd7a25b3d0b939d4e924db018916a5f8a13a81e55ebd1ce1acc548986e581d017ead9a08245a4af1ebdcd15536f082425ebe05f16eb4faad27d332e48482
 SHA512 
9fa0b1f9bba50f889d4542825c9543fb3b34c13b4cc0e18940a66fafd130749574bfa2c2663d8b39f0b4ed2b298bf130367cda1b17b2929093d64b386730cbc5

diff --git a/sci-libs/htslib/htslib-1.15.1.ebuild 
b/sci-libs/htslib/htslib-1.15.1.ebuild
deleted file mode 100644
index c4bd910685de..
--- a/sci-libs/htslib/htslib-1.15.1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
-
-LICENSE="MIT"
-SLOT="0/3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma"
-
-RDEPEND="
-   sys-libs/zlib
-   bzip2? ( app-arch/bzip2 )
-   curl? ( net-misc/curl )
-   lzma? ( app-arch/xz-utils )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-   default
-
-   # upstream injects LDFLAGS into the .pc file,
-   # which is a big nono for QA
-   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
-   -i htslib.pc.in || die
-}
-
-src_configure() {
-   econf \
-   --disable-gcs \
-   --disable-plugins \
-   --disable-s3 \
-   $(use_enable bzip2 bz2) \
-   $(use_enable curl libcurl) \
-   $(use_enable lzma)
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   # doesn't use libtool, can't disable static libraries
-   find "${ED}" -name '*.a' -delete || die
-}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2022-12-26 Thread David Seifert 
commit: 19c25897b24fd3699dc126bfb89af9d409ff0a71
Author: David Seifert  gentoo  org>
AuthorDate: Tue Dec 27 00:06:43 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Dec 27 00:06:43 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=19c25897

sci-libs/htslib: add 1.16

Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest   |  1 +
 sci-libs/htslib/htslib-1.16.ebuild | 52 ++
 2 files changed, 53 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index f5b37a27ae5a..b8eaa4248e7d 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1 +1,2 @@
 DIST htslib-1.15.1.tar.bz2 4141140 BLAKE2B 
312f67c8916586199b32b7703b43a9fd365b8af22802bf4d63fc40960c62b956915e7c60bbd777a8b179066608cd3a281929a10b60eef21d6eedb4caf8c147c1
 SHA512 
69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620
+DIST htslib-1.16.tar.bz2 4466776 BLAKE2B 
4957dd7a25b3d0b939d4e924db018916a5f8a13a81e55ebd1ce1acc548986e581d017ead9a08245a4af1ebdcd15536f082425ebe05f16eb4faad27d332e48482
 SHA512 
9fa0b1f9bba50f889d4542825c9543fb3b34c13b4cc0e18940a66fafd130749574bfa2c2663d8b39f0b4ed2b298bf130367cda1b17b2929093d64b386730cbc5

diff --git a/sci-libs/htslib/htslib-1.16.ebuild 
b/sci-libs/htslib/htslib-1.16.ebuild
new file mode 100644
index ..c4bd910685de
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.16.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+   sys-libs/zlib
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+   -i htslib.pc.in || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   # doesn't use libtool, can't disable static libraries
+   find "${ED}" -name '*.a' -delete || die
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2022-12-26 Thread David Seifert 
commit: 5dfb769a155875e234939d43f42bed9631dfbb59
Author: David Seifert  gentoo  org>
AuthorDate: Tue Dec 27 00:06:44 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Tue Dec 27 00:06:44 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5dfb769a

sci-libs/htslib: update remote-id

Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/metadata.xml | 14 +++---
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/sci-libs/htslib/metadata.xml b/sci-libs/htslib/metadata.xml
index 003b4a9e53f3..1950263f31e1 100644
--- a/sci-libs/htslib/metadata.xml
+++ b/sci-libs/htslib/metadata.xml
@@ -1,11 +1,11 @@
 
 https://www.gentoo.org/dtd/metadata.dtd;>
 
-  
-sci-biol...@gentoo.org
-Gentoo Biology Project
-  
-  
-samtools
-  
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+   
+   samtools/htslib
+

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2022-06-19 Thread David Seifert 
commit: b1d57c4d6a1a0838f716fadedb0160fc8e08dc55
Author: David Seifert  gentoo  org>
AuthorDate: Sun Jun 19 08:08:46 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Jun 19 08:08:46 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b1d57c4d

sci-libs/htslib: drop 1.13, 1.15

Closes: https://github.com/gentoo/gentoo/pull/25964
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest   |  2 --
 sci-libs/htslib/htslib-1.13.ebuild | 52 --
 sci-libs/htslib/htslib-1.15.ebuild | 52 --
 3 files changed, 106 deletions(-)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 4e08554f1289..f5b37a27ae5a 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,3 +1 @@
-DIST htslib-1.13.tar.bz2 4226834 BLAKE2B 
ae1f64e564f0f7bea80ea9d276b5d5b2b04fa3c8bd58f2c68966225b4324962f34d8a26b74267ab90dc530dfced1b9c01702d25918fd7a7c74e13913f00d5007
 SHA512 
16a3d61c115b71406bc4411a0c1176909166b52c4f7bb11614e398df4defaec4d09763413053e4d0d5916921c866d20019096d8fed866e77f9f1cafbd1e95b16
 DIST htslib-1.15.1.tar.bz2 4141140 BLAKE2B 
312f67c8916586199b32b7703b43a9fd365b8af22802bf4d63fc40960c62b956915e7c60bbd777a8b179066608cd3a281929a10b60eef21d6eedb4caf8c147c1
 SHA512 
69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620
-DIST htslib-1.15.tar.bz2 4141168 BLAKE2B 
20462b01e065b65de2b7df883cf61f9beb9ccca6fa3dc159c0aa7b303daf7c3779938f5eadbd3320e85ec19de105dc55e238c47a922ff6ace6fcaea2b0e95c19
 SHA512 
b87ce3eaa63a731d812953129f1c9aa857fe896ea9e924b7eb92173d8e624dd45e5582b3a97e7120ff7fe339e4d40148077424029626f50372b3f164093aa6cc

diff --git a/sci-libs/htslib/htslib-1.13.ebuild 
b/sci-libs/htslib/htslib-1.13.ebuild
deleted file mode 100644
index cfd9cfb3263e..
--- a/sci-libs/htslib/htslib-1.13.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0/3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma"
-
-RDEPEND="
-   sys-libs/zlib
-   bzip2? ( app-arch/bzip2 )
-   curl? ( net-misc/curl )
-   lzma? ( app-arch/xz-utils )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-   default
-
-   # upstream injects LDFLAGS into the .pc file,
-   # which is a big nono for QA
-   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
-   -i htslib.pc.in || die
-}
-
-src_configure() {
-   econf \
-   --disable-gcs \
-   --disable-plugins \
-   --disable-s3 \
-   $(use_enable bzip2 bz2) \
-   $(use_enable curl libcurl) \
-   $(use_enable lzma)
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   # doesn't use libtool, can't disable static libraries
-   find "${ED}" -name '*.a' -delete || die
-}

diff --git a/sci-libs/htslib/htslib-1.15.ebuild 
b/sci-libs/htslib/htslib-1.15.ebuild
deleted file mode 100644
index e651576d8a81..
--- a/sci-libs/htslib/htslib-1.15.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0/3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma"
-
-RDEPEND="
-   sys-libs/zlib
-   bzip2? ( app-arch/bzip2 )
-   curl? ( net-misc/curl )
-   lzma? ( app-arch/xz-utils )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-   default
-
-   # upstream injects LDFLAGS into the .pc file,
-   # which is a big nono for QA
-   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
-   -i htslib.pc.in || die
-}
-
-src_configure() {
-   econf \
-   --disable-gcs \
-   --disable-plugins \
-   --disable-s3 \
-   $(use_enable bzip2 bz2) \
-   $(use_enable curl libcurl) \
-   $(use_enable lzma)
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   # doesn't use libtool, can't disable static libraries
-   find "${ED}" -name '*.a' -delete || die
-}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2022-06-10 Thread David Seifert 
commit: 4ffaed7e16ee38e8b8edbda16aa559cd21cc382c
Author: David Seifert  gentoo  org>
AuthorDate: Fri Jun 10 12:41:45 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Jun 10 12:41:45 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4ffaed7e

sci-libs/htslib: add 1.15.1

Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest |  1 +
 sci-libs/htslib/htslib-1.15.1.ebuild | 52 
 2 files changed, 53 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 6cf20146c588..4e08554f1289 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,2 +1,3 @@
 DIST htslib-1.13.tar.bz2 4226834 BLAKE2B 
ae1f64e564f0f7bea80ea9d276b5d5b2b04fa3c8bd58f2c68966225b4324962f34d8a26b74267ab90dc530dfced1b9c01702d25918fd7a7c74e13913f00d5007
 SHA512 
16a3d61c115b71406bc4411a0c1176909166b52c4f7bb11614e398df4defaec4d09763413053e4d0d5916921c866d20019096d8fed866e77f9f1cafbd1e95b16
+DIST htslib-1.15.1.tar.bz2 4141140 BLAKE2B 
312f67c8916586199b32b7703b43a9fd365b8af22802bf4d63fc40960c62b956915e7c60bbd777a8b179066608cd3a281929a10b60eef21d6eedb4caf8c147c1
 SHA512 
69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620
 DIST htslib-1.15.tar.bz2 4141168 BLAKE2B 
20462b01e065b65de2b7df883cf61f9beb9ccca6fa3dc159c0aa7b303daf7c3779938f5eadbd3320e85ec19de105dc55e238c47a922ff6ace6fcaea2b0e95c19
 SHA512 
b87ce3eaa63a731d812953129f1c9aa857fe896ea9e924b7eb92173d8e624dd45e5582b3a97e7120ff7fe339e4d40148077424029626f50372b3f164093aa6cc

diff --git a/sci-libs/htslib/htslib-1.15.1.ebuild 
b/sci-libs/htslib/htslib-1.15.1.ebuild
new file mode 100644
index ..c4bd910685de
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.15.1.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2;
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+   sys-libs/zlib
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+   -i htslib.pc.in || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   # doesn't use libtool, can't disable static libraries
+   find "${ED}" -name '*.a' -delete || die
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2022-03-19 Thread David Seifert 
commit: 88f4424986b92b35e86a44e5d0fc67d4cedef2aa
Author: David Seifert  gentoo  org>
AuthorDate: Sat Mar 19 11:38:03 2022 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Mar 19 11:38:03 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=88f44249

sci-libs/htslib: add 1.15

Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest   |  1 +
 sci-libs/htslib/htslib-1.15.ebuild | 52 ++
 2 files changed, 53 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 230f4325182c..6cf20146c588 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1 +1,2 @@
 DIST htslib-1.13.tar.bz2 4226834 BLAKE2B 
ae1f64e564f0f7bea80ea9d276b5d5b2b04fa3c8bd58f2c68966225b4324962f34d8a26b74267ab90dc530dfced1b9c01702d25918fd7a7c74e13913f00d5007
 SHA512 
16a3d61c115b71406bc4411a0c1176909166b52c4f7bb11614e398df4defaec4d09763413053e4d0d5916921c866d20019096d8fed866e77f9f1cafbd1e95b16
+DIST htslib-1.15.tar.bz2 4141168 BLAKE2B 
20462b01e065b65de2b7df883cf61f9beb9ccca6fa3dc159c0aa7b303daf7c3779938f5eadbd3320e85ec19de105dc55e238c47a922ff6ace6fcaea2b0e95c19
 SHA512 
b87ce3eaa63a731d812953129f1c9aa857fe896ea9e924b7eb92173d8e624dd45e5582b3a97e7120ff7fe339e4d40148077424029626f50372b3f164093aa6cc

diff --git a/sci-libs/htslib/htslib-1.15.ebuild 
b/sci-libs/htslib/htslib-1.15.ebuild
new file mode 100644
index ..e651576d8a81
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.15.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+   sys-libs/zlib
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+   -i htslib.pc.in || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   # doesn't use libtool, can't disable static libraries
+   find "${ED}" -name '*.a' -delete || die
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2021-10-11 Thread David Seifert 
commit: fac85a0681906115f21e878305e44c0243e0c686
Author: David Seifert  gentoo  org>
AuthorDate: Mon Oct 11 14:55:11 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Oct 11 14:55:11 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fac85a06

sci-libs/htslib: drop 1.10.2

Bug: https://bugs.gentoo.org/799788
Signed-off-by: David Seifert  gentoo.org>
Closes: https://github.com/gentoo/gentoo/pull/22556
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest |  1 -
 sci-libs/htslib/htslib-1.10.2.ebuild | 51 
 2 files changed, 52 deletions(-)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 9e65f247fdf..230f4325182 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,2 +1 @@
-DIST htslib-1.10.2.tar.bz2 1306320 BLAKE2B 
f877bd9c160921f498f4160f687094a1a369732bc9f61cd94a3c9ca311fa9f865505a205e38e0d348a1010b627f1ef07b590cd7e69c945df1d804133b17b2fd1
 SHA512 
3ecb83b0abccf731cd42b889e352e10dd922524f6e78bcafb04f8c6c71457b0dc1f5f22690b36f03cce7d97a6a905db286243ef4858138068dcac368e4ae1075
 DIST htslib-1.13.tar.bz2 4226834 BLAKE2B 
ae1f64e564f0f7bea80ea9d276b5d5b2b04fa3c8bd58f2c68966225b4324962f34d8a26b74267ab90dc530dfced1b9c01702d25918fd7a7c74e13913f00d5007
 SHA512 
16a3d61c115b71406bc4411a0c1176909166b52c4f7bb11614e398df4defaec4d09763413053e4d0d5916921c866d20019096d8fed866e77f9f1cafbd1e95b16

diff --git a/sci-libs/htslib/htslib-1.10.2.ebuild 
b/sci-libs/htslib/htslib-1.10.2.ebuild
deleted file mode 100644
index 67a341be70e..000
--- a/sci-libs/htslib/htslib-1.10.2.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0/3"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma"
-
-RDEPEND="
-   bzip2? ( app-arch/bzip2:= )
-   curl? ( net-misc/curl )
-   lzma? ( app-arch/xz-utils:= )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-   default
-
-   # upstream injects LDFLAGS into the .pc file,
-   # which is a big nono for QA
-   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
-   -i htslib.pc.in || die
-}
-
-src_configure() {
-   econf \
-   --disable-gcs \
-   --disable-plugins \
-   --disable-s3 \
-   $(use_enable bzip2 bz2) \
-   $(use_enable curl libcurl) \
-   $(use_enable lzma)
-}
-
-src_compile() {
-   emake AR="$(tc-getAR)"
-}
-
-src_install() {
-   default
-
-   # doesn't use libtool, can't disable static libraries
-   find "${ED}" -name '*.a' -delete || die
-}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2021-10-03 Thread David Seifert 
commit: a7e45d492762de669f6e84b5df12aaf95cae1a1d
Author: David Seifert  gentoo  org>
AuthorDate: Sun Oct  3 17:41:36 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Oct  3 17:41:36 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a7e45d49

sci-libs/htslib: add 1.13

Bug: https://bugs.gentoo.org/799788
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest   |  1 +
 sci-libs/htslib/htslib-1.13.ebuild | 52 ++
 2 files changed, 53 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 3aac577a0cf..9e65f247fdf 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1 +1,2 @@
 DIST htslib-1.10.2.tar.bz2 1306320 BLAKE2B 
f877bd9c160921f498f4160f687094a1a369732bc9f61cd94a3c9ca311fa9f865505a205e38e0d348a1010b627f1ef07b590cd7e69c945df1d804133b17b2fd1
 SHA512 
3ecb83b0abccf731cd42b889e352e10dd922524f6e78bcafb04f8c6c71457b0dc1f5f22690b36f03cce7d97a6a905db286243ef4858138068dcac368e4ae1075
+DIST htslib-1.13.tar.bz2 4226834 BLAKE2B 
ae1f64e564f0f7bea80ea9d276b5d5b2b04fa3c8bd58f2c68966225b4324962f34d8a26b74267ab90dc530dfced1b9c01702d25918fd7a7c74e13913f00d5007
 SHA512 
16a3d61c115b71406bc4411a0c1176909166b52c4f7bb11614e398df4defaec4d09763413053e4d0d5916921c866d20019096d8fed866e77f9f1cafbd1e95b16

diff --git a/sci-libs/htslib/htslib-1.13.ebuild 
b/sci-libs/htslib/htslib-1.13.ebuild
new file mode 100644
index 000..cfd9cfb3263
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.13.ebuild
@@ -0,0 +1,52 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+   sys-libs/zlib
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+   -i htslib.pc.in || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   # doesn't use libtool, can't disable static libraries
+   find "${ED}" -name '*.a' -delete || die
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2020-12-10 Thread David Seifert 
commit: 448c220d0c712520c92dcfa6a3ce9aea31deb75c
Author: David Seifert  gentoo  org>
AuthorDate: Thu Dec 10 13:44:23 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Dec 10 13:44:23 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=448c220d

sci-libs/htslib: Remove old 1.9

Closes: https://bugs.gentoo.org/725270
Closes: https://github.com/gentoo/gentoo/pull/18592
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest  |  1 -
 sci-libs/htslib/htslib-1.9.ebuild | 45 ---
 2 files changed, 46 deletions(-)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index e89bbbd8301..3aac577a0cf 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,2 +1 @@
 DIST htslib-1.10.2.tar.bz2 1306320 BLAKE2B 
f877bd9c160921f498f4160f687094a1a369732bc9f61cd94a3c9ca311fa9f865505a205e38e0d348a1010b627f1ef07b590cd7e69c945df1d804133b17b2fd1
 SHA512 
3ecb83b0abccf731cd42b889e352e10dd922524f6e78bcafb04f8c6c71457b0dc1f5f22690b36f03cce7d97a6a905db286243ef4858138068dcac368e4ae1075
-DIST htslib-1.9.tar.bz2 1178859 BLAKE2B 
a0229313d3572717101f4f23d39fa124f3bb38d8b2e65055f4f801dbb5f1549df95115e8beadd8fa024171b3ff8a874d20087bf71819c36700666f168dbe41ab
 SHA512 
ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7

diff --git a/sci-libs/htslib/htslib-1.9.ebuild 
b/sci-libs/htslib/htslib-1.9.ebuild
deleted file mode 100644
index ea70899c061..000
--- a/sci-libs/htslib/htslib-1.9.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
-
-SLOT="0/2"
-LICENSE="MIT"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma static-libs"
-
-RDEPEND="
-   bzip2? ( app-arch/bzip2:= )
-   curl? ( net-misc/curl )
-   lzma? ( app-arch/xz-utils:= )"
-DEPEND="${RDEPEND}"
-
-src_prepare() {
-   default
-
-   # upstream injects LDFLAGS into the .pc file,
-   # which is a big nono for QA
-   sed 's/private_LIBS=$LDFLAGS/private_LIBS=""/g' -i configure || die
-}
-
-src_configure() {
-   econf \
-   --disable-gcs \
-   --disable-plugins \
-   --disable-s3 \
-   $(use_enable bzip2 bz2) \
-   $(use_enable curl libcurl) \
-   $(use_enable lzma)
-}
-
-src_install() {
-   default
-
-   if ! use static-libs; then
-   find "${D}" -name '*.a' -delete || die
-   fi
-}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2020-08-03 Thread David Seifert 
commit: b63825b8f4636cdcdb7066279b4a743b19e530f8
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 21:11:21 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 21:11:21 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b63825b8

sci-libs/htslib: Remove old

Closes: https://github.com/gentoo/gentoo/pull/16982
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest  |  1 -
 sci-libs/htslib/htslib-1.5.ebuild | 37 -
 2 files changed, 38 deletions(-)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index dce2a3b0b7b..e89bbbd8301 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,3 +1,2 @@
 DIST htslib-1.10.2.tar.bz2 1306320 BLAKE2B 
f877bd9c160921f498f4160f687094a1a369732bc9f61cd94a3c9ca311fa9f865505a205e38e0d348a1010b627f1ef07b590cd7e69c945df1d804133b17b2fd1
 SHA512 
3ecb83b0abccf731cd42b889e352e10dd922524f6e78bcafb04f8c6c71457b0dc1f5f22690b36f03cce7d97a6a905db286243ef4858138068dcac368e4ae1075
-DIST htslib-1.5.tar.bz2 1051132 BLAKE2B 
90c6aeeaa2a2692228aa1f530d775a6e81f9275d321e8b2d6005b86b9a25e5967acca19dd898311a5bc4f3c17d4e8ea36d18da4602e18fadee47666350122077
 SHA512 
fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917
 DIST htslib-1.9.tar.bz2 1178859 BLAKE2B 
a0229313d3572717101f4f23d39fa124f3bb38d8b2e65055f4f801dbb5f1549df95115e8beadd8fa024171b3ff8a874d20087bf71819c36700666f168dbe41ab
 SHA512 
ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7

diff --git a/sci-libs/htslib/htslib-1.5.ebuild 
b/sci-libs/htslib/htslib-1.5.ebuild
deleted file mode 100644
index d9957ce3a17..000
--- a/sci-libs/htslib/htslib-1.5.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
-
-SLOT="0/2"
-LICENSE="MIT"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma static-libs"
-
-RDEPEND="
-   bzip2? ( app-arch/bzip2 )
-   curl? ( net-misc/curl )
-   lzma? ( app-arch/xz-utils )"
-DEPEND="${RDEPEND}"
-
-src_configure() {
-   econf \
-   --disable-gcs \
-   --disable-plugins \
-   --disable-s3 \
-   $(use_enable bzip2 bz2) \
-   $(use_enable curl libcurl) \
-   $(use_enable lzma)
-}
-
-src_install() {
-   default
-
-   if ! use static-libs; then
-   find "${D}" -name '*.a' -delete || die
-   fi
-}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2020-08-03 Thread David Seifert 
commit: 5e82d24704dfce8efb91971c96031756d46fe0c2
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 16:54:20 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 16:54:20 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5e82d247

sci-libs/htslib: Bump to version 1.10.2

Bug: https://bugs.gentoo.org/725270
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-libs/htslib/Manifest |  1 +
 sci-libs/htslib/htslib-1.10.2.ebuild | 51 
 2 files changed, 52 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index e818f35f147..dce2a3b0b7b 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,2 +1,3 @@
+DIST htslib-1.10.2.tar.bz2 1306320 BLAKE2B 
f877bd9c160921f498f4160f687094a1a369732bc9f61cd94a3c9ca311fa9f865505a205e38e0d348a1010b627f1ef07b590cd7e69c945df1d804133b17b2fd1
 SHA512 
3ecb83b0abccf731cd42b889e352e10dd922524f6e78bcafb04f8c6c71457b0dc1f5f22690b36f03cce7d97a6a905db286243ef4858138068dcac368e4ae1075
 DIST htslib-1.5.tar.bz2 1051132 BLAKE2B 
90c6aeeaa2a2692228aa1f530d775a6e81f9275d321e8b2d6005b86b9a25e5967acca19dd898311a5bc4f3c17d4e8ea36d18da4602e18fadee47666350122077
 SHA512 
fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917
 DIST htslib-1.9.tar.bz2 1178859 BLAKE2B 
a0229313d3572717101f4f23d39fa124f3bb38d8b2e65055f4f801dbb5f1549df95115e8beadd8fa024171b3ff8a874d20087bf71819c36700666f168dbe41ab
 SHA512 
ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7

diff --git a/sci-libs/htslib/htslib-1.10.2.ebuild 
b/sci-libs/htslib/htslib-1.10.2.ebuild
new file mode 100644
index 000..67a341be70e
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.10.2.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit toolchain-funcs
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0/3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma"
+
+RDEPEND="
+   bzip2? ( app-arch/bzip2:= )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils:= )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed -e '/^\(static_l\|Libs.private\|Requires.private\)/d' \
+   -i htslib.pc.in || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_compile() {
+   emake AR="$(tc-getAR)"
+}
+
+src_install() {
+   default
+
+   # doesn't use libtool, can't disable static libraries
+   find "${ED}" -name '*.a' -delete || die
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2020-03-20 Thread Agostino Sarubbo 
commit: 63df71b9c5b962de7ef92d4956f88bfdf8fe1e7d
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Fri Mar 20 09:04:35 2020 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Fri Mar 20 09:04:52 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=63df71b9

sci-libs/htslib: x86 stable wrt bug #713236

Package-Manager: Portage-2.3.89, Repoman-2.3.20
RepoMan-Options: --include-arches="x86"
Signed-off-by: Agostino Sarubbo  gentoo.org>

 sci-libs/htslib/htslib-1.9.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-libs/htslib/htslib-1.9.ebuild 
b/sci-libs/htslib/htslib-1.9.ebuild
index 327ffeed1ef..ea70899c061 100644
--- a/sci-libs/htslib/htslib-1.9.ebuild
+++ b/sci-libs/htslib/htslib-1.9.ebuild
@@ -9,7 +9,7 @@ SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
 
 SLOT="0/2"
 LICENSE="MIT"
-KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE="+bzip2 curl +lzma static-libs"
 
 RDEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2020-03-20 Thread Agostino Sarubbo 
commit: 8d367cf57a082dc88d24a5bf22aadb90c18709a3
Author: Agostino Sarubbo  gentoo  org>
AuthorDate: Fri Mar 20 08:59:04 2020 +
Commit: Agostino Sarubbo  gentoo  org>
CommitDate: Fri Mar 20 08:59:04 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8d367cf5

sci-libs/htslib: amd64 stable wrt bug #713236

Package-Manager: Portage-2.3.89, Repoman-2.3.20
RepoMan-Options: --include-arches="amd64"
Signed-off-by: Agostino Sarubbo  gentoo.org>

 sci-libs/htslib/htslib-1.9.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/htslib/htslib-1.9.ebuild 
b/sci-libs/htslib/htslib-1.9.ebuild
index 69df48a332f..327ffeed1ef 100644
--- a/sci-libs/htslib/htslib-1.9.ebuild
+++ b/sci-libs/htslib/htslib-1.9.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -9,7 +9,7 @@ SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
 
 SLOT="0/2"
 LICENSE="MIT"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="+bzip2 curl +lzma static-libs"
 
 RDEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2018-10-28 Thread David Seifert 
commit: 85fad26e8efb7e2fc01de49e59a0d7e0b210c5bc
Author: David Seifert  gentoo  org>
AuthorDate: Sun Oct 28 20:24:33 2018 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Oct 28 20:24:33 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=85fad26e

sci-libs/htslib: Version bump to 1.9

Bug: https://bugs.gentoo.org/647714
Signed-off-by: David Seifert  gentoo.org>
Package-Manager: Portage-2.3.50, Repoman-2.3.11

 sci-libs/htslib/Manifest  |  1 +
 sci-libs/htslib/htslib-1.9.ebuild | 45 +++
 2 files changed, 46 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 6841d0a69fb..e818f35f147 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1 +1,2 @@
 DIST htslib-1.5.tar.bz2 1051132 BLAKE2B 
90c6aeeaa2a2692228aa1f530d775a6e81f9275d321e8b2d6005b86b9a25e5967acca19dd898311a5bc4f3c17d4e8ea36d18da4602e18fadee47666350122077
 SHA512 
fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917
+DIST htslib-1.9.tar.bz2 1178859 BLAKE2B 
a0229313d3572717101f4f23d39fa124f3bb38d8b2e65055f4f801dbb5f1549df95115e8beadd8fa024171b3ff8a874d20087bf71819c36700666f168dbe41ab
 SHA512 
ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7

diff --git a/sci-libs/htslib/htslib-1.9.ebuild 
b/sci-libs/htslib/htslib-1.9.ebuild
new file mode 100644
index 000..69df48a332f
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.9.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+SLOT="0/2"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma static-libs"
+
+RDEPEND="
+   bzip2? ( app-arch/bzip2:= )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils:= )"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+   default
+
+   # upstream injects LDFLAGS into the .pc file,
+   # which is a big nono for QA
+   sed 's/private_LIBS=$LDFLAGS/private_LIBS=""/g' -i configure || die
+}
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_install() {
+   default
+
+   if ! use static-libs; then
+   find "${D}" -name '*.a' -delete || die
+   fi
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2017-09-02 Thread David Seifert 
commit: 8414705ae146126e4745b343cd33e71a405cb166
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 11:07:41 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 12:37:06 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8414705a

sci-libs/htslib: Remove old

Package-Manager: Portage-2.3.8, Repoman-2.3.3
Closes: https://github.com/gentoo/gentoo/pull/5593

 sci-libs/htslib/Manifest|  5 -
 sci-libs/htslib/htslib-1.0.ebuild   | 44 -
 sci-libs/htslib/htslib-1.1.ebuild   | 42 ---
 sci-libs/htslib/htslib-1.2.1.ebuild | 20 -
 sci-libs/htslib/htslib-1.3.1.ebuild | 20 -
 sci-libs/htslib/htslib-1.3.ebuild   | 20 -
 6 files changed, 151 deletions(-)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 728098018cc..fbf89b440a9 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,6 +1 @@
-DIST htslib-1.0.tar.bz2 842174 SHA256 
3d53fb081fafd930cadfee6f950faacc1993a0f4a9fa329fc897865fc6b331bc SHA512 
aee7080a31c3fe5bd1fe4a16102da4aef7d415fd022781c1a5bdc1316ca50f8fcabbb95a39adc867e4eb5ac2d8ed63ab15ceafcd768e840d2593282916313507
 WHIRLPOOL 
512f4a95e98129151fef34fb90294138bc0aec40d5c2345d15d49ded02810c4663b8ff65726ced9f0d9ceb300295da066f6025d2b1966224937fc9ff58f2b58f
-DIST htslib-1.1.tar.bz2 844870 SHA256 
204e894074d9a864d27b607fda19f6240c5da351bb61bfc6c94beaa8790e4d58 SHA512 
cde0b01583035f139203b8e9884dc97846bdf02fbb6dd2af74d0829270c2141ac490d0ca3ece4f9afd9d66d6af235452d3e94bbe0ea6e1a8625405735a813271
 WHIRLPOOL 
56e986cd7ee29d2d680ef55fd9128d4e43bacff4d72bc83df7b8c1e6c8d53b4a726c576d690dee272397778a6796096072fc3fffe4a4f1cbc0179a91fe9405b6
-DIST htslib-1.2.1.tar.bz2 911326 SHA256 
bddb1372b9215b32e0f21d8394bab859c57cb00324a8dc06775cdac5b4d662b0 SHA512 
23db1861cd08b503223f14dcbbdf9c6ae24dec648c987816abc47cc85fa7287c2405be72193cf492fff4f5991ff7b1f55dc386004588971a0e43a2f1c7355199
 WHIRLPOOL 
d81f1cc74bb7e70d538f3e616f290a50017c56c517d9986f84c897b75524848135dd1788f92ff983c701ab7d5e84163123c570a200b83bea6a7922f4c1293107
-DIST htslib-1.3.1.tar.bz2 983165 SHA256 
49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6 SHA512 
cdc34166d36a3bf4479d020a2352fe6e8fb7ad92c3205b3fbde3e83b0916cffcfdcf2f28a68a4937e58b903ea8913558ae3a90c2445212da1f25a3b30c43d786
 WHIRLPOOL 
474de4015cf4f8c2b469f45693ba3e677be246b946a8ba70205219dd25f16ce85def7c062c4073326aa0a795a732e84664ab7df2c002cca6e47abceb145c
-DIST htslib-1.3.tar.bz2 952864 SHA256 
f203af750ccc80fd421c70a04d90a03097d2ef2abe0e6d8f0ae6435d6c11aeab SHA512 
1a96fd22632b4a593596645b3a40aa59a9f342f97ec8c1807fe4058576420ba2c6279594d00bfc67db93aa858bd63bf3e2cf1a63e79605791c6f8aef097c
 WHIRLPOOL 
49140830c525cea21533cc9924a5f0a5e6aecef24cf7ac58ddc959faac205b1bcc2d6f423daab6d6ff8cb5c9ad5b750cfef9e7181a68485ab35e10b7932ab4a6
 DIST htslib-1.5.tar.bz2 1051132 SHA256 
a02b515ea51d86352b089c63d778fb5e8b9d784937cf157e587189cb97ad922d SHA512 
fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917
 WHIRLPOOL 
fb7026c26816db6746006d1b5ade235ce10181a633c9bab8ed3d9f72aaa152d0b68fd69d8988d69fef2bd2d57f9676de0761b2577ef0dd1d334da5d028cb64ee

diff --git a/sci-libs/htslib/htslib-1.0.ebuild 
b/sci-libs/htslib/htslib-1.0.ebuild
deleted file mode 100644
index d5c594b0cfb..000
--- a/sci-libs/htslib/htslib-1.0.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit multilib toolchain-funcs
-
-DESCRIPTION="C library for high-throughput sequencing data formats"
-HOMEPAGE="http://www.htslib.org/;
-SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
-
-SLOT="0"
-LICENSE="MIT"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-src_prepare() {
-   sed \
-   -e "/libdir/s:lib$:$(get_libdir):g" \
-   -i Makefile || die
-}
-
-src_compile() {
-   emake \
-   AR="$(tc-getAR)" \
-   CC="$(tc-getCC)" \
-   CFLAGS="${CFLAGS}" \
-   LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-   emake \
-   DESTDIR="${D}" \
-   prefix="${EPREFIX}/usr" \
-   install
-
-   rm "${ED}/usr/share/man/man1/libhts.so.1" || die
-
-   if ! use static-libs; then
-   find "${ED}" -type f -name "*.a" -delete || die
-   fi
-
-   dodoc README
-}

diff --git a/sci-libs/htslib/htslib-1.1.ebuild 
b/sci-libs/htslib/htslib-1.1.ebuild
deleted file mode 100644
index 5f9d646c827..000
--- a/sci-libs/htslib/htslib-1.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit multilib toolchain-funcs
-
-DESCRIPTION="C library for

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2017-07-29 Thread David Seifert 
commit: a4708f79ea39cabbf7231fdedecf6ee8a525a3e6
Author: David Seifert  gentoo  org>
AuthorDate: Sat Jul 29 09:17:59 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Jul 29 09:19:06 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a4708f79

sci-libs/htslib: Bump to version 1.5

Package-Manager: Portage-2.3.6, Repoman-2.3.3

 sci-libs/htslib/Manifest  |  1 +
 sci-libs/htslib/htslib-1.5.ebuild | 37 +
 2 files changed, 38 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 79fe19162ed..728098018cc 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -3,3 +3,4 @@ DIST htslib-1.1.tar.bz2 844870 SHA256 
204e894074d9a864d27b607fda19f6240c5da351bb
 DIST htslib-1.2.1.tar.bz2 911326 SHA256 
bddb1372b9215b32e0f21d8394bab859c57cb00324a8dc06775cdac5b4d662b0 SHA512 
23db1861cd08b503223f14dcbbdf9c6ae24dec648c987816abc47cc85fa7287c2405be72193cf492fff4f5991ff7b1f55dc386004588971a0e43a2f1c7355199
 WHIRLPOOL 
d81f1cc74bb7e70d538f3e616f290a50017c56c517d9986f84c897b75524848135dd1788f92ff983c701ab7d5e84163123c570a200b83bea6a7922f4c1293107
 DIST htslib-1.3.1.tar.bz2 983165 SHA256 
49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6 SHA512 
cdc34166d36a3bf4479d020a2352fe6e8fb7ad92c3205b3fbde3e83b0916cffcfdcf2f28a68a4937e58b903ea8913558ae3a90c2445212da1f25a3b30c43d786
 WHIRLPOOL 
474de4015cf4f8c2b469f45693ba3e677be246b946a8ba70205219dd25f16ce85def7c062c4073326aa0a795a732e84664ab7df2c002cca6e47abceb145c
 DIST htslib-1.3.tar.bz2 952864 SHA256 
f203af750ccc80fd421c70a04d90a03097d2ef2abe0e6d8f0ae6435d6c11aeab SHA512 
1a96fd22632b4a593596645b3a40aa59a9f342f97ec8c1807fe4058576420ba2c6279594d00bfc67db93aa858bd63bf3e2cf1a63e79605791c6f8aef097c
 WHIRLPOOL 
49140830c525cea21533cc9924a5f0a5e6aecef24cf7ac58ddc959faac205b1bcc2d6f423daab6d6ff8cb5c9ad5b750cfef9e7181a68485ab35e10b7932ab4a6
+DIST htslib-1.5.tar.bz2 1051132 SHA256 
a02b515ea51d86352b089c63d778fb5e8b9d784937cf157e587189cb97ad922d SHA512 
fd58552ddbd178f9797123fdaf47914ccd0e2aefd055fc6557ac8f479c600775616107cfa871c3acd93079f45974a19f443941a79f2acfd2a8c2983ef35b8917
 WHIRLPOOL 
fb7026c26816db6746006d1b5ade235ce10181a633c9bab8ed3d9f72aaa152d0b68fd69d8988d69fef2bd2d57f9676de0761b2577ef0dd1d334da5d028cb64ee

diff --git a/sci-libs/htslib/htslib-1.5.ebuild 
b/sci-libs/htslib/htslib-1.5.ebuild
new file mode 100644
index 000..d9957ce3a17
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.5.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+SLOT="0/2"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma static-libs"
+
+RDEPEND="
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   lzma? ( app-arch/xz-utils )"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+   econf \
+   --disable-gcs \
+   --disable-plugins \
+   --disable-s3 \
+   $(use_enable bzip2 bz2) \
+   $(use_enable curl libcurl) \
+   $(use_enable lzma)
+}
+
+src_install() {
+   default
+
+   if ! use static-libs; then
+   find "${D}" -name '*.a' -delete || die
+   fi
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2016-07-30 Thread David Seifert 
commit: 61be48515eb9adb8d4513e4ad52faec15586d984
Author: David Seifert  gentoo  org>
AuthorDate: Fri Jul 29 17:24:58 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Jul 30 08:25:44 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=61be4851

sci-libs/htslib: version bump

Package-Manager: portage-2.3.0

 sci-libs/htslib/Manifest|  1 +
 sci-libs/htslib/htslib-1.3.1.ebuild | 21 +
 2 files changed, 22 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 480f325..79fe191 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,4 +1,5 @@
 DIST htslib-1.0.tar.bz2 842174 SHA256 
3d53fb081fafd930cadfee6f950faacc1993a0f4a9fa329fc897865fc6b331bc SHA512 
aee7080a31c3fe5bd1fe4a16102da4aef7d415fd022781c1a5bdc1316ca50f8fcabbb95a39adc867e4eb5ac2d8ed63ab15ceafcd768e840d2593282916313507
 WHIRLPOOL 
512f4a95e98129151fef34fb90294138bc0aec40d5c2345d15d49ded02810c4663b8ff65726ced9f0d9ceb300295da066f6025d2b1966224937fc9ff58f2b58f
 DIST htslib-1.1.tar.bz2 844870 SHA256 
204e894074d9a864d27b607fda19f6240c5da351bb61bfc6c94beaa8790e4d58 SHA512 
cde0b01583035f139203b8e9884dc97846bdf02fbb6dd2af74d0829270c2141ac490d0ca3ece4f9afd9d66d6af235452d3e94bbe0ea6e1a8625405735a813271
 WHIRLPOOL 
56e986cd7ee29d2d680ef55fd9128d4e43bacff4d72bc83df7b8c1e6c8d53b4a726c576d690dee272397778a6796096072fc3fffe4a4f1cbc0179a91fe9405b6
 DIST htslib-1.2.1.tar.bz2 911326 SHA256 
bddb1372b9215b32e0f21d8394bab859c57cb00324a8dc06775cdac5b4d662b0 SHA512 
23db1861cd08b503223f14dcbbdf9c6ae24dec648c987816abc47cc85fa7287c2405be72193cf492fff4f5991ff7b1f55dc386004588971a0e43a2f1c7355199
 WHIRLPOOL 
d81f1cc74bb7e70d538f3e616f290a50017c56c517d9986f84c897b75524848135dd1788f92ff983c701ab7d5e84163123c570a200b83bea6a7922f4c1293107
+DIST htslib-1.3.1.tar.bz2 983165 SHA256 
49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6 SHA512 
cdc34166d36a3bf4479d020a2352fe6e8fb7ad92c3205b3fbde3e83b0916cffcfdcf2f28a68a4937e58b903ea8913558ae3a90c2445212da1f25a3b30c43d786
 WHIRLPOOL 
474de4015cf4f8c2b469f45693ba3e677be246b946a8ba70205219dd25f16ce85def7c062c4073326aa0a795a732e84664ab7df2c002cca6e47abceb145c
 DIST htslib-1.3.tar.bz2 952864 SHA256 
f203af750ccc80fd421c70a04d90a03097d2ef2abe0e6d8f0ae6435d6c11aeab SHA512 
1a96fd22632b4a593596645b3a40aa59a9f342f97ec8c1807fe4058576420ba2c6279594d00bfc67db93aa858bd63bf3e2cf1a63e79605791c6f8aef097c
 WHIRLPOOL 
49140830c525cea21533cc9924a5f0a5e6aecef24cf7ac58ddc959faac205b1bcc2d6f423daab6d6ff8cb5c9ad5b750cfef9e7181a68485ab35e10b7932ab4a6

diff --git a/sci-libs/htslib/htslib-1.3.1.ebuild 
b/sci-libs/htslib/htslib-1.3.1.ebuild
new file mode 100644
index 000..79e7d9d
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.3.1.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="static-libs"
+
+src_install() {
+   default
+   if ! use static-libs; then
+   find "${ED}" -type f -name "*.a" -delete || die
+   fi
+}

[gentoo-commits] repo/gentoo:master commit in: sci-libs/htslib/

2016-03-27 Thread David Seifert 
commit: 6d547d1a204d6ff97d90e74949b6f710ef106630
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 21:00:23 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 22:39:43 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6d547d1a

sci-libs/htslib: Version bump to 1.3

Package-Manager: portage-2.2.28

 sci-libs/htslib/Manifest  |  1 +
 sci-libs/htslib/htslib-1.3.ebuild | 21 +
 2 files changed, 22 insertions(+)

diff --git a/sci-libs/htslib/Manifest b/sci-libs/htslib/Manifest
index 1618f6e..480f325 100644
--- a/sci-libs/htslib/Manifest
+++ b/sci-libs/htslib/Manifest
@@ -1,3 +1,4 @@
 DIST htslib-1.0.tar.bz2 842174 SHA256 
3d53fb081fafd930cadfee6f950faacc1993a0f4a9fa329fc897865fc6b331bc SHA512 
aee7080a31c3fe5bd1fe4a16102da4aef7d415fd022781c1a5bdc1316ca50f8fcabbb95a39adc867e4eb5ac2d8ed63ab15ceafcd768e840d2593282916313507
 WHIRLPOOL 
512f4a95e98129151fef34fb90294138bc0aec40d5c2345d15d49ded02810c4663b8ff65726ced9f0d9ceb300295da066f6025d2b1966224937fc9ff58f2b58f
 DIST htslib-1.1.tar.bz2 844870 SHA256 
204e894074d9a864d27b607fda19f6240c5da351bb61bfc6c94beaa8790e4d58 SHA512 
cde0b01583035f139203b8e9884dc97846bdf02fbb6dd2af74d0829270c2141ac490d0ca3ece4f9afd9d66d6af235452d3e94bbe0ea6e1a8625405735a813271
 WHIRLPOOL 
56e986cd7ee29d2d680ef55fd9128d4e43bacff4d72bc83df7b8c1e6c8d53b4a726c576d690dee272397778a6796096072fc3fffe4a4f1cbc0179a91fe9405b6
 DIST htslib-1.2.1.tar.bz2 911326 SHA256 
bddb1372b9215b32e0f21d8394bab859c57cb00324a8dc06775cdac5b4d662b0 SHA512 
23db1861cd08b503223f14dcbbdf9c6ae24dec648c987816abc47cc85fa7287c2405be72193cf492fff4f5991ff7b1f55dc386004588971a0e43a2f1c7355199
 WHIRLPOOL 
d81f1cc74bb7e70d538f3e616f290a50017c56c517d9986f84c897b75524848135dd1788f92ff983c701ab7d5e84163123c570a200b83bea6a7922f4c1293107
+DIST htslib-1.3.tar.bz2 952864 SHA256 
f203af750ccc80fd421c70a04d90a03097d2ef2abe0e6d8f0ae6435d6c11aeab SHA512 
1a96fd22632b4a593596645b3a40aa59a9f342f97ec8c1807fe4058576420ba2c6279594d00bfc67db93aa858bd63bf3e2cf1a63e79605791c6f8aef097c
 WHIRLPOOL 
49140830c525cea21533cc9924a5f0a5e6aecef24cf7ac58ddc959faac205b1bcc2d6f423daab6d6ff8cb5c9ad5b750cfef9e7181a68485ab35e10b7932ab4a6

diff --git a/sci-libs/htslib/htslib-1.3.ebuild 
b/sci-libs/htslib/htslib-1.3.ebuild
new file mode 100644
index 000..79e7d9d
--- /dev/null
+++ b/sci-libs/htslib/htslib-1.3.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="C library for high-throughput sequencing data formats"
+HOMEPAGE="http://www.htslib.org/;
+SRC_URI="mirror://sourceforge/samtools/${PV}/${P}.tar.bz2"
+
+SLOT="0"
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="static-libs"
+
+src_install() {
+   default
+   if ! use static-libs; then
+   find "${ED}" -type f -name "*.a" -delete || die
+   fi
+}