New upstream version

Package-Manager: portage-2.1-r1

19 files changed, 170 insertions, 8 deletions

diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog
index e9d176b07cf7..72c1a33d4380 100644
--- a/sci-biology/embassy-domainatrix/ChangeLog
+++ b/sci-biology/embassy-domainatrix/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/embassy-domainatrix
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.15 2006/07/20 21:00:24 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.16 2006/07/21 14:51:20 ribosome Exp $
+
+*embassy-domainatrix-0.1.0-r1 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-domainatrix-0.1.0-r1.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
 
   20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
   embassy-domainatrix-0.1.0.ebuild:
diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r1.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r1.ebuild
new file mode 100644
index 000000000000..8d966a232671
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r1.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.0-r1.ebuild,v 1.1 2006/07/21 14:51:20 ribosome Exp $
+
+EBOV="4.0.0"
+
+inherit embassy
+
+DESCRIPTION="Protein domain analysis add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+	mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="~ppc ~ppc-macos ~x86"
diff --git a/sci-biology/embassy-domainatrix/files/digest-embassy-domainatrix-0.1.0-r1 b/sci-biology/embassy-domainatrix/files/digest-embassy-domainatrix-0.1.0-r1
new file mode 100644
index 000000000000..e51c275c70ad
--- /dev/null
+++ b/sci-biology/embassy-domainatrix/files/digest-embassy-domainatrix-0.1.0-r1
@@ -0,0 +1,6 @@
+MD5 2ef912cfde4903129f2424d23d6da0d2 EMBOSS-4.0.0.tar.gz 17651607
+RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 EMBOSS-4.0.0.tar.gz 17651607
+SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 EMBOSS-4.0.0.tar.gz 17651607
+MD5 5893d3e5f101783050cbbc44766fe7d8 embassy-4.0.0-domainatrix-0.1.0.tar.gz 405474
+RMD160 65f60a617d1d59b2de530d7cdf0be6e77416a0b6 embassy-4.0.0-domainatrix-0.1.0.tar.gz 405474
+SHA256 efeb08f29cfd18a87fb54a448eb5b13a5805ae0d3a2d067563c8ff86feb1a1d7 embassy-4.0.0-domainatrix-0.1.0.tar.gz 405474
diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog
index 51ad18f6498c..0ba4c0b23f04 100644
--- a/sci-biology/embassy-domalign/ChangeLog
+++ b/sci-biology/embassy-domalign/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/embassy-domalign
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.5 2006/07/20 21:12:53 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.6 2006/07/21 14:52:32 ribosome Exp $
+
+*embassy-domalign-0.1.0-r1 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-domalign-0.1.0-r1.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
 
   20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
   embassy-domalign-0.1.0.ebuild:
diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r1.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r1.ebuild
new file mode 100644
index 000000000000..c89b46fc1362
--- /dev/null
+++ b/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r1.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/embassy-domalign-0.1.0-r1.ebuild,v 1.1 2006/07/21 14:52:32 ribosome Exp $
+
+EBOV="4.0.0"
+
+inherit embassy
+
+DESCRIPTION="Protein domain alignment add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+	mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="~ppc ~ppc-macos ~x86"
diff --git a/sci-biology/embassy-domalign/files/digest-embassy-domalign-0.1.0-r1 b/sci-biology/embassy-domalign/files/digest-embassy-domalign-0.1.0-r1
new file mode 100644
index 000000000000..8a4b499e844f
--- /dev/null
+++ b/sci-biology/embassy-domalign/files/digest-embassy-domalign-0.1.0-r1
@@ -0,0 +1,6 @@
+MD5 2ef912cfde4903129f2424d23d6da0d2 EMBOSS-4.0.0.tar.gz 17651607
+RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 EMBOSS-4.0.0.tar.gz 17651607
+SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 EMBOSS-4.0.0.tar.gz 17651607
+MD5 38ab9e0a0158cf923668d0e863606b54 embassy-4.0.0-domalign-0.1.0.tar.gz 440714
+RMD160 252202a6263d8da1166166610db836037f205ea3 embassy-4.0.0-domalign-0.1.0.tar.gz 440714
+SHA256 9abf35023e64229a103039d505bda23b0d3eef45d7cd79bdac14f2fe133764b6 embassy-4.0.0-domalign-0.1.0.tar.gz 440714
diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog
index 0dd257468938..b63d97bae7f5 100644
--- a/sci-biology/embassy-domsearch/ChangeLog
+++ b/sci-biology/embassy-domsearch/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/embassy-domsearch
 # Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.5 2006/07/20 21:19:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.6 2006/07/21 14:53:43 ribosome Exp $
+
+*embassy-domsearch-0.1.0-r1 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-domsearch-0.1.0-r1.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
 
   20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
   embassy-domsearch-0.1.0.ebuild:
diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r1.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r1.ebuild
new file mode 100644
index 000000000000..3e932e5fa0c2
--- /dev/null
+++ b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r1.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/embassy-domsearch-0.1.0-r1.ebuild,v 1.1 2006/07/21 14:53:43 ribosome Exp $
+
+EBOV="4.0.0"
+
+inherit embassy
+
+DESCRIPTION="Protein domain search add-on package for EMBOSS"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+	mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="~ppc ~ppc-macos ~x86"
diff --git a/sci-biology/embassy-domsearch/files/digest-embassy-domsearch-0.1.0-r1 b/sci-biology/embassy-domsearch/files/digest-embassy-domsearch-0.1.0-r1
new file mode 100644
index 000000000000..295864ec80bb
--- /dev/null
+++ b/sci-biology/embassy-domsearch/files/digest-embassy-domsearch-0.1.0-r1
@@ -0,0 +1,6 @@
+MD5 2ef912cfde4903129f2424d23d6da0d2 EMBOSS-4.0.0.tar.gz 17651607
+RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 EMBOSS-4.0.0.tar.gz 17651607
+SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 EMBOSS-4.0.0.tar.gz 17651607
+MD5 d214f124dd2806aa2eb163682dc7be7f embassy-4.0.0-domsearch-0.1.0.tar.gz 452839
+RMD160 8e7821127b1234708f9b03da9bdbca38e21666f2 embassy-4.0.0-domsearch-0.1.0.tar.gz 452839
+SHA256 d285d85b18dc34062a2c1ff3ec57bae552782ad982ca9cb0f7e5481e862fbbe3 embassy-4.0.0-domsearch-0.1.0.tar.gz 452839
diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog
index ec44cb77ff59..34ccbfec9ec7 100644
--- a/sci-biology/embassy-emnu/ChangeLog
+++ b/sci-biology/embassy-emnu/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/embassy-emnu
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.15 2006/07/20 19:36:45 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.16 2006/07/21 14:55:28 ribosome Exp $
+
+*embassy-emnu-1.05-r3 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-emnu-1.05-r3.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
 
   20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
   embassy-emnu-1.05-r2.ebuild:
diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05-r3.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05-r3.ebuild
new file mode 100644
index 000000000000..a2815b765e26
--- /dev/null
+++ b/sci-biology/embassy-emnu/embassy-emnu-1.05-r3.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/embassy-emnu-1.05-r3.ebuild,v 1.1 2006/07/21 14:55:28 ribosome Exp $
+
+EBOV="4.0.0"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS Menu is Not UNIX - Simple menu of EMBOSS applications"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+	mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="~ppc ~ppc-macos ~x86"
+
+RDEPEND="sys-libs/ncurses
+	${RDEPEND}"
+
+DEPEND="sys-libs/ncurses
+	${DEPEND}"
diff --git a/sci-biology/embassy-emnu/files/digest-embassy-emnu-1.05-r3 b/sci-biology/embassy-emnu/files/digest-embassy-emnu-1.05-r3
new file mode 100644
index 000000000000..330da100ca2c
--- /dev/null
+++ b/sci-biology/embassy-emnu/files/digest-embassy-emnu-1.05-r3
@@ -0,0 +1,6 @@
+MD5 2ef912cfde4903129f2424d23d6da0d2 EMBOSS-4.0.0.tar.gz 17651607
+RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 EMBOSS-4.0.0.tar.gz 17651607
+SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 EMBOSS-4.0.0.tar.gz 17651607
+MD5 3ef6e2ac28f55b167b7f2f3614015618 embassy-4.0.0-emnu-1.05.tar.gz 377734
+RMD160 7c82e48085b711e27d026476f73524f9afac3275 embassy-4.0.0-emnu-1.05.tar.gz 377734
+SHA256 f826eb3e8a782ba00f5e565015468fd2032d43ac9800fe31634f4ec107a7bd01 embassy-4.0.0-emnu-1.05.tar.gz 377734
diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog
index 3062407604bd..709dbbc1edaf 100644
--- a/sci-biology/embassy-esim4/ChangeLog
+++ b/sci-biology/embassy-esim4/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/embassy-esim4
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.15 2006/07/20 20:18:12 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.16 2006/07/21 14:56:46 ribosome Exp $
+
+*embassy-esim4-1.0.0-r3 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  +embassy-esim4-1.0.0-r3.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
 
   20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
   embassy-esim4-1.0.0-r2.ebuild:
diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r3.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r3.ebuild
new file mode 100644
index 000000000000..c9ce03997e78
--- /dev/null
+++ b/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r3.ebuild
@@ -0,0 +1,13 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/embassy-esim4-1.0.0-r3.ebuild,v 1.1 2006/07/21 14:56:46 ribosome Exp $
+
+EBOV="4.0.0"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS integrated version of sim4 - Alignment of cDNA and genomic DNA"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+	mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="~ppc ~ppc-macos ~x86"
diff --git a/sci-biology/embassy-esim4/files/digest-embassy-esim4-1.0.0-r3 b/sci-biology/embassy-esim4/files/digest-embassy-esim4-1.0.0-r3
new file mode 100644
index 000000000000..a9f1b556b3c0
--- /dev/null
+++ b/sci-biology/embassy-esim4/files/digest-embassy-esim4-1.0.0-r3
@@ -0,0 +1,6 @@
+MD5 2ef912cfde4903129f2424d23d6da0d2 EMBOSS-4.0.0.tar.gz 17651607
+RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 EMBOSS-4.0.0.tar.gz 17651607
+SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 EMBOSS-4.0.0.tar.gz 17651607
+MD5 35b0f661043bd9c03aaba22f7bffc321 embassy-4.0.0-esim4-1.0.0.tar.gz 417724
+RMD160 76aaffa27b6a20c5734ec575346f58428974c36e embassy-4.0.0-esim4-1.0.0.tar.gz 417724
+SHA256 94c864bc0c2d12b01987f098470437b0535b4f8d2a7a275d29e4034ee07ebe7e embassy-4.0.0-esim4-1.0.0.tar.gz 417724
diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog
index 787ae8aa0429..afd0808f5544 100644
--- a/sci-biology/embassy-hmmer/ChangeLog
+++ b/sci-biology/embassy-hmmer/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/embassy-hmmer
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.16 2006/07/20 21:06:52 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.17 2006/07/21 14:58:40 ribosome Exp $
+
+*embassy-hmmer-2.3.2 (21 Jul 2006)
+
+  21 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
+  embassy-hmmer-2.1.1-r2.ebuild, +embassy-hmmer-2.3.2.ebuild:
+  New upstream version building against EMBOSS 4.0.0.
 
   20 Jul 2006; Olivier Fisette <ribosome@gentoo.org>
   embassy-hmmer-2.1.1-r2.ebuild:
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.1.1-r2.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.1.1-r2.ebuild
index bb06ccff1cef..7bfdee2482a4 100644
--- a/sci-biology/embassy-hmmer/embassy-hmmer-2.1.1-r2.ebuild
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.1.1-r2.ebuild
@@ -1,13 +1,13 @@
 # Copyright 1999-2006 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.1.1-r2.ebuild,v 1.5 2006/07/20 21:06:52 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.1.1-r2.ebuild,v 1.6 2006/07/21 14:58:40 ribosome Exp $
 
 EBOV="3.0.0"
 
 inherit embassy
 
 DESCRIPTION="EMBOSS integrated version of HMMER - Biological sequence analysis with profile HMMs"
-SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/EMBOSS-${EBOV}.tar.gz
 	ftp://emboss.open-bio.org/pub/EMBOSS/old/${EBOV}/${EF}.tar.gz"
 
 RESTRICT="mirror"
diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.ebuild
new file mode 100644
index 000000000000..b67cb9091de0
--- /dev/null
+++ b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.ebuild
@@ -0,0 +1,19 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.ebuild,v 1.1 2006/07/21 14:58:40 ribosome Exp $
+
+EBOV="4.0.0"
+
+inherit embassy
+
+DESCRIPTION="EMBOSS integrated version of HMMER - Biological sequence analysis with profile HMMs"
+SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EBOV}.tar.gz
+	mirror://gentoo/embassy-${EBOV}-${PN:8}-${PV}.tar.gz"
+
+KEYWORDS="~ppc ~ppc-macos ~x86"
+
+src_install() {
+	embassy_src_install
+	insinto /usr/include/emboss/hmmer
+	doins src/*.h
+}
diff --git a/sci-biology/embassy-hmmer/files/digest-embassy-hmmer-2.3.2 b/sci-biology/embassy-hmmer/files/digest-embassy-hmmer-2.3.2
new file mode 100644
index 000000000000..98afe222e94c
--- /dev/null
+++ b/sci-biology/embassy-hmmer/files/digest-embassy-hmmer-2.3.2
@@ -0,0 +1,6 @@
+MD5 2ef912cfde4903129f2424d23d6da0d2 EMBOSS-4.0.0.tar.gz 17651607
+RMD160 5b29ac2946a1315928581bf0e40a0f6b5023c599 EMBOSS-4.0.0.tar.gz 17651607
+SHA256 bbfd127adc064a5211542f3b5400cbb13c7f74d9171fd16b8531cee9fd11b231 EMBOSS-4.0.0.tar.gz 17651607
+MD5 967454c708ecaa0cbd47deda66b78e65 embassy-4.0.0-hmmer-2.3.2.tar.gz 546870
+RMD160 2bde7ce9240fdeb1c1f14440f56db02266ac52c1 embassy-4.0.0-hmmer-2.3.2.tar.gz 546870
+SHA256 87c2ac5ae9d62bbf5e60c7b61f777ac0790b74a1ac825ac7960d29b11ae5f7c7 embassy-4.0.0-hmmer-2.3.2.tar.gz 546870