* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/, sci-biology/amos/files/
@ 2015-03-31 20:19 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-03-31 20:19 UTC (permalink / raw
To: gentoo-commits
commit: 8e3157e581a2503912b86bb5e48fb73e82c26cc9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 31 20:18:38 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 31 20:18:38 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e3157e5
sci-biology/amos: fix installation process and dependencies
Package-Manager: portage-2.2.18
sci-biology/amos/ChangeLog | 9 ++-
sci-biology/amos/amos-3.1.0-r2.ebuild | 66 ++++++++++++++++++++++
sci-biology/amos/amos-9999.ebuild | 27 ++++++++-
sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 +++++
...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 ++++++++
5 files changed, 138 insertions(+), 4 deletions(-)
diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog
index 7d1df6d..9bdce77 100644
--- a/sci-biology/amos/ChangeLog
+++ b/sci-biology/amos/ChangeLog
@@ -1,7 +1,14 @@
# ChangeLog for sci-biology/amos
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*amos-3.1.0-r2 (31 Mar 2015)
+
+ 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +amos-3.1.0-r2.ebuild, +files/amos-3.1.0-gcc-4.7.patch,
+ +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, amos-9999.ebuild:
+ sci-biology/amos: fix installation process and dependencies
+
29 Dec 2013; Justin Lecher <jlec@gentoo.org> -amos-3.1.0-r1.ebuild,
amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch,
-files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch,
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
new file mode 100644
index 0000000..b814791
--- /dev/null
+++ b/sci-biology/amos/amos-3.1.0-r2.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0-r1.ebuild,v 1.1 2013/12/29 00:24:16 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils python-r1
+
+DESCRIPTION="A Modular, Open-Source whole genome assembler"
+HOMEPAGE="http://amos.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="qt4"
+
+DEPEND="
+ dev-libs/boost
+ qt4? ( dev-qt/qtcore:4 )"
+RDEPEND="${DEPEND}
+ dev-lang/perl
+ dev-perl/DBI
+ dev-perl/Statistics-Descriptive
+ sci-biology/blat
+ sci-biology/mummer"
+
+MAKEOPTS+=" -j1"
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-gcc-4.7.patch \
+ "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch
+}
+
+# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/DotLib.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/Bambus/Untangler/AsmLib.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAreader.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosFoundation.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/Foundation.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/AmosLib.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTArecord.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/ParseFasta.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/xfig.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAwriter.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAgrammar.pm
+# amos-3.1.0-r2/work/amos-3.1.0/src/PerlModules/FASTAiterator.pm
+
+# --with-jellyfish location of Jellyfish headers
+
+src_install() {
+ default
+ python_replicate_script "${ED}"/usr/bin/goBambus2
+ # bambus needs TIGR::FASTAreader.pm and others
+ # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
+ mkdir -p "${D}"/usr/share/"${PN}"/perl/AMOS || die
+ mv "${D}"/usr/lib64/AMOS/*.pm "${D}"/usr/share/"${PN}"/perl/AMOS || die
+ mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}" || die
+ # move also /usr/lib64/AMOS/AMOS.py to /usr/bin
+ mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index baecc2f..610c3d6 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -16,11 +16,32 @@ EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
LICENSE="Artistic"
SLOT="0"
KEYWORDS=""
-IUSE=""
+IUSE="mpi qt4"
DEPEND="
+ mpi? ( virtual/mpi )
dev-libs/boost
- dev-qt/qtcore:4"
+ qt4? ( dev-qt/qtcore:4 )
+ sci-biology/blat
+ sci-biology/jellyfish"
RDEPEND="${DEPEND}
dev-perl/DBI
+ dev-perl/Statistics-Descriptive
sci-biology/mummer"
+
+# --with-jellyfish location of Jellyfish headers
+
+src_install() {
+ default
+ python_replicate_script "${ED}"/usr/bin/goBambus2
+ # bambus needs TIGR::FASTAreader.pm and others
+ # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
+ mkdir -p "${D}/usr/share/${PN}/perl/AMOS" || die
+ mv "${D}"/usr/lib64/AMOS/*.pm "${D}/usr/share/${PN}/perl/AMOS" || die
+ mkdir -p "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ mv "${D}"/usr/lib64/TIGR/*.pm "${D}"/usr/share/"${PN}"/perl/TIGR || die
+ echo "PERL5LIB=/usr/share/${PN}/perl" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}" || die
+ # move also /usr/lib64/AMOS/AMOS.py to /usr/bin
+ mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
+}
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
new file mode 100644
index 0000000..de2a411
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ src/Align/find-tandem.cc | 1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
+index ddf1cab..a29e21e 100644
+--- a/src/Align/find-tandem.cc
++++ b/src/Align/find-tandem.cc
+@@ -7,6 +7,7 @@
+ #include <vector>
+ #include <ctime>
+ #include <sys/time.h>
++#include <unistd.h>
+ using namespace std;
+
+ const int OFFSET_TABLE_SIZE = 100;
diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
new file mode 100644
index 0000000..97a8f59
--- /dev/null
+++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
@@ -0,0 +1,25 @@
+--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200
++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200
+@@ -1,7 +1,7 @@
+ #pipeline script for assembly + Bambus 2
+ #contributed by Todd J Treangen
+
+-import string, sys, os, subprocess#, spincursor
++import sys, os, subprocess#, spincursor
+
+ RED = "\033[0;31m"
+ GREEN = "\033[0;32m"
+@@ -360,7 +360,7 @@
+ print "\t\t%s...failed%s"%(RED,NONE)
+ sys.exit(1)
+
+- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
+
+ if xopt_dict["verbose"] == 1:
+ print "10) running OutputResults"
+@@ -388,4 +388,3 @@
+ else:
+ print "\t\t%s...failed%s"%(RED,NONE)
+ sys.exit(1)
+-)
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/, sci-biology/amos/files/
@ 2018-03-07 12:29 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2018-03-07 12:29 UTC (permalink / raw
To: gentoo-commits
commit: 2b34e4019d8a95ce7efd7db67337571a8dfd18be
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 7 12:29:13 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 7 12:29:13 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b34e401
sci-biology/amos: fix include path from -I$(top_builddir) to -I$(top_builddir)
The include path is wrong when we use separate build directory.
In file included from src/Bambus/Bundler/Utilities_Bundler.cc:4:0:
src/Bambus/Bundler/Utilities_Bundler.hh:16:26: fatal error: Contig_AMOS.hh: No such file or directory
https://sourceforge.net/p/amos/mailman/amos-help/thread/197db37d-d83e-1371-022b-2866c5686bd9%40fold.natur.cuni.cz/#msg36246774
Package-Manager: Portage-2.3.24, Repoman-2.3.6
sci-biology/amos/amos-9999.ebuild | 14 +++++++++++++-
sci-biology/amos/files/amos-9999-fix-include-paths.patch | 13 +++++++++++++
2 files changed, 26 insertions(+), 1 deletion(-)
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
index 97ae851a3..2c911603d 100644
--- a/sci-biology/amos/amos-9999.ebuild
+++ b/sci-biology/amos/amos-9999.ebuild
@@ -3,8 +3,10 @@
EAPI=5
+PYTHON_COMPAT=( python2_7 )
+
PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-module eutils toolchain-funcs autotools flag-o-matic python-single-r1 qmake-utils
AUTOTOOLS_AUTORECONF=true
inherit autotools-utils git-r3
@@ -37,6 +39,16 @@ RDEPEND="${DEPEND}
# ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
# $
+src_prepare() {
+ epatch "${FILESDIR}"/"${P}"-fix-include-paths.patch
+ default
+ eautoreconf
+
+ # prevent GCC 6 log pollution due
+ # to hash_map deprecation in C++11
+ append-cxxflags -Wno-cpp
+}
+
src_install() {
default
python_replicate_script "${ED}"/usr/bin/goBambus2
diff --git a/sci-biology/amos/files/amos-9999-fix-include-paths.patch b/sci-biology/amos/files/amos-9999-fix-include-paths.patch
new file mode 100644
index 000000000..a6e8dc9f0
--- /dev/null
+++ b/sci-biology/amos/files/amos-9999-fix-include-paths.patch
@@ -0,0 +1,13 @@
+--- src/Bambus/Bundler/Makefile.am.old 2018-07-03 12:52:17.306095693 +0200
++++ src/Bambus/Bundler/Makefile.am 2018-07-03 12:52:19.506101530 +0200
+@@ -78,8 +78,8 @@
+ ##-- libBundler.a
+ libBundler_a_CPPFLAGS = \
+ $(BOOST_CXXFLAGS) \
+- -I$(top_builddir)/src/GNU \
+- -I$(top_builddir)/src/AMOS
++ -I$(top_srcdir)/src/GNU \
++ -I$(top_srcdir)/src/AMOS
+ ## because some system headers will be built if necessary
+ libBundler_a_LIBADD = \
+ $(LIBOBJS:%=$(top_builddir)/src/GNU/%) \
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/amos/, sci-biology/amos/files/
@ 2020-02-03 4:02 Benda XU
0 siblings, 0 replies; 3+ messages in thread
From: Benda XU @ 2020-02-03 4:02 UTC (permalink / raw
To: gentoo-commits
commit: 435cdfbb48bf8efd38cb3198230758bd599aeac3
Author: Benda Xu <heroxbd <AT> gentoo <DOT> org>
AuthorDate: Mon Feb 3 03:22:24 2020 +0000
Commit: Benda XU <heroxbd <AT> gentoo <DOT> org>
CommitDate: Mon Feb 3 04:02:34 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=435cdfbb
sci-biology/amos: remove from tree.
1. No upstream development since 2011.
2. Does not support Python 3.
Bug: https://bugs.gentoo.org/707558
Signed-off-by: Benda Xu <heroxbd <AT> gentoo.org>
sci-biology/amos/amos-3.1.0-r2.ebuild | 76 ----------------------
sci-biology/amos/amos-9999.ebuild | 76 ----------------------
sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 -----
...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 -------
.../files/amos-3.1.0-rename_to_jellyfish1.patch | 43 ------------
.../amos/files/amos-9999-fix-include-paths.patch | 13 ----
sci-biology/amos/metadata.xml | 21 ------
7 files changed, 269 deletions(-)
diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild
deleted file mode 100644
index 951f12c1b..000000000
--- a/sci-biology/amos/amos-3.1.0-r2.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-inherit eutils python-r1
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
-
-DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
-HOMEPAGE="http://amos.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi qt5"
-
-DEPEND="
- mpi? ( virtual/mpi )
- dev-libs/boost
- qt5? ( dev-qt/qtcore:5 )
- sci-biology/blat
- sci-biology/jellyfish:1"
-RDEPEND="${DEPEND}
- dev-lang/perl
- dev-perl/DBI
- dev-perl/Statistics-Descriptive
- sci-biology/mummer"
-
-MAKEOPTS+=" -j1"
-
-src_prepare() {
- epatch \
- "${FILESDIR}"/${P}-gcc-4.7.patch \
- "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch \
- "${FILESDIR}"/${P}-rename_to_jellyfish1.patch
- # $ gap-links
- # ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
- # $
- sh ./bootstrap || die
- default
- eautoreconf
- # prevent GCC 6 log pollution due to hash_map deprecation in C++11
- # shutdown gcc-8.2.0 messages too
- append-cxxflags -Wno-cpp -Wno-narrowing
-}
-
-src_configure() {
- local myconf
- use X && myconf+=( --with-x )
- econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all
-}
-
-src_install() {
- default
- python_replicate_script "${ED}"/usr/bin/goBambus2
- # bambus needs TIGR::FASTAreader.pm and others
- # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
- perl_set_version
- insinto ${VENDOR_LIB}/AMOS
- doins "${D}"/usr/lib64/AMOS/*.pm
- insinto ${VENDOR_LIB}/TIGR
- doins "${D}"/usr/lib64/TIGR/*.pm
- # move also /usr/lib64/AMOS/AMOS.py to /usr/bin
- mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
- # zap the mis-placed files ('make install' is at fault)
- rm -f "${D}"/usr/lib64/AMOS/*.pm
- rm -rf "${D}"/usr/lib64/TIGR
- echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
- mkdir -p "${ED}"/etc || die
- touch "${ED}"/etc/amos.acf || die
- doenvd "${S}/99amos"
-}
diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild
deleted file mode 100644
index 923ac5978..000000000
--- a/sci-biology/amos/amos-9999.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs autotools flag-o-matic python-single-r1 qmake-utils
-
-AUTOTOOLS_AUTORECONF=true
-inherit autotools-utils git-r3
-
-DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies"
-HOMEPAGE="http://sourceforge.net/projects/amos"
-SRC_URI=""
-EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-IUSE="mpi qt5 X"
-
-DEPEND="
- mpi? ( virtual/mpi )
- dev-libs/boost
- qt5? ( dev-qt/qtcore:5 )
- sci-biology/blat
- sci-biology/jellyfish:1"
-RDEPEND="${DEPEND}
- dev-perl/DBI
- dev-perl/Statistics-Descriptive
- sci-biology/mummer"
-
-# $ gap-links
-# ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/
-# $
-
-src_prepare() {
- epatch "${FILESDIR}"/"${P}"-fix-include-paths.patch
- epatch "${FILESDIR}"/amos-3.1.0-rename_to_jellyfish1.patch
- sh ./bootstrap || die
- default
- eautoreconf
-
- # prevent GCC 6 log pollution due to hash_map deprecation in C++11
- # shutdown gcc-8.2.0 messages too
- append-cxxflags -Wno-cpp -Wno-narrowing
-}
-
-src_configure() {
- local myconf
- use X && myconf+=( --with-x )
- econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all
-}
-
-src_install() {
- default
- python_replicate_script "${ED}"/usr/bin/goBambus2
- # bambus needs TIGR::FASTAreader.pm and others
- # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it
- perl_set_version
- insinto ${VENDOR_LIB}/AMOS
- doins "${D}"/usr/lib64/AMOS/*.pm
- insinto ${VENDOR_LIB}/TIGR
- doins "${D}"/usr/lib64/TIGR/*.pm
- # move also /usr/lib64/AMOS/AMOS.py to /usr/bin
- mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die
- # zap the mis-placed files ('make install' is at fault)
- rm -f "${D}"/usr/lib64/AMOS/*.pm
- rm -rf "${D}"/usr/lib64/TIGR
- echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die
- mkdir -p "${ED}"/etc || die
- touch "${ED}"/etc/amos.acf || die
- doenvd "${S}/99amos"
-}
diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
deleted file mode 100644
index de2a41184..000000000
--- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch
+++ /dev/null
@@ -1,15 +0,0 @@
- src/Align/find-tandem.cc | 1 +
- 1 files changed, 1 insertions(+), 0 deletions(-)
-
-diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc
-index ddf1cab..a29e21e 100644
---- a/src/Align/find-tandem.cc
-+++ b/src/Align/find-tandem.cc
-@@ -7,6 +7,7 @@
- #include <vector>
- #include <ctime>
- #include <sys/time.h>
-+#include <unistd.h>
- using namespace std;
-
- const int OFFSET_TABLE_SIZE = 100;
diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
deleted file mode 100644
index 97a8f59d0..000000000
--- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200
-+++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200
-@@ -1,7 +1,7 @@
- #pipeline script for assembly + Bambus 2
- #contributed by Todd J Treangen
-
--import string, sys, os, subprocess#, spincursor
-+import sys, os, subprocess#, spincursor
-
- RED = "\033[0;31m"
- GREEN = "\033[0;32m"
-@@ -360,7 +360,7 @@
- print "\t\t%s...failed%s"%(RED,NONE)
- sys.exit(1)
-
-- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
-+ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile)
-
- if xopt_dict["verbose"] == 1:
- print "10) running OutputResults"
-@@ -388,4 +388,3 @@
- else:
- print "\t\t%s...failed%s"%(RED,NONE)
- sys.exit(1)
--)
diff --git a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch
deleted file mode 100644
index 4b52c5640..000000000
--- a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- config/amos.m4 2018-09-11 13:23:14.478444129 +0200
-+++ config/amos.m4 2018-09-11 13:36:36.697612245 +0200
-@@ -695,15 +695,15 @@
- else
- jellyfish_unspecified=no
- fi
--if ! test -f "$jellyfish_dir/jellyfish/mer_counting.hpp"; then
-+if ! test -f "$jellyfish_dir/jellyfish1/mer_counting.hpp"; then
- if test $jellyfish_unspecified = no; then
-- AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish/compacted_hash.hpp"])
-+ AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish1/compacted_hash.hpp"])
- fi
- JELLYFISH_LDADD=
- JELLYFISH_CPPFLAGS=
- AC_MSG_RESULT([not found])
- else
-- JELLYFISH_LDADD="-ljellyfish -lpthread"
-+ JELLYFISH_LDADD="-ljellyfish-1.1 -lpthread"
- JELLYFISH_CPPFLAGS="-I $jellyfish_dir"
- AC_DEFINE([WITH_JELLYFISH], [1], [Define to 1 if using Jellyfish])
- cppflags_save="$CPPFLAGS"
-@@ -715,7 +715,7 @@
- AC_LANG_PUSH([C++])
- AC_LINK_IFELSE([
- AC_LANG_PROGRAM([
--#include <jellyfish/mer_counting.hpp>
-+#include <jellyfish1/mer_counting.hpp>
- #include <string>
- ], [
- std::string s;
---- src/Align/kmer-cov-plot.cc 2018-09-11 13:23:15.079443556 +0200
-+++ src/Align/kmer-cov-plot.cc 2018-09-11 13:36:36.831612096 +0200
-@@ -388,8 +388,8 @@
-
- #ifdef WITH_JELLYFISH
-
--#include <jellyfish/compacted_hash.hpp>
--#include <jellyfish/mer_counting.hpp>
-+#include <jellyfish1/compacted_hash.hpp>
-+#include <jellyfish1/mer_counting.hpp>
-
- // Assert that jellyfish is using the expected kmer representation
- static void jellyfish_check()
diff --git a/sci-biology/amos/files/amos-9999-fix-include-paths.patch b/sci-biology/amos/files/amos-9999-fix-include-paths.patch
deleted file mode 100644
index a6e8dc9f0..000000000
--- a/sci-biology/amos/files/amos-9999-fix-include-paths.patch
+++ /dev/null
@@ -1,13 +0,0 @@
---- src/Bambus/Bundler/Makefile.am.old 2018-07-03 12:52:17.306095693 +0200
-+++ src/Bambus/Bundler/Makefile.am 2018-07-03 12:52:19.506101530 +0200
-@@ -78,8 +78,8 @@
- ##-- libBundler.a
- libBundler_a_CPPFLAGS = \
- $(BOOST_CXXFLAGS) \
-- -I$(top_builddir)/src/GNU \
-- -I$(top_builddir)/src/AMOS
-+ -I$(top_srcdir)/src/GNU \
-+ -I$(top_srcdir)/src/AMOS
- ## because some system headers will be built if necessary
- libBundler_a_LIBADD = \
- $(LIBOBJS:%=$(top_builddir)/src/GNU/%) \
diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml
deleted file mode 100644
index ddba4784f..000000000
--- a/sci-biology/amos/metadata.xml
+++ /dev/null
@@ -1,21 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <longdescription>
-AMOS is collection of tools and class interfaces for the assembly of DNA
-sequencing reads. The package includes a robust infrastructure, modular assembly
-pipelines, and tools for overlapping, consensus generation, contigging, and
-assembly manipulation
-</longdescription>
- <upstream>
- <remote-id type="sourceforge">amos</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
end of thread, other threads:[~2020-02-03 4:02 UTC | newest]
Thread overview: 3+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2018-03-07 12:29 [gentoo-commits] proj/sci:master commit in: sci-biology/amos/, sci-biology/amos/files/ Martin Mokrejs
-- strict thread matches above, loose matches on Subject: below --
2020-02-03 4:02 Benda XU
2015-03-31 20:19 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox