* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2015-01-09 16:13 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-01-09 16:13 UTC (permalink / raw
To: gentoo-commits
commit: 04e413e188afb955661634805f602e744d3ec5c4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 9 16:12:34 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 9 16:12:34 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=04e413e1
sci-biology/ESTate: new package
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 9 +++++++++
sci-biology/ESTate/ESTate-0.5.ebuild | 32 ++++++++++++++++++++++++++++++++
sci-biology/ESTate/metadata.xml | 9 +++++++++
3 files changed, 50 insertions(+)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
new file mode 100644
index 0000000..52cfa8c
--- /dev/null
+++ b/sci-biology/ESTate/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/ESTate
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ESTate-0.5 (09 Jan 2015)
+
+ 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +ESTate-0.5.ebuild,
+ +metadata.xml:
+ sci-biology/ESTate: new package
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
new file mode 100644
index 0000000..5b9f468
--- /dev/null
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="EST clustering tools (estcluster, usage counter, revcomp and translate)"
+HOMEPAGE="http://www.ebi.ac.uk/~guy/estate"
+SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/estate
+
+src_prepare(){
+ sed -e "s/^CC/#CC/" -e "s/^LDFLAGS/#LDFLAGS/" -e "s/^CFLAGS/#CFLAGS/" -e "s/LDFLAGS/CFLAGS/" -i src/Makefile || die
+}
+
+src_install(){
+ dobin bin/*
+ doman doc/man/man1/*.1 doc/man/man7/*.7
+ insinto /usr/share/ESTate/etc
+ doins etc/ESTaterc
+ dodoc ANNOUNCE.txt README.txt
+ einfo "Additionally you may want to install sci-biology/wcd which can be used by ESTate"
+}
diff --git a/sci-biology/ESTate/metadata.xml b/sci-biology/ESTate/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/ESTate/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2015-01-09 17:15 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-01-09 17:15 UTC (permalink / raw
To: gentoo-commits
commit: 319bfe2c5fe2d5ffc011000547a814696300a8ff
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 9 17:14:11 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 9 17:14:11 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=319bfe2c
add the PhD thesis itself as documentation
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 4 +++-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 52cfa8c..6ae928b 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
+ add the PhD thesis itself as documentation
+
*ESTate-0.5 (09 Jan 2015)
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +ESTate-0.5.ebuild,
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
index 5b9f468..989e5f2 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -6,7 +6,8 @@ EAPI=5
DESCRIPTION="EST clustering tools (estcluster, usage counter, revcomp and translate)"
HOMEPAGE="http://www.ebi.ac.uk/~guy/estate"
-SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz"
+SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz
+ http://www.ebi.ac.uk/~guy/estate/thesis.ps.gz"
LICENSE="GPL-2"
SLOT="0"
@@ -28,5 +29,6 @@ src_install(){
insinto /usr/share/ESTate/etc
doins etc/ESTaterc
dodoc ANNOUNCE.txt README.txt
+ dodoc "${DISTDIR}"/thesis.ps.gz
einfo "Additionally you may want to install sci-biology/wcd which can be used by ESTate"
}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2015-01-09 17:30 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-01-09 17:30 UTC (permalink / raw
To: gentoo-commits
commit: 72826ae7fd740933822987a2922daaa22dbb26d8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 9 17:29:47 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 9 17:29:47 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=72826ae7
add the probability matrices
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 2 ++
2 files changed, 5 insertions(+)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 6ae928b..628daf7 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -3,6 +3,9 @@
# $Header: $
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
+ add the probability matrices
+
+ 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
add the PhD thesis itself as documentation
*ESTate-0.5 (09 Jan 2015)
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
index 989e5f2..54704d4 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -28,6 +28,8 @@ src_install(){
doman doc/man/man1/*.1 doc/man/man7/*.7
insinto /usr/share/ESTate/etc
doins etc/ESTaterc
+ doins /usr/share/ESTate/example
+ doins example/embl59* example/drosophila*
dodoc ANNOUNCE.txt README.txt
dodoc "${DISTDIR}"/thesis.ps.gz
einfo "Additionally you may want to install sci-biology/wcd which can be used by ESTate"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2015-01-09 17:34 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-01-09 17:34 UTC (permalink / raw
To: gentoo-commits
commit: 74d14fc07ea7c08a447ef8f9d5e14b360f868af2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 9 17:33:22 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 9 17:33:22 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=74d14fc0
use 'insinto' and not 'doins'
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 628daf7..c5cae89 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -3,6 +3,9 @@
# $Header: $
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
+ use 'insinto' and not 'doins'
+
+ 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
add the probability matrices
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
index 54704d4..7fc7970 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -28,7 +28,7 @@ src_install(){
doman doc/man/man1/*.1 doc/man/man7/*.7
insinto /usr/share/ESTate/etc
doins etc/ESTaterc
- doins /usr/share/ESTate/example
+ insinto /usr/share/ESTate/example
doins example/embl59* example/drosophila*
dodoc ANNOUNCE.txt README.txt
dodoc "${DISTDIR}"/thesis.ps.gz
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2015-01-09 17:56 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-01-09 17:56 UTC (permalink / raw
To: gentoo-commits
commit: 1665dd570b59a6962d18316b9e65f672747f1c88
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jan 9 17:55:46 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 9 17:55:46 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1665dd57
improve description and emphasize the ORF finder can overcome frameshifts in CDS
Package-Manager: portage-2.2.7
---
sci-biology/ESTate/ChangeLog | 4 ++++
sci-biology/ESTate/ESTate-0.5.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index c5cae89..0e86bdb 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -3,6 +3,10 @@
# $Header: $
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
+ improve description and emphasize the ORF finder can overcome frameshifts in
+ CDS
+
+ 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
use 'insinto' and not 'doins'
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
index 7fc7970..3e459b0 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -4,7 +4,7 @@
EAPI=5
-DESCRIPTION="EST clustering tools (estcluster, usage counter, revcomp and translate)"
+DESCRIPTION="ORF finding despite frameshifts, EST clustering (framefinder, estcluster, usage counter, revcomp and translate)"
HOMEPAGE="http://www.ebi.ac.uk/~guy/estate"
SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz
http://www.ebi.ac.uk/~guy/estate/thesis.ps.gz"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2015-01-10 14:37 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-01-10 14:37 UTC (permalink / raw
To: gentoo-commits
commit: fb4ef931e8f0177f06753635416595180b789995
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 14:17:58 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 14:17:58 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fb4ef931
sci-biology/ESTate: Soma QA and polishing
Package-Manager: portage-2.2.15
---
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 28 +++++++++++++++++++---------
2 files changed, 22 insertions(+), 9 deletions(-)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 0e86bdb..879e7b4 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> ESTate-0.5.ebuild:
+ Soma QA and polishing
+
09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
improve description and emphasize the ORF finder can overcome frameshifts in
CDS
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
index 3e459b0..1622516 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -4,9 +4,12 @@
EAPI=5
-DESCRIPTION="ORF finding despite frameshifts, EST clustering (framefinder, estcluster, usage counter, revcomp and translate)"
+inherit eutils
+
+DESCRIPTION="ORF finding despite frameshifts, EST clustering"
HOMEPAGE="http://www.ebi.ac.uk/~guy/estate"
-SRC_URI="http://www.ebi.ac.uk/~guy/estate/estate.tar.gz
+SRC_URI="
+ http://www.ebi.ac.uk/~guy/estate/estate.tar.gz
http://www.ebi.ac.uk/~guy/estate/thesis.ps.gz"
LICENSE="GPL-2"
@@ -14,23 +17,30 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND=""
-RDEPEND="${DEPEND}"
-
S="${WORKDIR}"/estate
src_prepare(){
- sed -e "s/^CC/#CC/" -e "s/^LDFLAGS/#LDFLAGS/" -e "s/^CFLAGS/#CFLAGS/" -e "s/LDFLAGS/CFLAGS/" -i src/Makefile || die
+ sed \
+ -e "s/^CC/#CC/" \
+ -e "s/^LDFLAGS/#LDFLAGS/" \
+ -e "s/^CFLAGS/#CFLAGS/" \
+ -e "s/LDFLAGS/CFLAGS/" \
+ -i src/Makefile || die
}
src_install(){
dobin bin/*
doman doc/man/man1/*.1 doc/man/man7/*.7
+
insinto /usr/share/ESTate/etc
doins etc/ESTaterc
+
insinto /usr/share/ESTate/example
doins example/embl59* example/drosophila*
- dodoc ANNOUNCE.txt README.txt
- dodoc "${DISTDIR}"/thesis.ps.gz
- einfo "Additionally you may want to install sci-biology/wcd which can be used by ESTate"
+
+ dodoc ANNOUNCE.txt README.txt "${DISTDIR}"/thesis.ps.gz
+}
+
+pkg_postinst() {
+ optfeature "additional features" sci-biology/wcd
}
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2015-04-18 0:55 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2015-04-18 0:55 UTC (permalink / raw
To: gentoo-commits
commit: 8bbbf78fcf81607816082c4e36840c972fde539d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 18 00:02:28 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 18 00:02:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8bbbf78f
sci-biology/ESTate: track file collision
Package-Manager: portage-2.2.18
sci-biology/ESTate/ChangeLog | 3 +++
sci-biology/ESTate/ESTate-0.5.ebuild | 5 +++++
2 files changed, 8 insertions(+)
diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog
index 879e7b4..7d523e9 100644
--- a/sci-biology/ESTate/ChangeLog
+++ b/sci-biology/ESTate/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild:
+ sci-biology/ESTate: track file collision
+
10 Jan 2015; Justin Lecher <jlec@gentoo.org> ESTate-0.5.ebuild:
Soma QA and polishing
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
index 1622516..63c8966 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -28,6 +28,11 @@ src_prepare(){
-i src/Makefile || die
}
+# Detected file collision(s) versus sci-biology/hmmer-2.3.2-r2:
+# * sci-biology/ESTate-0.5:0::science
+# * /usr/bin/revcomp
+# * /usr/bin/translate
+
src_install(){
dobin bin/*
doman doc/man/man1/*.1 doc/man/man7/*.7
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ESTate/
@ 2017-01-10 0:59 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2017-01-10 0:59 UTC (permalink / raw
To: gentoo-commits
commit: 932231c6e6287f4f77189a6ae65b5885e1c7419a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 00:31:44 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 00:31:44 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=932231c6
sci-biology/ESTate: avoid file collisions
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/ESTate/ESTate-0.5.ebuild | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild
index f48399d..aa66bcd 100644
--- a/sci-biology/ESTate/ESTate-0.5.ebuild
+++ b/sci-biology/ESTate/ESTate-0.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -28,12 +28,12 @@ src_prepare(){
-i src/Makefile || die
}
-# Detected file collision(s) versus sci-biology/hmmer-2.3.2-r2:
-# * sci-biology/ESTate-0.5:0::science
-# * /usr/bin/revcomp
-# * /usr/bin/translate
-
src_install(){
+ # prevent file collision with sci-biology/hmmer-2.3.2
+ newbin bin/{revcomp,revcomp_ESTate}
+ rm bin/revcomp || die
+ newbin bin/{translate,translate_ESTate}
+ rm bin/translate || die
dobin bin/*
doman doc/man/man1/*.1 doc/man/man7/*.7
^ permalink raw reply related [flat|nested] 8+ messages in thread
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