[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/
commit: f5a3b3f1fc417be8e9577e8e7a85d2aa6fa5db42
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Jan 25 13:10:25 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Jan 25 13:10:25 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f5a3b3f1
sci-biology/primerD: drop dead package
last update 2012!
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/primerD/metadata.xml | 12 -
sci-biology/primerD/primerD-1.0.0.ebuild | 42
2 files changed, 54 deletions(-)
diff --git a/sci-biology/primerD/metadata.xml b/sci-biology/primerD/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/primerD/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild
b/sci-biology/primerD/primerD-1.0.0.ebuild
deleted file mode 100644
index 6d46832a9..0
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Design degenerate primers"
-HOMEPAGE="https://mblab.wustl.edu/software.html;
-SRC_URI="primerD.tar.gz"
-#SRC_URI="https://mblab.wustl.edu/software/download/primerD.tar.gz ->
primerD-1.0.tar.gz"
-# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon
RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
-# Unable to locally verify the issuer's authority.
-# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
-RESTRICT="fetch"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-# make: *** No rule to make target '/usr/include/linux/new.h', needed by
'Main.o'. Stop.
-KEYWORDS=""
-
-S="${WORKDIR}"/primerD
-
-src_prepare(){
- default
- sed -i -e "s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}:" \
- -e
"s:/usr/include/g++-3/stl_algobase.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/bits/stl_algobase.h:g" \
- -e
"s:/usr/include/g++-3/stl_relops.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/bits/stl_relops.h:g" \
- -e
"s:/usr/include/g++-3/stl_pair.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/bits/stl_pair.h:g" \
- -e
"s:/usr/include/g++-3/type_traits.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/ext/type_traits.h:g" \
- -e
"s:/usr/include/g++-3/stl_config.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/pstl/pstl_config.h:g" \
- -e
"s:/usr/include/g++-3/:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/:g" \
- -e "s:/usr/include/_G_config.h:/usr/include/stdio.h:g" \
- -e
"s:/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/:/usr/include/linux/:g" \
- Makefile || die
-
-}
-
-src_install(){
- dodoc README
- dobin primerD
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/
commit: 66034a17eb03ca7e7d8ef90bcaabd5adcc5ed8cf Author: Andrew Ammerlaan gentoo org> AuthorDate: Tue Aug 31 09:39:17 2021 + Commit: Andrew Ammerlaan gentoo org> CommitDate: Tue Aug 31 09:39:17 2021 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=66034a17 sci-biology/primerD: move RESTRICT Package-Manager: Portage-3.0.22, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/primerD/primerD-1.0.0.ebuild | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild b/sci-biology/primerD/primerD-1.0.0.ebuild index b5365336a..6d46832a9 100644 --- a/sci-biology/primerD/primerD-1.0.0.ebuild +++ b/sci-biology/primerD/primerD-1.0.0.ebuild @@ -7,12 +7,12 @@ inherit toolchain-funcs DESCRIPTION="Design degenerate primers" HOMEPAGE="https://mblab.wustl.edu/software.html; +SRC_URI="primerD.tar.gz" #SRC_URI="https://mblab.wustl.edu/software/download/primerD.tar.gz -> primerD-1.0.tar.gz" # ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’: # Unable to locally verify the issuer's authority. # To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'. RESTRICT="fetch" -SRC_URI="primerD.tar.gz" LICENSE="LGPL-2.1" SLOT="0"
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/
commit: 38747aba5b528c356618d31da8f9275c0d7b618d
Author: Andrew Ammerlaan riseup net>
AuthorDate: Wed Feb 3 06:33:43 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Wed Feb 3 06:33:43 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=38747aba
sci-biology/primerD: fix some include statements
though it still does not compile
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/primerD/primerD-1.0.0.ebuild | 14 +-
1 file changed, 13 insertions(+), 1 deletion(-)
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild
b/sci-biology/primerD/primerD-1.0.0.ebuild
index 1aefce6cb..b5365336a 100644
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ b/sci-biology/primerD/primerD-1.0.0.ebuild
@@ -16,12 +16,24 @@ SRC_URI="primerD.tar.gz"
LICENSE="LGPL-2.1"
SLOT="0"
+# make: *** No rule to make target '/usr/include/linux/new.h', needed by
'Main.o'. Stop.
KEYWORDS=""
S="${WORKDIR}"/primerD
src_prepare(){
- sed -e "s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}:" -i Makefile
|| die
+ default
+ sed -i -e "s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}:" \
+ -e
"s:/usr/include/g++-3/stl_algobase.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/bits/stl_algobase.h:g" \
+ -e
"s:/usr/include/g++-3/stl_relops.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/bits/stl_relops.h:g" \
+ -e
"s:/usr/include/g++-3/stl_pair.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/bits/stl_pair.h:g" \
+ -e
"s:/usr/include/g++-3/type_traits.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/ext/type_traits.h:g" \
+ -e
"s:/usr/include/g++-3/stl_config.h:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/pstl/pstl_config.h:g" \
+ -e
"s:/usr/include/g++-3/:/usr/lib/gcc/${CHOST}/$(gcc-fullversion)/include/g++-v$(gcc-major-version
)/:g" \
+ -e "s:/usr/include/_G_config.h:/usr/include/stdio.h:g" \
+ -e
"s:/usr/lib/gcc-lib/i386-redhat-linux/2.96/include/:/usr/include/linux/:g" \
+ Makefile || die
+
}
src_install(){
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/
commit: db6da9e797597d6c9ea43fce8adf4af218c013fc
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Fri Feb 13 21:50:14 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Fri Feb 13 21:50:14 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=db6da9e7
edit the bundled Makefile
Package-Manager: portage-2.2.15
---
sci-biology/primerD/ChangeLog| 5 -
sci-biology/primerD/primerD-1.0.0.ebuild | 13 +
2 files changed, 17 insertions(+), 1 deletion(-)
diff --git a/sci-biology/primerD/ChangeLog b/sci-biology/primerD/ChangeLog
index 55298f3..f98ebf8 100644
--- a/sci-biology/primerD/ChangeLog
+++ b/sci-biology/primerD/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 13 Feb 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+ primerD-1.0.0.ebuild:
+ edit the bundled Makefile
+
10 Jan 2015; Justin Lecher j...@gentoo.org primerD-1.0.0.ebuild:
Fix license
@@ -10,4 +14,3 @@
07 Jan 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+primerD-1.0.0.ebuild, +metadata.xml:
ebuild skeleton
-
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild
b/sci-biology/primerD/primerD-1.0.0.ebuild
index 2dbabc8..a77c039 100644
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ b/sci-biology/primerD/primerD-1.0.0.ebuild
@@ -4,6 +4,8 @@
EAPI=5
+inherit toolchain-funcs
+
DESCRIPTION=Design degenerate primers
HOMEPAGE=http://mblab.wustl.edu/software.html;
SRC_URI=http://mblab.wustl.edu/software/download/primerD.tar.gz -
primerD-1.0.tar.gz
@@ -12,3 +14,14 @@ LICENSE=LGPL-2.1
SLOT=0
KEYWORDS=
IUSE=
+
+S=${WORKDIR}/primerD
+
+src_prepare(){
+ sed -e s:CC=g++:CC=$(tc-getCXX):; s:-Wall -g:${CFLAGS}: -i Makefile
|| die
+}
+
+src_install(){
+ dodoc README
+ dobin primerD
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/
commit: 682702ad64751e60f5208af904c5f900f3931c5d
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Sat Jan 10 14:35:02 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sat Jan 10 14:35:02 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=682702ad
sci-biology/primerD: Fix license
Package-Manager: portage-2.2.15
---
sci-biology/primerD/ChangeLog| 3 +++
sci-biology/primerD/primerD-1.0.0.ebuild | 5 +
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/primerD/ChangeLog b/sci-biology/primerD/ChangeLog
index f75108a..55298f3 100644
--- a/sci-biology/primerD/ChangeLog
+++ b/sci-biology/primerD/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Justin Lecher j...@gentoo.org primerD-1.0.0.ebuild:
+ Fix license
+
*primerD-1.0.0 (07 Jan 2015)
07 Jan 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild
b/sci-biology/primerD/primerD-1.0.0.ebuild
index 21163db..2dbabc8 100644
--- a/sci-biology/primerD/primerD-1.0.0.ebuild
+++ b/sci-biology/primerD/primerD-1.0.0.ebuild
@@ -8,10 +8,7 @@ DESCRIPTION=Design degenerate primers
HOMEPAGE=http://mblab.wustl.edu/software.html;
SRC_URI=http://mblab.wustl.edu/software/download/primerD.tar.gz -
primerD-1.0.tar.gz
-LICENSE=
+LICENSE=LGPL-2.1
SLOT=0
KEYWORDS=
IUSE=
-
-DEPEND=
-RDEPEND=${DEPEND}
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/, sci-biology/InterMine/, sci-biology/ucsc-genome-browser/, ...
commit: 2c54fbea31de3d8b20ca965d780805fdf20dd018
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Wed Jan 7 20:42:52 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Wed Jan 7 20:42:52 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2c54fbea
Revert sci-biology/blue: Initial ebuild, does not install the *.exe.so files.
Do we need them?
This reverts commit b79af8f82794f511181ab43aa0c20871a4d39723.
---
sci-biology/Atlas/Atlas-2005.ebuild| 18
sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild | 22 -
sci-biology/CAutils/CAutils-20120126.ebuild| 20
sci-biology/InterMine/InterMine-0.98.ebuild| 3 -
sci-biology/MochiView/MochiView-1.45.ebuild| 18
.../ampliconnoise/ampliconnoise-1.27.ebuild| 20
sci-biology/bioperl/bioperl-1.6.901.ebuild | 81
sci-biology/bioperl/metadata.xml | 5 -
sci-biology/blue/ChangeLog | 10 --
sci-biology/blue/blue-1.1.2.ebuild | 31 --
sci-biology/blue/metadata.xml | 9 --
sci-biology/ePCR/ePCR-2.3.12.ebuild| 34 ---
sci-biology/ePCR/files/config.mk.patch | 18
sci-biology/est2assembly/est2assembly-1.08.ebuild | 26 -
sci-biology/jigsaw/jigsaw-3.2.10.ebuild| 2 -
sci-biology/pb-honey/pb-honey-14.1.15.ebuild | 25 -
sci-biology/pb-jelly/pb-jelly-14.1.14.ebuild | 22 -
sci-biology/primerD/primerD-1.0.0.ebuild | 3 -
sci-biology/pvmsx/metadata.xml | 9 --
sci-biology/pvmsx/pvmsx-0.1.ebuild | 46 -
.../tigr-closure/tigr-closure-20080106.ebuild | 66 -
sci-biology/ucsc-genome-browser/metadata.xml | 12 ---
.../ucsc-genome-browser-260.ebuild | 106 -
23 files changed, 606 deletions(-)
diff --git a/sci-biology/Atlas/Atlas-2005.ebuild
b/sci-biology/Atlas/Atlas-2005.ebuild
deleted file mode 100644
index 8400820..000
--- a/sci-biology/Atlas/Atlas-2005.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION=Atlas Whole Genome Assembly Suite
-HOMEPAGE=https://www.hgsc.bcm.edu/software/atlas-whole-genome-assembly-suite;
-SRC_URI=https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas-src.tgz;
-#
https://www.hgsc.bcm.edu/sites/default/files/software/Atlas/atlas2005-linux.tgz
-
-LICENSE=
-SLOT=0
-KEYWORDS=~amd64
-IUSE=
-
-DEPEND=
-RDEPEND=${DEPEND}
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
deleted file mode 100644
index b918714..000
--- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=5
-
-DESCRIPTION=Close gaps using BWA-identified reads and reassemble using Phrap,
Newbler, Velvet, compare by cross_match
-HOMEPAGE=https://www.hgsc.bcm.edu/software/atlas-gapfill;
-SRC_URI=https://www.hgsc.bcm.edu/sites/default/files/software/ATLAS_GapFill_V2_2/ATLAS_GapFill_V2.2_release.tar.bz2;
-
-LICENSE=
-SLOT=0
-KEYWORDS=~amd64
-IUSE=
-
-# is there an ebuild for newbler?
-DEPEND=dev-lang/perl
- (sys-cluster/torque || sys/cluster/openpbs)
- sci-biology/phrap
- sci-biology/bwa
- sci-biology/velvet
-RDEPEND=${DEPEND}
diff --git a/sci-biology/CAutils/CAutils-20120126.ebuild
b/sci-biology/CAutils/CAutils-20120126.ebuild
deleted file mode 100644
index 7b1ca7b..000
--- a/sci-biology/CAutils/CAutils-20120126.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=3
-
-DESCRIPTION=Additional utilities for Celera assembler (wgs-assembler) from
UMD
-HOMEPAGE=http://www.cbcb.umd.edu/research/CeleraAssembler.shtml;
-SRC_URI=ftp://ftp.cbcb.umd.edu/pub/software/CAutils.tar.gz;
-
-LICENSE=
-SLOT=0
-KEYWORDS=~amd64 ~x86
-IUSE=
-
-DEPEND=
-RDEPEND=${DEPEND}
- dev-lang/perl
-
-# is partially included in amos-3.1.0
diff --git a/sci-biology/InterMine/InterMine-0.98.ebuild
b/sci-biology/InterMine/InterMine-0.98.ebuild
deleted file mode 100644
index a06fba7..000
--- a/sci-biology/InterMine/InterMine-0.98.ebuild
+++ /dev/null
@@ -1,3 +0,0 @@
-http://intermine.org/
-svn co svn://subversion.flymine.org/branches/intermine_0_98
-LGPL-3
diff --git a/sci-biology/MochiView/MochiView-1.45.ebuild
b/sci-biology/MochiView/MochiView-1.45.ebuild
deleted file mode 100644
index 5e9344a..000
--- a/sci-biology/MochiView/MochiView-1.45.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2012
[gentoo-commits] proj/sci:master commit in: sci-biology/primerD/
commit: 92575f215ce3ea9efcfa46326947ba00e4676742
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Wed Jan 7 21:41:02 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Wed Jan 7 21:41:02 2015 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=92575f21
ebuild skeleton
---
sci-biology/primerD/ChangeLog| 10 ++
sci-biology/primerD/metadata.xml | 9 +
sci-biology/primerD/primerD-1.0.0.ebuild | 17 +
3 files changed, 36 insertions(+)
diff --git a/sci-biology/primerD/ChangeLog b/sci-biology/primerD/ChangeLog
new file mode 100644
index 000..f75108a
--- /dev/null
+++ b/sci-biology/primerD/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/primerD
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*primerD-1.0.0 (07 Jan 2015)
+
+ 07 Jan 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+ +primerD-1.0.0.ebuild, +metadata.xml:
+ ebuild skeleton
+
diff --git a/sci-biology/primerD/metadata.xml b/sci-biology/primerD/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/primerD/metadata.xml
@@ -0,0 +1,9 @@
+?xml version=1.0 encoding=UTF-8?
+!DOCTYPE pkgmetadata SYSTEM http://www.gentoo.org/dtd/metadata.dtd;
+pkgmetadata
+ herdsci-biology/herd
+ maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin Mokrejs/name
+ /maintainer
+/pkgmetadata
diff --git a/sci-biology/primerD/primerD-1.0.0.ebuild
b/sci-biology/primerD/primerD-1.0.0.ebuild
new file mode 100644
index 000..21163db
--- /dev/null
+++ b/sci-biology/primerD/primerD-1.0.0.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION=Design degenerate primers
+HOMEPAGE=http://mblab.wustl.edu/software.html;
+SRC_URI=http://mblab.wustl.edu/software/download/primerD.tar.gz -
primerD-1.0.tar.gz
+
+LICENSE=
+SLOT=0
+KEYWORDS=
+IUSE=
+
+DEPEND=
+RDEPEND=${DEPEND}
