[gentoo-commits] proj/sci:master commit in: sci-biology/mgblast/
commit: 2175a5c65e6a29e243f25f7d1e237874d08020f0
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Tue Aug 31 09:28:05 2021 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Tue Aug 31 09:28:05 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2175a5c6
sci-biology/mgblast: remove last-rited pack
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/mgblast/metadata.xml | 12
sci-biology/mgblast/mgblast-0.1.ebuild | 34 --
2 files changed, 46 deletions(-)
diff --git a/sci-biology/mgblast/metadata.xml b/sci-biology/mgblast/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/mgblast/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/mgblast/mgblast-0.1.ebuild
b/sci-biology/mgblast/mgblast-0.1.ebuild
deleted file mode 100644
index 9eb877c27..0
--- a/sci-biology/mgblast/mgblast-0.1.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Customized version of megablast from TIGR Gene Indices project"
-HOMEPAGE="https://web.archive.org/web/20140726030702/http://compbio.dfci.harvard.edu/tgi/software/;
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz
-> ${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="sci-biology/ncbi-tools"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-# mgblast needs old version of ncbi-tools unpacked and compiled during its own
compilation
-# from newer tools you need to include blfmtutl.h but the next error is no go
for me:
-# mgblast.c:2205: error: too few arguments to function
‘BXMLBuildOneQueryIteration’
-
-# Quoting from mgblast/README: the present package was built and tested only
with the release 20060507
-
-src_prepare(){
- # mgblast cannot be compiled against newer ncbi-tools but let's try
- mv makefile Makefile 2>/dev/null || true
- sed -i -e 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#' \
- -e's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' \
- -e's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#' \
- -e 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' \
- -e "s#-I-#-iquote#" Makefile || die # a PATH to NCBI-TOOLKIT
(/usr/lib) while NOT /usr/lib/ncbi-tools++ !
- default
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/mgblast/
commit: 601aa9b78c9e572dd6676cf00942de9e1c0ec2b0
Author: Andrew Ammerlaan riseup net>
AuthorDate: Mon Feb 1 11:19:09 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Mon Feb 1 11:19:09 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=601aa9b7
sci-biology/mgblast: EAPI bump
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/mgblast/mgblast-0.1.ebuild | 29 +
1 file changed, 9 insertions(+), 20 deletions(-)
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild
b/sci-biology/mgblast/mgblast-0.1.ebuild
index 354836e22..3a2d3d7a6 100644
--- a/sci-biology/mgblast/mgblast-0.1.ebuild
+++ b/sci-biology/mgblast/mgblast-0.1.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
DESCRIPTION="Customized version of megablast from TIGR Gene Indices project"
HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/;
@@ -9,14 +9,12 @@
SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz
LICENSE="Artistic"
SLOT="0"
-KEYWORDS="" # upstream binary is provided by sci-biology/tgicl currently
-#KEYWORDS="~amd64 ~x86"
-IUSE=""
+KEYWORDS=""
DEPEND="sci-biology/ncbi-tools"
RDEPEND="${DEPEND}"
-S="${WORKDIR}"
+S="${WORKDIR}/${PN}"
# mgblast needs old version of ncbi-tools unpacked and compiled during its own
compilation
# from newer tools you need to include blfmtutl.h but the next error is no go
for me:
@@ -26,20 +24,11 @@ S="${WORKDIR}"
src_prepare(){
# mgblast cannot be compiled against newer ncbi-tools but let's try
- mv mgblast/makefile mgblast/Makefile 2>/dev/null || true
- sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#'
mgblast/Makefile || die
- sed -i 's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' mgblast/Makefile
|| die
- sed -i 's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#'
mgblast/Makefile || die
- sed -i 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' mgblast/Makefile ||
die # a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ !
- sed -i "s#-I-#-iquote#" mgblast/Makefile || die
-}
-
-src_compile(){
- cd "${S}"/mgblast || die
+ mv makefile Makefile 2>/dev/null || true
+ sed -i -e 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#' \
+ -e's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' \
+ -e's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#' \
+ -e 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' \
+ -e "s#-I-#-iquote#" Makefile || die # a PATH to NCBI-TOOLKIT
(/usr/lib) while NOT /usr/lib/ncbi-tools++ !
default
}
-
-src_install(){
- cd "${S}"/mgblast || die
- dobin mgblast
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/mgblast/
commit: 7cad083e4ed170d3fb56323e672a8c364eed6cb5
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 19 16:23:06 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 19 16:23:06 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7cad083e
sci-biology/mgblast: properly name tarball
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/mgblast/mgblast-0.1.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild
b/sci-biology/mgblast/mgblast-0.1.ebuild
index 1f7a63ec8..354836e22 100644
--- a/sci-biology/mgblast/mgblast-0.1.ebuild
+++ b/sci-biology/mgblast/mgblast-0.1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
DESCRIPTION="Customized version of megablast from TIGR Gene Indices project"
HOMEPAGE="http://compbio.dfci.harvard.edu/tgi/software/;
-SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz;
+SRC_URI="ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz
-> ${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
[gentoo-commits] proj/sci:master commit in: sci-biology/mgblast/
commit: aada253938880482eb9e52d146948e062aaea848
Author: Christoph Junghans ottxor AT gentoo DOT org
AuthorDate: Tue Sep 16 16:24:23 2014 +
Commit: Christoph Junghans ottxor AT gentoo DOT org
CommitDate: Tue Sep 16 16:24:23 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aada2539
clean up
Package-Manager: portage-2.2.8-r1
---
sci-biology/mgblast/ChangeLog | 4 +++-
sci-biology/mgblast/mgblast-0.1.ebuild | 20 ++--
2 files changed, 13 insertions(+), 11 deletions(-)
diff --git a/sci-biology/mgblast/ChangeLog b/sci-biology/mgblast/ChangeLog
index 5b62270..8a87f81 100644
--- a/sci-biology/mgblast/ChangeLog
+++ b/sci-biology/mgblast/ChangeLog
@@ -2,10 +2,12 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Sep 2014; Christoph Junghans ott...@gentoo.org mgblast-0.1.ebuild:
+ clean up
+
*mgblast-0.1 (24 Mar 2014)
24 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+mgblast-0.1.ebuild, +metadata.xml:
initial ebuild but while it needs an old version of ncbi-tools source tree to
build ... it is not tested yet
-
diff --git a/sci-biology/mgblast/mgblast-0.1.ebuild
b/sci-biology/mgblast/mgblast-0.1.ebuild
index 8b7011a..4638e9b 100644
--- a/sci-biology/mgblast/mgblast-0.1.ebuild
+++ b/sci-biology/mgblast/mgblast-0.1.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
DESCRIPTION=Customized version of megablast from TIGR Gene Indices project
used by tgicl and gicl utilities
HOMEPAGE=http://compbio.dfci.harvard.edu/tgi/software/;
@@ -17,7 +17,7 @@ IUSE=
DEPEND=sci-biology/ncbi-tools
RDEPEND=${DEPEND}
-S=${WORKDIR}
+S=${WORKDIR}
# mgblast needs old version of ncbi-tools unpacked and compiled during its own
compilation
# from newer tools you need to include blfmtutl.h but the next error is no go
for me:
@@ -28,19 +28,19 @@ S=${WORKDIR}
src_prepare(){
# mgblast cannot be compiled against newer ncbi-tools but let's try
mv mgblast/makefile mgblast/Makefile 2/dev/null || true
- sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#'
mgblast/Makefile
- sed -i 's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' mgblast/Makefile
- sed -i 's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#'
mgblast/Makefile
- sed -i 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' mgblast/Makefile #
a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ !
- sed -i s#-I-#-iquote# mgblast/Makefile
+ sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#'
mgblast/Makefile || die
+ sed -i 's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' mgblast/Makefile
|| die
+ sed -i 's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#'
mgblast/Makefile || die
+ sed -i 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' mgblast/Makefile ||
die # a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ !
+ sed -i s#-I-#-iquote# mgblast/Makefile || die
}
src_compile(){
- cd ${S}/mgblast || die
+ cd ${S}/mgblast || die
emake || die mgblast really needs an older ncbi-toolkit version so we
are out of luck, install the binary provided by upstream instead from
mgblast-bin package
}
src_install(){
- cd ${S}/mgblast || die
- dobin mgblast || die
+ cd ${S}/mgblast || die
+ dobin mgblast
}
[gentoo-commits] proj/sci:master commit in: sci-biology/mgblast/
commit: 2c576304e6b594c5423610448a39bb68e75d47ea
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Mon Mar 24 11:53:41 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Mon Mar 24 11:53:41 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2c576304
sci-biology/mgblast: initial ebuild but while it needs an old version of
ncbi-tools source tree to build ... it is not tested yet
---
sci-biology/mgblast/ChangeLog | 11
sci-biology/mgblast/metadata.xml | 9 +++
sci-biology/mgblast/mgblast-0.1.ebuild | 46 ++
3 files changed, 66 insertions(+)
diff --git a/sci-biology/mgblast/ChangeLog b/sci-biology/mgblast/ChangeLog
new file mode 100644
index 000..5b62270
--- /dev/null
+++ b/sci-biology/mgblast/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/mgblast
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mgblast-0.1 (24 Mar 2014)
+
+ 24 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+ +mgblast-0.1.ebuild, +metadata.xml:
+ initial ebuild but while it needs an old version of ncbi-tools source tree to
+ build ... it is not tested yet
+
diff --git a/sci-biology/mgblast/metadata.xml b/sci-biology/mgblast/metadata.xml
new file mode 100644
index 000..07b5255
--- /dev/null
+++ b/sci-biology/mgblast/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/mgblast/mgblast-0.1.ebuild
b/sci-biology/mgblast/mgblast-0.1.ebuild
new file mode 100644
index 000..8b7011a
--- /dev/null
+++ b/sci-biology/mgblast/mgblast-0.1.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION=Customized version of megablast from TIGR Gene Indices project
used by tgicl and gicl utilities
+HOMEPAGE=http://compbio.dfci.harvard.edu/tgi/software/;
+SRC_URI=ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/mgblast.tar.gz;
+
+LICENSE=Artistic
+SLOT=0
+KEYWORDS= # upstream binary is provided by sci-biology/tgicl currently
+#KEYWORDS=~amd64 ~x86
+IUSE=
+
+DEPEND=sci-biology/ncbi-tools
+RDEPEND=${DEPEND}
+
+S=${WORKDIR}
+
+# mgblast needs old version of ncbi-tools unpacked and compiled during its own
compilation
+# from newer tools you need to include blfmtutl.h but the next error is no go
for me:
+# mgblast.c:2205: error: too few arguments to function
‘BXMLBuildOneQueryIteration’
+
+# Quoting from mgblast/README: the present package was built and tested only
with the release 20060507
+
+src_prepare(){
+ # mgblast cannot be compiled against newer ncbi-tools but let's try
+ mv mgblast/makefile mgblast/Makefile 2/dev/null || true
+ sed -i 's#/usr/local/projects/tgi/ncbitoolkit/ncbi#/usr#'
mgblast/Makefile
+ sed -i 's#NCBIDIR = /mylocal/src/ncbi#NCBIDIR = /usr#' mgblast/Makefile
+ sed -i 's#NCBI_INCDIR = .*#NCBI_INCDIR = /usr/include/ncbi#'
mgblast/Makefile
+ sed -i 's#NCBI_LIBDIR = .*#NCBI_LIBDIR = /usr/lib#' mgblast/Makefile #
a PATH to NCBI-TOOLKIT (/usr/lib) while NOT /usr/lib/ncbi-tools++ !
+ sed -i s#-I-#-iquote# mgblast/Makefile
+}
+
+src_compile(){
+ cd ${S}/mgblast || die
+ emake || die mgblast really needs an older ncbi-toolkit version so we
are out of luck, install the binary provided by upstream instead from
mgblast-bin package
+}
+
+src_install(){
+ cd ${S}/mgblast || die
+ dobin mgblast || die
+}
