| 1 |
commit: 458e1564c2fa03fefffd8a8f9dc8975d95f26c3f |
| 2 |
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 3 |
AuthorDate: Tue Jan 22 15:17:58 2019 +0000 |
| 4 |
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 5 |
CommitDate: Tue Jan 22 15:17:58 2019 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=458e1564 |
| 7 |
|
| 8 |
sci-libs/libmaus2: upstream moved from github to gitlab |
| 9 |
|
| 10 |
https://github.com/gt1/libmaus2/issues/28#issuecomment-456336598 |
| 11 |
|
| 12 |
Package-Manager: Portage-2.3.56, Repoman-2.3.12 |
| 13 |
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz> |
| 14 |
|
| 15 |
.../{libmaus2-2.0.499.ebuild => libmaus2-2.0.587.ebuild} | 15 +++++++-------- |
| 16 |
sci-libs/libmaus2/libmaus2-9999.ebuild | 11 +++++------ |
| 17 |
2 files changed, 12 insertions(+), 14 deletions(-) |
| 18 |
|
| 19 |
diff --git a/sci-libs/libmaus2/libmaus2-2.0.499.ebuild b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild |
| 20 |
similarity index 70% |
| 21 |
rename from sci-libs/libmaus2/libmaus2-2.0.499.ebuild |
| 22 |
rename to sci-libs/libmaus2/libmaus2-2.0.587.ebuild |
| 23 |
index cebe44161..1c61df056 100644 |
| 24 |
--- a/sci-libs/libmaus2/libmaus2-2.0.499.ebuild |
| 25 |
+++ b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild |
| 26 |
@@ -1,4 +1,4 @@ |
| 27 |
-# Copyright 1999-2018 Gentoo Authors |
| 28 |
+# Copyright 2019 Gentoo Authors |
| 29 |
# Distributed under the terms of the GNU General Public License v2 |
| 30 |
|
| 31 |
EAPI=7 |
| 32 |
@@ -7,36 +7,35 @@ inherit autotools |
| 33 |
|
| 34 |
DESCRIPTION="Library for biobambam2" |
| 35 |
HOMEPAGE="https://github.com/gt1/libmaus" |
| 36 |
-SRC_URI="https://github.com/gt1/libmaus2/archive/2.0.499-release-20180606122508.tar.gz" |
| 37 |
+SRC_URI="https://gitlab.com/german.tischler/libmaus2/-/archive/master/${P}.tar.gz" |
| 38 |
|
| 39 |
LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS |
| 40 |
SLOT="0" |
| 41 |
-KEYWORDS="" |
| 42 |
+KEYWORDS="~amd64 ~x86" |
| 43 |
IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2" |
| 44 |
|
| 45 |
DEPEND=" |
| 46 |
!sci-libs/libmaus |
| 47 |
- sci-libs/io_lib |
| 48 |
+ >=sci-libs/io_lib-1.14.11 |
| 49 |
app-arch/snappy |
| 50 |
- sci-biology/seqan |
| 51 |
sci-libs/fftw |
| 52 |
sci-libs/hdf5 |
| 53 |
net-libs/gnutls |
| 54 |
dev-libs/nettle" |
| 55 |
# --with-daligner |
| 56 |
# --with-irods |
| 57 |
-S="${WORKDIR}"/libmaus2-2.0.499-release-20180606122508 |
| 58 |
+S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901 |
| 59 |
|
| 60 |
src_configure(){ |
| 61 |
local CONFIG_OPTS |
| 62 |
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 ) |
| 63 |
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 ) |
| 64 |
- econf --with-snappy --with-seqan --with-io_lib $CONFIG_OPTS \ |
| 65 |
+ econf --with-snappy --with-io_lib $CONFIG_OPTS \ |
| 66 |
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw |
| 67 |
} |
| 68 |
|
| 69 |
pkg_postinst(){ |
| 70 |
- einfo "The io_lib, snappy and seqan dependencies are not strictly needed" |
| 71 |
+ einfo "The io_lib, snappy dependencies are not strictly needed" |
| 72 |
einfo "but were forced for optimal libmaus2 performance." |
| 73 |
einfo "igzip is only used if gzip level is set to 11." |
| 74 |
} |
| 75 |
|
| 76 |
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild |
| 77 |
index 01aa74a92..c371d5432 100644 |
| 78 |
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild |
| 79 |
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild |
| 80 |
@@ -1,4 +1,4 @@ |
| 81 |
-# Copyright 1999-2018 Gentoo Authors |
| 82 |
+# Copyright 2019 Gentoo Authors |
| 83 |
# Distributed under the terms of the GNU General Public License v2 |
| 84 |
|
| 85 |
EAPI=7 |
| 86 |
@@ -7,7 +7,7 @@ inherit autotools git-r3 |
| 87 |
|
| 88 |
DESCRIPTION="Library for biobambam2" |
| 89 |
HOMEPAGE="https://github.com/gt1/libmaus" |
| 90 |
-EGIT_REPO_URI="https://github.com/gt1/libmaus2.git" |
| 91 |
+EGIT_REPO_URI="https://gitlab.com/german.tischler/libmaus2" |
| 92 |
|
| 93 |
LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS |
| 94 |
SLOT="0" |
| 95 |
@@ -16,9 +16,8 @@ IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2" |
| 96 |
|
| 97 |
DEPEND=" |
| 98 |
!sci-libs/libmaus |
| 99 |
- sci-libs/io_lib |
| 100 |
+ >=sci-libs/io_lib-1.14.11 |
| 101 |
app-arch/snappy |
| 102 |
- sci-biology/seqan |
| 103 |
sci-libs/fftw |
| 104 |
sci-libs/hdf5 |
| 105 |
net-libs/gnutls |
| 106 |
@@ -35,12 +34,12 @@ src_configure(){ |
| 107 |
local CONFIG_OPTS |
| 108 |
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 ) |
| 109 |
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 ) |
| 110 |
- econf --with-snappy --with-seqan --with-io_lib $CONFIG_OPTS \ |
| 111 |
+ econf --with-snappy --with-io_lib $CONFIG_OPTS \ |
| 112 |
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw |
| 113 |
} |
| 114 |
|
| 115 |
pkg_postinst(){ |
| 116 |
- einfo "The io_lib, snappy and seqan dependencies are not strictly needed" |
| 117 |
+ einfo "The io_lib, snappy dependencies are not strictly needed" |
| 118 |
einfo "but were forced for optimal libmaus2 performance." |
| 119 |
einfo "igzip is only used if gzip level is set to 11." |
| 120 |
} |
Archives