* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2016-07-14 18:42 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2016-07-14 18:42 UTC (permalink / raw
To: gentoo-commits
commit: ec639407519c52105c86906c2909ecbeb3a25665
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 14 18:42:06 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jul 14 18:42:06 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ec639407
sci-libs/libmaus2: new package although a version bump of sci-libs/libmaus
I think this and the parental libmaus package will need a fix on the LICENSE
line (they are not only GPL-v3).
Package-Manager: portage-2.2.28
sci-libs/libmaus2/libmaus2-9999.ebuild | 27 +++++++++++++++++++++++++++
sci-libs/libmaus2/metadata.xml | 20 ++++++++++++++++++++
2 files changed, 47 insertions(+)
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
new file mode 100644
index 0000000..ae02d15
--- /dev/null
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+inherit autotools git-r3
+
+DESCRIPTION="Library for biobambam"
+HOMEPAGE="https://github.com/gt1/libmaus"
+EGIT_REPO_URI="https://github.com/gt1/libmaus2.git"
+
+LICENSE="GPL-3" # BUG: a mix of licenses, see AUTHORS
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+ !sci-libs/libmaus
+ sci-libs/io_lib
+ app-arch/snappy
+ sci-biology/seqan"
+
+src_prepare() {
+ eautoreconf
+ eapply_user
+}
diff --git a/sci-libs/libmaus2/metadata.xml b/sci-libs/libmaus2/metadata.xml
new file mode 100644
index 0000000..1541e62
--- /dev/null
+++ b/sci-libs/libmaus2/metadata.xml
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <longdescription lang="en">
+libmaus is a collection of data structures and algorithms. It contains
+
+I/O classes (single byte and UTF-8)
+ bitio classes (input, output and various forms of bit level manipulation)
+ text indexing classes (suffix and LCP array, fulltext and minute (FM), ...)
+ BAM sequence alignment files input/output (simple and collating)
+ and many lower level support classes.
+</longdescription>
+ <upstream>
+ <remote-id type="github">gt1/libmaus</remote-id>
+ </upstream>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2016-07-15 9:06 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2016-07-15 9:06 UTC (permalink / raw
To: gentoo-commits
commit: e842de446a9e5dfa46b57f023e3e7fe878bdf168
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 15 09:06:33 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 15 09:06:33 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e842de44
sc-libs/libmaus2: minor polishing
Package-Manager: portage-2.2.28
sci-libs/libmaus2/libmaus2-9999.ebuild | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
index ae02d15..ebbf8ca 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -6,7 +6,7 @@ EAPI=6
inherit autotools git-r3
-DESCRIPTION="Library for biobambam"
+DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus"
EGIT_REPO_URI="https://github.com/gt1/libmaus2.git"
@@ -25,3 +25,8 @@ src_prepare() {
eautoreconf
eapply_user
}
+
+pkg_postinst(){
+ einfo "The io_lib, snappy and seqan dependencies are not strictly needed"
+ einfo "but were forced for optimal libmaus2 performance."
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2017-04-18 12:09 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2017-04-18 12:09 UTC (permalink / raw
To: gentoo-commits
commit: 51fe11a3b2a3519a325f9cb86f1b27ea0cf9ec62
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 18 12:09:06 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 18 12:09:06 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=51fe11a3
sci-libs/libmaus2: make configure to enable optional but highly wanted features
The configure by default has a number of features disables, and does not enable
the option. It somehow does not even try to look for headers and libs from say
snappy unless --enable-snappy was passed.
Try to blindly enable most of the features although it is not clear whether say
gnutls should be preferred over nettle, likewise when --enable-sse4 is any better
--enable-sse3 (and should not be enabled concurrently with it).
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-libs/libmaus2/libmaus2-9999.ebuild | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
index ab60eeb60..fcf29886d 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -12,19 +12,33 @@ EGIT_REPO_URI="https://github.com/gt1/libmaus2.git"
LICENSE="GPL-3" # BUG: a mix of licenses, see AUTHORS
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
DEPEND="
!sci-libs/libmaus
sci-libs/io_lib
app-arch/snappy
- sci-biology/seqan"
+ sci-biology/seqan
+ sci-libs/fftw
+ sci-libs/hdf5
+ net-libs/gnutls
+ dev-libs/nettle"
+# --with-daligner
+# --with-irods
src_prepare() {
eautoreconf
eapply_user
}
+src_configure(){
+ local CONFIG_OPTS
+ use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
+ ( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
+ econf --with-snappy --with-seqan --with-io_lib $CONFIG_OPTS \
+ --with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
+}
+
pkg_postinst(){
einfo "The io_lib, snappy and seqan dependencies are not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2017-04-29 19:25 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2017-04-29 19:25 UTC (permalink / raw
To: gentoo-commits
commit: 27def088978a406b829e839584cead93eb9a38c8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 29 19:25:37 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 29 19:25:37 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=27def088
sci-libs/libmaus2: Improve einfo based on upstream issue #19
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-libs/libmaus2/libmaus2-9999.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
index fcf29886d..d68a5d0e0 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -42,4 +42,5 @@ src_configure(){
pkg_postinst(){
einfo "The io_lib, snappy and seqan dependencies are not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
+ einfo "igzip is only used if gzip level is set to 11."
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2018-12-14 11:41 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2018-12-14 11:41 UTC (permalink / raw
To: gentoo-commits
commit: 4fdad4d5229ce714a6a2c7e91338be89c14e7fc4
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 14 11:40:50 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 14 11:40:50 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4fdad4d5
sci-libs/libmaus2: bring in a release, add more LICENSEs
The list of licenses is still incomplete and somebody more
comfortable with interpretation of them inside *.asm and other
files needs to poke over this before unmasking. See AUTHORS
file for their listing.
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
.../{libmaus2-9999.ebuild => libmaus2-2.0.499.ebuild} | 16 ++++++----------
sci-libs/libmaus2/libmaus2-9999.ebuild | 6 +++---
2 files changed, 9 insertions(+), 13 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-2.0.499.ebuild
similarity index 76%
copy from sci-libs/libmaus2/libmaus2-9999.ebuild
copy to sci-libs/libmaus2/libmaus2-2.0.499.ebuild
index d68a5d0e0..cebe44161 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.499.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-inherit autotools git-r3
+inherit autotools
DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus"
-EGIT_REPO_URI="https://github.com/gt1/libmaus2.git"
+SRC_URI="https://github.com/gt1/libmaus2/archive/2.0.499-release-20180606122508.tar.gz"
-LICENSE="GPL-3" # BUG: a mix of licenses, see AUTHORS
+LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
SLOT="0"
KEYWORDS=""
IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
@@ -25,11 +25,7 @@ DEPEND="
dev-libs/nettle"
# --with-daligner
# --with-irods
-
-src_prepare() {
- eautoreconf
- eapply_user
-}
+S="${WORKDIR}"/libmaus2-2.0.499-release-20180606122508
src_configure(){
local CONFIG_OPTS
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
index d68a5d0e0..01aa74a92 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit autotools git-r3
@@ -9,7 +9,7 @@ DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus"
EGIT_REPO_URI="https://github.com/gt1/libmaus2.git"
-LICENSE="GPL-3" # BUG: a mix of licenses, see AUTHORS
+LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
SLOT="0"
KEYWORDS=""
IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2019-01-22 15:18 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2019-01-22 15:18 UTC (permalink / raw
To: gentoo-commits
commit: 458e1564c2fa03fefffd8a8f9dc8975d95f26c3f
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 22 15:17:58 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 22 15:17:58 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=458e1564
sci-libs/libmaus2: upstream moved from github to gitlab
https://github.com/gt1/libmaus2/issues/28#issuecomment-456336598
Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
.../{libmaus2-2.0.499.ebuild => libmaus2-2.0.587.ebuild} | 15 +++++++--------
sci-libs/libmaus2/libmaus2-9999.ebuild | 11 +++++------
2 files changed, 12 insertions(+), 14 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-2.0.499.ebuild b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
similarity index 70%
rename from sci-libs/libmaus2/libmaus2-2.0.499.ebuild
rename to sci-libs/libmaus2/libmaus2-2.0.587.ebuild
index cebe44161..1c61df056 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.499.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,36 +7,35 @@ inherit autotools
DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus"
-SRC_URI="https://github.com/gt1/libmaus2/archive/2.0.499-release-20180606122508.tar.gz"
+SRC_URI="https://gitlab.com/german.tischler/libmaus2/-/archive/master/${P}.tar.gz"
LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
DEPEND="
!sci-libs/libmaus
- sci-libs/io_lib
+ >=sci-libs/io_lib-1.14.11
app-arch/snappy
- sci-biology/seqan
sci-libs/fftw
sci-libs/hdf5
net-libs/gnutls
dev-libs/nettle"
# --with-daligner
# --with-irods
-S="${WORKDIR}"/libmaus2-2.0.499-release-20180606122508
+S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
src_configure(){
local CONFIG_OPTS
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
- econf --with-snappy --with-seqan --with-io_lib $CONFIG_OPTS \
+ econf --with-snappy --with-io_lib $CONFIG_OPTS \
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
}
pkg_postinst(){
- einfo "The io_lib, snappy and seqan dependencies are not strictly needed"
+ einfo "The io_lib, snappy dependencies are not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
einfo "igzip is only used if gzip level is set to 11."
}
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
index 01aa74a92..c371d5432 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -7,7 +7,7 @@ inherit autotools git-r3
DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus"
-EGIT_REPO_URI="https://github.com/gt1/libmaus2.git"
+EGIT_REPO_URI="https://gitlab.com/german.tischler/libmaus2"
LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
SLOT="0"
@@ -16,9 +16,8 @@ IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
DEPEND="
!sci-libs/libmaus
- sci-libs/io_lib
+ >=sci-libs/io_lib-1.14.11
app-arch/snappy
- sci-biology/seqan
sci-libs/fftw
sci-libs/hdf5
net-libs/gnutls
@@ -35,12 +34,12 @@ src_configure(){
local CONFIG_OPTS
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
- econf --with-snappy --with-seqan --with-io_lib $CONFIG_OPTS \
+ econf --with-snappy --with-io_lib $CONFIG_OPTS \
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
}
pkg_postinst(){
- einfo "The io_lib, snappy and seqan dependencies are not strictly needed"
+ einfo "The io_lib, snappy dependencies are not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
einfo "igzip is only used if gzip level is set to 11."
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2019-12-30 15:14 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2019-12-30 15:14 UTC (permalink / raw
To: gentoo-commits
commit: 6a52a6c327152d555ec8699271d8d4445a27f285
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 30 15:14:45 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 30 15:14:45 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6a52a6c3
sci-libs/libmaus2: update the ebuild for gitlab.com site
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-libs/libmaus2/libmaus2-2.0.587.ebuild | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
index 1c61df056..593fe083f 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
@@ -5,9 +5,10 @@ EAPI=7
inherit autotools
+release_data="20190122104826"
DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus"
-SRC_URI="https://gitlab.com/german.tischler/libmaus2/-/archive/master/${P}.tar.gz"
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz -> ${P}.tar.gz"
LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
SLOT="0"
@@ -24,7 +25,10 @@ DEPEND="
dev-libs/nettle"
# --with-daligner
# --with-irods
-S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
+# old github.com release tarballs
+# S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
+# current gitlab.com release tarballs
+S="${WORKDIR}/${P}-release-${release_data}"
src_configure(){
local CONFIG_OPTS
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2019-12-30 15:20 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2019-12-30 15:20 UTC (permalink / raw
To: gentoo-commits
commit: 08a272766f1feb9206762a4c51839c55a9c7637d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 30 15:20:32 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 30 15:20:32 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=08a27276
sci-libs/libmaus2: version bump to 2.0.689
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-libs/libmaus2/libmaus2-2.0.689.ebuild | 45 +++++++++++++++++++++++++++++++
1 file changed, 45 insertions(+)
diff --git a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
new file mode 100644
index 000000000..50b82d5aa
--- /dev/null
+++ b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+release_data="20191120141844"
+DESCRIPTION="Library for biobambam2"
+HOMEPAGE="https://github.com/gt1/libmaus"
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
+
+DEPEND="
+ !sci-libs/libmaus
+ >=sci-libs/io_lib-1.14.11
+ app-arch/snappy
+ sci-libs/fftw
+ sci-libs/hdf5
+ net-libs/gnutls
+ dev-libs/nettle"
+# --with-daligner
+# --with-irods
+# old github.com release tarballs
+# S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
+# current gitlab.com release tarballs
+S="${WORKDIR}/${P}-release-${release_data}"
+
+src_configure(){
+ local CONFIG_OPTS
+ use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
+ ( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
+ econf --with-snappy --with-io_lib $CONFIG_OPTS \
+ --with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
+}
+
+pkg_postinst(){
+ einfo "The io_lib, snappy dependencies are not strictly needed"
+ einfo "but were forced for optimal libmaus2 performance."
+ einfo "igzip is only used if gzip level is set to 11."
+}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2019-12-30 15:37 Martin Mokrejs
0 siblings, 0 replies; 12+ messages in thread
From: Martin Mokrejs @ 2019-12-30 15:37 UTC (permalink / raw
To: gentoo-commits
commit: 14d6fe3e3263ff60126348989714159e9731e2a5
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 30 15:37:44 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 30 15:37:44 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=14d6fe3e
sci-libs/libmaus2: point to libmaus2 and to gitlab
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-libs/libmaus2/metadata.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-libs/libmaus2/metadata.xml b/sci-libs/libmaus2/metadata.xml
index 80f68639f..4b4685854 100644
--- a/sci-libs/libmaus2/metadata.xml
+++ b/sci-libs/libmaus2/metadata.xml
@@ -15,6 +15,6 @@ BAM sequence alignment files input/output (simple and collating)
and many lower level support classes.
</longdescription>
<upstream>
- <remote-id type="github">gt1/libmaus</remote-id>
+ <remote-id type="gitlab">german.tischler/libmaus2</remote-id>
</upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2020-09-28 7:31 Horea Christian
0 siblings, 0 replies; 12+ messages in thread
From: Horea Christian @ 2020-09-28 7:31 UTC (permalink / raw
To: gentoo-commits
commit: b886b4e53916c3c3ebf31f07c1fc1f375a128c40
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 07:17:54 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 07:17:54 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b886b4e5
sci-libs/libmaus2: updated dependencies
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-libs/libmaus2/libmaus2-2.0.587.ebuild | 13 +++++--------
sci-libs/libmaus2/libmaus2-2.0.689.ebuild | 13 +++++--------
sci-libs/libmaus2/libmaus2-9999.ebuild | 10 +++++-----
3 files changed, 15 insertions(+), 21 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
index 593fe083f..9be955b71 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -16,8 +16,6 @@ KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
DEPEND="
- !sci-libs/libmaus
- >=sci-libs/io_lib-1.14.11
app-arch/snappy
sci-libs/fftw
sci-libs/hdf5
@@ -25,21 +23,20 @@ DEPEND="
dev-libs/nettle"
# --with-daligner
# --with-irods
-# old github.com release tarballs
-# S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
-# current gitlab.com release tarballs
S="${WORKDIR}/${P}-release-${release_data}"
src_configure(){
local CONFIG_OPTS
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
- econf --with-snappy --with-io_lib $CONFIG_OPTS \
+ econf --with-snappy $CONFIG_OPTS \
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
+ # --with-io_lib
+ # will require >=sci-libs/io_lib-1.14.11 which is not yet available in ::gentoo
}
pkg_postinst(){
- einfo "The io_lib, snappy dependencies are not strictly needed"
+ einfo "The snappy dependency is not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
einfo "igzip is only used if gzip level is set to 11."
}
diff --git a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
index 50b82d5aa..ff5583090 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -16,8 +16,6 @@ KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
DEPEND="
- !sci-libs/libmaus
- >=sci-libs/io_lib-1.14.11
app-arch/snappy
sci-libs/fftw
sci-libs/hdf5
@@ -25,21 +23,20 @@ DEPEND="
dev-libs/nettle"
# --with-daligner
# --with-irods
-# old github.com release tarballs
-# S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
-# current gitlab.com release tarballs
S="${WORKDIR}/${P}-release-${release_data}"
src_configure(){
local CONFIG_OPTS
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
- econf --with-snappy --with-io_lib $CONFIG_OPTS \
+ econf --with-snappy $CONFIG_OPTS \
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
+ # --with-io_lib
+ # will require >=sci-libs/io_lib-1.14.11 which is not yet available in ::gentoo
}
pkg_postinst(){
- einfo "The io_lib, snappy dependencies are not strictly needed"
+ einfo "The snappy dependency is not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
einfo "igzip is only used if gzip level is set to 11."
}
diff --git a/sci-libs/libmaus2/libmaus2-9999.ebuild b/sci-libs/libmaus2/libmaus2-9999.ebuild
index c371d5432..d2cbd9439 100644
--- a/sci-libs/libmaus2/libmaus2-9999.ebuild
+++ b/sci-libs/libmaus2/libmaus2-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 2019 Gentoo Authors
+# Copyright 2019-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -15,8 +15,6 @@ KEYWORDS=""
IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
DEPEND="
- !sci-libs/libmaus
- >=sci-libs/io_lib-1.14.11
app-arch/snappy
sci-libs/fftw
sci-libs/hdf5
@@ -34,12 +32,14 @@ src_configure(){
local CONFIG_OPTS
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
- econf --with-snappy --with-io_lib $CONFIG_OPTS \
+ econf --with-snappy $CONFIG_OPTS \
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
+ # --with-io_lib
+ # will require >=sci-libs/io_lib-1.14.11 which is not yet available in ::gentoo
}
pkg_postinst(){
- einfo "The io_lib, snappy dependencies are not strictly needed"
+ einfo "The snappy dependency is not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
einfo "igzip is only used if gzip level is set to 11."
}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2020-09-28 7:31 Horea Christian
0 siblings, 0 replies; 12+ messages in thread
From: Horea Christian @ 2020-09-28 7:31 UTC (permalink / raw
To: gentoo-commits
commit: 6b93c27115efc381ba6dc195e2a4d32b98a23177
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Sep 28 07:28:26 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Sep 28 07:28:26 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6b93c271
sci-libs/libmaus2: dropped old version
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-libs/libmaus2/libmaus2-2.0.587.ebuild | 42 -------------------------------
1 file changed, 42 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
deleted file mode 100644
index 9be955b71..000000000
--- a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 2019-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit autotools
-
-release_data="20190122104826"
-DESCRIPTION="Library for biobambam2"
-HOMEPAGE="https://github.com/gt1/libmaus"
-SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see AUTHORS
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
-
-DEPEND="
- app-arch/snappy
- sci-libs/fftw
- sci-libs/hdf5
- net-libs/gnutls
- dev-libs/nettle"
-# --with-daligner
-# --with-irods
-S="${WORKDIR}/${P}-release-${release_data}"
-
-src_configure(){
- local CONFIG_OPTS
- use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
- ( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && CONFIG_OPTS+=( --enable-sse4 )
- econf --with-snappy $CONFIG_OPTS \
- --with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp --with-fftw
- # --with-io_lib
- # will require >=sci-libs/io_lib-1.14.11 which is not yet available in ::gentoo
-}
-
-pkg_postinst(){
- einfo "The snappy dependency is not strictly needed"
- einfo "but were forced for optimal libmaus2 performance."
- einfo "igzip is only used if gzip level is set to 11."
-}
^ permalink raw reply related [flat|nested] 12+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
@ 2021-12-16 10:57 Andrew Ammerlaan
0 siblings, 0 replies; 12+ messages in thread
From: Andrew Ammerlaan @ 2021-12-16 10:57 UTC (permalink / raw
To: gentoo-commits
commit: 3dd3af665fd88792a77b7a3b40ed8f2052e1ef4d
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 16 10:46:16 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Dec 16 10:46:16 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3dd3af66
sci-libs/libmaus2: drop UnusedInherits
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-libs/libmaus2/libmaus2-2.0.689.ebuild | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
index ff5583090..4b50c2030 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
@@ -1,10 +1,8 @@
-# Copyright 2019-2020 Gentoo Authors
+# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-inherit autotools
-
release_data="20191120141844"
DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus"
^ permalink raw reply related [flat|nested] 12+ messages in thread
end of thread, other threads:[~2021-12-16 10:57 UTC | newest]
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2020-09-28 7:31 Horea Christian
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2019-01-22 15:18 Martin Mokrejs
2018-12-14 11:41 Martin Mokrejs
2017-04-29 19:25 Martin Mokrejs
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