New upstream version (5.05). Removed 4.45 as sources are no longer available.

Package-Manager: portage-2.1.2.7

5 files changed, 39 insertions, 30 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index 1a630c6a439d..693b81f16bc8 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/t-coffee
 # Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.17 2007/03/09 02:43:13 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.18 2007/05/21 15:26:35 ribosome Exp $
+
+*t-coffee-5.05 (21 May 2007)
+
+  21 May 2007; Olivier Fisette <ribosome@gentoo.org> -t-coffee-4.45.ebuild,
+  +t-coffee-5.05.ebuild:
+  New upstream version (5.05). Removed 4.45 as sources are no longer available.
 
 *t-coffee-4.96 (09 Mar 2007)
 
diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
index 35c18c0a9b6b..0dd24199d49f 100644
--- a/sci-biology/t-coffee/Manifest
+++ b/sci-biology/t-coffee/Manifest
@@ -1,22 +1,22 @@
 DIST T-COFFEE_distribution_Version_3.84.tar.gz 1625217 RMD160 cda295fd0c2c432c8f802739a3748fcb01f40389 SHA1 b1ddedc7a1d756c6265c20a870e101d75942a1aa SHA256 1c062fe67b1817570fdce8f57999ce637863cc91b4feb91053ef805cc3f48eab
-DIST T-COFFEE_distribution_Version_4.45.tar.gz 2735436 RMD160 f05110dff0d05c852b9a72be7247ebe527a4649c SHA1 85f2608f220376f4a9793d1b6be7f99247cafbb1 SHA256 256675fdb3e438839a179c2ca5019a14045fcb346836c9c9c54581e7694d4ca3
 DIST T-COFFEE_distribution_Version_4.96.tar.gz 2863327 RMD160 d6a7722f1fe3b2a8b186fad49e8bc136d812b610 SHA1 b8ae0be131ae470f5aa596369afa9fc9fbc18701 SHA256 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213
+DIST T-COFFEE_distribution_Version_5.05.tar.gz 2869348 RMD160 edc62c922280ac627089d44997ce859b56950955 SHA1 be137ec323630dc3795deddc71663ece907ef0e8 SHA256 494be7bfca83ee9701fb0fc5aba829fff0592c11173b95f239e39390ca3eeae8
 EBUILD t-coffee-3.84.ebuild 1814 RMD160 2f89d06ef91f1946a0cb0178caeff16924f35dd3 SHA1 89744ef5e82c61bf0f77cad88f09d0806245fd16 SHA256 aad58deacb8762799f5dc443a1b34be4fa06fb54c0b42980ec23cbf5e4736595
 MD5 93fd7a0d063210749ad2817dca89df98 t-coffee-3.84.ebuild 1814
 RMD160 2f89d06ef91f1946a0cb0178caeff16924f35dd3 t-coffee-3.84.ebuild 1814
 SHA256 aad58deacb8762799f5dc443a1b34be4fa06fb54c0b42980ec23cbf5e4736595 t-coffee-3.84.ebuild 1814
-EBUILD t-coffee-4.45.ebuild 1882 RMD160 63d60a1c6fd7de29f8c5b10de9f66249a0918d11 SHA1 0c9bfd4742d8161df2a8e8c7df45ae6c35e0e64f SHA256 1e6cb93c8839abe8823e90e59fbf24acad28a49784a3786fe17526244db4523d
-MD5 05d9b62a0da700a27a5b180ac4799b03 t-coffee-4.45.ebuild 1882
-RMD160 63d60a1c6fd7de29f8c5b10de9f66249a0918d11 t-coffee-4.45.ebuild 1882
-SHA256 1e6cb93c8839abe8823e90e59fbf24acad28a49784a3786fe17526244db4523d t-coffee-4.45.ebuild 1882
 EBUILD t-coffee-4.96.ebuild 2005 RMD160 2d2fc3b8efac91c9701ef6324c9745d6eb77f194 SHA1 e1dbcaa2d1e1ca432f5e8301d30f410ec1debbdf SHA256 431fe23ac6bac5c85538658619041cbd7c2c7c5bd0e4381350323662d7f813b1
 MD5 e8914d250401ad84c7abdf9ba3907665 t-coffee-4.96.ebuild 2005
 RMD160 2d2fc3b8efac91c9701ef6324c9745d6eb77f194 t-coffee-4.96.ebuild 2005
 SHA256 431fe23ac6bac5c85538658619041cbd7c2c7c5bd0e4381350323662d7f813b1 t-coffee-4.96.ebuild 2005
-MISC ChangeLog 2584 RMD160 c1d40253336ab1809fb94a887b3f2076b7d38e0b SHA1 d800935c83b571df47cab77dccbfa3123b3e168a SHA256 bf4ec6936c46f6d7b662ef19dec1a26247e59c4891a17e5d8aeaf06b9e92e36e
-MD5 e52ad059fd1f9a9f1788512592769b2f ChangeLog 2584
-RMD160 c1d40253336ab1809fb94a887b3f2076b7d38e0b ChangeLog 2584
-SHA256 bf4ec6936c46f6d7b662ef19dec1a26247e59c4891a17e5d8aeaf06b9e92e36e ChangeLog 2584
+EBUILD t-coffee-5.05.ebuild 2005 RMD160 c665bdb7ab535e892890c3f90a061d54b96f98b6 SHA1 393764d445552fcdacfef490110cc306c6343b9a SHA256 42b03b515deffcd59d5c39f52d4dd285610a3906d1ff66b289880fca8e2b307e
+MD5 de625fecc1501313b1ea88169530896f t-coffee-5.05.ebuild 2005
+RMD160 c665bdb7ab535e892890c3f90a061d54b96f98b6 t-coffee-5.05.ebuild 2005
+SHA256 42b03b515deffcd59d5c39f52d4dd285610a3906d1ff66b289880fca8e2b307e t-coffee-5.05.ebuild 2005
+MISC ChangeLog 2796 RMD160 a891aaf09fe9a6cf4bd3fbf55d2fede10e6c7867 SHA1 a4ef5a7781c3fe93131ea38614d53ab6e7ed381d SHA256 270cd47c24956bc351d8641b76ece4e75183d3da3d74f31967e82a29e5ba3c0e
+MD5 5ecb88ae00a657af9eda0d798db75c3b ChangeLog 2796
+RMD160 a891aaf09fe9a6cf4bd3fbf55d2fede10e6c7867 ChangeLog 2796
+SHA256 270cd47c24956bc351d8641b76ece4e75183d3da3d74f31967e82a29e5ba3c0e ChangeLog 2796
 MISC metadata.xml 763 RMD160 1163b25c489923e806ccf77dd3b4b5a486da0c28 SHA1 9a6b86bfa165e9b7c0a9b8631990bbfb727fe410 SHA256 8ff6c199eb54e1a49903130ed1aebbe32a0c0b1698aaec2044530c27533270a2
 MD5 d5530b7c0b5defb31d0e1ad80fad02d6 metadata.xml 763
 RMD160 1163b25c489923e806ccf77dd3b4b5a486da0c28 metadata.xml 763
@@ -24,9 +24,9 @@ SHA256 8ff6c199eb54e1a49903130ed1aebbe32a0c0b1698aaec2044530c27533270a2 metadata
 MD5 8663d9c02294b9417b3c82f0e9d3a570 files/digest-t-coffee-3.84 307
 RMD160 e234918666e5de1a15e6a0ccb831d7597608a08a files/digest-t-coffee-3.84 307
 SHA256 6717825503db3a5cc4d64a2506dc81d25498dcc2625f37eb64c8df50c25462f9 files/digest-t-coffee-3.84 307
-MD5 d81db5e2bd9495765fd8434602d640a7 files/digest-t-coffee-4.45 307
-RMD160 511f979bf54572e7339a99d3b1f748c33667ba29 files/digest-t-coffee-4.45 307
-SHA256 b3b5f1aca6ea37a586fd0763776d63b5c228b12c15630cbc6b3b8d0e444d5520 files/digest-t-coffee-4.45 307
 MD5 f59bcfecf86c8b4729dc646cfe693047 files/digest-t-coffee-4.96 307
 RMD160 1813cba165d62ee51fcecbcc5f04fe587374a5c9 files/digest-t-coffee-4.96 307
 SHA256 2a6ffaf1bef9217315fb872171f49b5810002e900edb2ecc136d9a9f24503d7c files/digest-t-coffee-4.96 307
+MD5 56d859aa293b43ac7c981e8e10b5dbc0 files/digest-t-coffee-5.05 307
+RMD160 b35e86ce914c46e0f661a07dcd54896e1a92027c files/digest-t-coffee-5.05 307
+SHA256 6caf3d7baff8202f79d5201ee4ab95ccba5cac470e67827c28aa8c7e32c5f9b5 files/digest-t-coffee-5.05 307
diff --git a/sci-biology/t-coffee/files/digest-t-coffee-4.45 b/sci-biology/t-coffee/files/digest-t-coffee-4.45
deleted file mode 100644
index fee157903763..000000000000
--- a/sci-biology/t-coffee/files/digest-t-coffee-4.45
+++ /dev/null
@@ -1,3 +0,0 @@
-MD5 5d3e15767206720f4aff82ffea8bfb40 T-COFFEE_distribution_Version_4.45.tar.gz 2735436
-RMD160 f05110dff0d05c852b9a72be7247ebe527a4649c T-COFFEE_distribution_Version_4.45.tar.gz 2735436
-SHA256 256675fdb3e438839a179c2ca5019a14045fcb346836c9c9c54581e7694d4ca3 T-COFFEE_distribution_Version_4.45.tar.gz 2735436
diff --git a/sci-biology/t-coffee/files/digest-t-coffee-5.05 b/sci-biology/t-coffee/files/digest-t-coffee-5.05
new file mode 100644
index 000000000000..c72c1bd320c8
--- /dev/null
+++ b/sci-biology/t-coffee/files/digest-t-coffee-5.05
@@ -0,0 +1,3 @@
+MD5 aee1a51c8a73580de4e1c9c2de140b9b T-COFFEE_distribution_Version_5.05.tar.gz 2869348
+RMD160 edc62c922280ac627089d44997ce859b56950955 T-COFFEE_distribution_Version_5.05.tar.gz 2869348
+SHA256 494be7bfca83ee9701fb0fc5aba829fff0592c11173b95f239e39390ca3eeae8 T-COFFEE_distribution_Version_5.05.tar.gz 2869348
diff --git a/sci-biology/t-coffee/t-coffee-4.45.ebuild b/sci-biology/t-coffee/t-coffee-5.05.ebuild
index 1af0091b2ebb..bbd2fef331d0 100644
--- a/sci-biology/t-coffee/t-coffee-4.45.ebuild
+++ b/sci-biology/t-coffee/t-coffee-5.05.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2006 Gentoo Foundation
+# Copyright 1999-2007 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-4.45.ebuild,v 1.1 2006/09/13 23:52:04 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-5.05.ebuild,v 1.1 2007/05/21 15:26:35 ribosome Exp $
 
 inherit toolchain-funcs flag-o-matic
 
 DESCRIPTION="A multiple sequence alignment package"
 LICENSE="t-coffee"
-HOMEPAGE="http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html"
-SRC_URI="http://igs-server.cnrs-mrs.fr/~cnotred/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz"
+HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_${PV}.tar.gz"
 
 SLOT="0"
 IUSE=""
@@ -42,18 +42,21 @@ src_compile() {
 }
 
 src_install() {
-	cd "${TCDIR}"/bin
-	dobin t_coffee || die "Failed to install program."
-	insinto /usr/share/${PN}/lib/html
-	doins ${TCDIR}/html/* || die "Failed to install HTML documentation,"
+	dobin "${TCDIR}"/bin/t_coffee || die "Failed to install program."
 
-	dodoc ${TCDIR}/doc/README4T-COFFEE || die \
-		"Failed to install basic documentation."
+	insinto /usr/share/${PN}/lib/html
+	doins "${TCDIR}"/html/* || die "Failed to install Web interface files."
+
+	cd "${TCDIR}"/doc
+	dodoc aln_compare.doc.txt README4T-COFFEE seq_reformat.doc.txt \
+			t_coffee_technical.txt t_coffee_tutorial.txt || die \
+			"Failed to install text documentation."
+	dohtml t_coffee_technical.htm t_coffee_tutorial.htm || die \
+			"Failed to install HTML documentation."
 	insinto /usr/share/doc/${PF}
-	doins ${TCDIR}/doc/t_coffee{_doc.{doc,pdf},.pdf} || die \
-		"Failed to install manuals and articles."
-	doins ${TCDIR}/doc/*.txt || die "Failed to install documentation."
+	doins t_coffee.pdf t_coffee_technical.doc t_coffee_tutorial.doc || die \
+	"Failed to install DOC and PDF documentation."
 
 	insinto /usr/share/${PN}/example
-	doins ${TCDIR}/example/* || die "Failed to install example files."
+	doins "${TCDIR}"/example/* || die "Failed to install example files."
 }