New version

Package-Manager: portage-2.0.54

diff --git a/sci-biology/prosite/ChangeLog b/sci-biology/prosite/ChangeLog
index a65f9cbd32b737e66ddd6d187e8c027e487f99c8..10c65dd79a4d0bbd6e898e26a97a9fb98b165870 100644 (file)
--- a/sci-biology/prosite/ChangeLog
+++ b/sci-biology/prosite/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/prosite
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/prosite/ChangeLog,v 1.75 2006/02/22 21:04:48 grobian Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/prosite/ChangeLog,v 1.76 2006/03/15 14:33:47 ribosome Exp $
+
+*prosite-19.22 (15 Mar 2006)
+
+  15 Mar 2006; Olivier Fisette <ribosome@gentoo.org> +prosite-19.22.ebuild:
+  New version.
 
   22 Feb 2006; Fabian Groffen <grobian@gentoo.org> prosite-19.18.ebuild:
   Marked ppc-macos stable (bug #123334)

diff --git a/sci-biology/prosite/Manifest b/sci-biology/prosite/Manifest
index 01786f972efef090417f9f0c91b5e520f7883480..710718488ea9d4b8b07404d9e09dd7525ebcdda4 100644 (file)
--- a/sci-biology/prosite/Manifest
+++ b/sci-biology/prosite/Manifest
@@ -1,36 +1,14 @@
 MD5 096b7d8e66a12a851726b5ab34a1f2fb ChangeLog 11705
-RMD160 efdc5863eed3443f20980dd8d99422e0f73c4d8d ChangeLog 11705
-SHA256 22c067c4af7021078c37746bb46346b5e7ec9b391e7908329bde9022247e48cd ChangeLog 11705
 MD5 2f35d065ff4b9256d80f3923fa864c5c files/digest-prosite-19.16 67
-RMD160 fe669c23fd4cad9e4bb61e3fe24cd11a544eee90 files/digest-prosite-19.16 67
-SHA256 bc527623b4a4462badfc534a31167d6481e0c6f9bdd7c692d79ad9ada2af5cbe files/digest-prosite-19.16 67
 MD5 88309b107f8fd9445fb2370e95506eff files/digest-prosite-19.17 67
-RMD160 4698c250c8d9fdf1b57ee8e7283a1cd12ee41858 files/digest-prosite-19.17 67
-SHA256 daa20d7935177e72692da67cc418684c719e7decda65e091ff1ccfafec48a7b6 files/digest-prosite-19.17 67
 MD5 a652d8b43037190415fe10e9282d838f files/digest-prosite-19.18 67
-RMD160 dbda98722b5c60df16cc2520ea5bd74bde7846eb files/digest-prosite-19.18 67
-SHA256 c08859bc6f93dd250ac7e19968c31467da734c4c408ae48d59b1b9c9a8a47603 files/digest-prosite-19.18 67
 MD5 db4add7ca9d25fb3c90e646c88d6f562 files/digest-prosite-19.19 67
-RMD160 46a87c396366cc756097815f2245153bc1cada79 files/digest-prosite-19.19 67
-SHA256 fd4788c8dc4520b4ffc54a20a33e73ea0cf0fceda2295860a115e6145ff39ce0 files/digest-prosite-19.19 67
 MD5 9676c19817d33959f3d396ba9bd29642 files/digest-prosite-19.20 67
-RMD160 bd84a5ac854848a646a1b8ea8865c76978e301e6 files/digest-prosite-19.20 67
-SHA256 a7b26bc40e915ed2ee01677c5d52dc7b5058d2990f0b62b402d13fc0f1cfc88a files/digest-prosite-19.20 67
+MD5 ce741f14b29ee8a8a5109073ea6940be files/digest-prosite-19.22 67
 MD5 81b73af5f2f4778bea2dde0b55620129 metadata.xml 810
-RMD160 a0acc8bc90197c6e5e9814044b11a02f15e4c398 metadata.xml 810
-SHA256 432b03b079022cf13e6cdbcb2455fb10ac5a95a8b3f41c63f76212a5e7f67c65 metadata.xml 810
 MD5 fd8571a2c6a6d2a8c66c39dfb6bcefe2 prosite-19.16.ebuild 1240
-RMD160 45814dfb20b6f877b9952ff6ef4f68e55c6e44a2 prosite-19.16.ebuild 1240
-SHA256 0fcf024a6c3f15a5e4d7db6db4063bfd604bb9d58e9ab5fdfa489d38050c315c prosite-19.16.ebuild 1240
 MD5 98de3c18be9fae196528dc1ae064a614 prosite-19.17.ebuild 1246
-RMD160 2d0794ca45fd388ec1283237db5e1088f06a5793 prosite-19.17.ebuild 1246
-SHA256 f93c4086e3fd3c6cce86fb191e1b8172e2305de3360eda55e29f064819b8759f prosite-19.17.ebuild 1246
 MD5 816bdf1daa3b43ac3e34ee2e29c30266 prosite-19.18.ebuild 1241
-RMD160 5584d647a481c05bfdee2bf5d80d8fc2cc540d04 prosite-19.18.ebuild 1241
-SHA256 f09a7c61dcee87e514b871bfa41990118cf7e8fa07bb6eb5524758cbefaf161f prosite-19.18.ebuild 1241
 MD5 4bc992bd06b47b580178c21734648c37 prosite-19.19.ebuild 1246
-RMD160 658320982caa1c7cde80b465e7b49d34be2392b7 prosite-19.19.ebuild 1246
-SHA256 9465431c4f32fe918b2c8f41144c1d4de5367d81814a4d56421e94d7b2fa9e43 prosite-19.19.ebuild 1246
 MD5 3521d2f54ad4949ea85492479fb905c9 prosite-19.20.ebuild 1246
-RMD160 f55a25984cfb7fccec7bcba50b2693a34c2328ee prosite-19.20.ebuild 1246
-SHA256 121f3266f4330d4e88bfe7814429c38cbd99413043eb9db44099965e91658fbd prosite-19.20.ebuild 1246
+MD5 3521d2f54ad4949ea85492479fb905c9 prosite-19.22.ebuild 1246

diff --git a/sci-biology/prosite/files/digest-prosite-19.22 b/sci-biology/prosite/files/digest-prosite-19.22
new file mode 100644 (file)
index 0000000..cde64b7
--- /dev/null
+++ b/sci-biology/prosite/files/digest-prosite-19.22
@@ -0,0 +1 @@
+MD5 f772e98f52e517b935ab80eec20872c8 prosite-19.22.tar.bz2 4015769

diff --git a/sci-biology/prosite/prosite-19.22.ebuild b/sci-biology/prosite/prosite-19.22.ebuild
new file mode 100644 (file)
index 0000000..1772df3
--- /dev/null
+++ b/sci-biology/prosite/prosite-19.22.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/prosite/prosite-19.22.ebuild,v 1.1 2006/03/15 14:33:47 ribosome Exp $
+
+DESCRIPTION="A protein families and domains database"
+LICENSE="swiss-prot"
+HOMEPAGE="http://ca.expasy.org/prosite"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="~amd64 ~ppc ~ppc-macos ~ppc64 ~x86"
+
+DEPEND="emboss? ( >=sci-biology/emboss-3.0.0 )"
+
+src_compile() {
+       if use emboss; then
+               mkdir PROSITE
+               echo
+               einfo "Indexing PROSITE for usage with EMBOSS."
+               EMBOSS_DATA="." prosextract -auto -prositedir "${S}" || die \
+                       "Indexing PROSITE failed."
+               echo
+       fi
+}
+
+src_install() {
+       if ! use minimal; then
+               insinto /usr/share/${PN}
+               doins ${PN}.{doc,dat,lis} || die "Installing raw database failed."
+       fi
+       dodoc *.txt || die "Documentation installation failed."
+       dohtml *.htm || die "HTML documentation installation failed."
+       if use emboss; then
+               insinto /usr/share/EMBOSS/data/PROSITE
+               doins PROSITE/* || die "Installing EMBOSS data files failed."
+       fi
+}

diff --git a/sci-biology/rebase/ChangeLog b/sci-biology/rebase/ChangeLog
index 78e576e9339fce88cfaaa147c72e00db870c3423..e0a7f9cf53dae0cbfa39fc6b91969c64f762fa78 100644 (file)
--- a/sci-biology/rebase/ChangeLog
+++ b/sci-biology/rebase/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-biology/rebase
 # Copyright 2000-2006 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/ChangeLog,v 1.58 2006/02/22 21:18:22 grobian Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/ChangeLog,v 1.59 2006/03/15 14:34:54 ribosome Exp $
+
+*rebase-603 (15 Mar 2006)
+
+  15 Mar 2006; Olivier Fisette <ribosome@gentoo.org> +rebase-603.ebuild:
+  New version.
 
   22 Feb 2006; Fabian Groffen <grobian@gentoo.org> rebase-601-r1.ebuild:
   Marked ppc-macos stable (bug #123332)

diff --git a/sci-biology/rebase/Manifest b/sci-biology/rebase/Manifest
index c7d28082daa629ccc90f42097f5e89ad0a364fc4..6a15fb6a5ae08deed365aeb8ed7f532d28dae887 100644 (file)
--- a/sci-biology/rebase/Manifest
+++ b/sci-biology/rebase/Manifest
@@ -1,24 +1,10 @@
 MD5 012c0d136bf544e7f0a630e24cb3a169 ChangeLog 8187
-RMD160 2ca25390e718a124a89dfe4db09b384b93391a82 ChangeLog 8187
-SHA256 bb35f6da576d86d08cdb0de933e53d69103b3ea71731f05b118f599e39117d4e ChangeLog 8187
 MD5 0327e485fe0040317dd1016583b0d76d files/digest-rebase-512 63
-RMD160 da0977a8bd82283fb9f713ada1bd99cf102261ce files/digest-rebase-512 63
-SHA256 13c140a92f51b0ea6c4901606fad7fb9f970680beee3904e9454132d699a90f7 files/digest-rebase-512 63
 MD5 9b37c587b84cf914d6f9a9b616c493db files/digest-rebase-601-r1 63
-RMD160 a3685b540b325e1e6f26caf1843a07476771dd59 files/digest-rebase-601-r1 63
-SHA256 d2c68d331d68ca3431d7f39ae76cea9c6972766b24d45c68fc6cbe617d0a36e2 files/digest-rebase-601-r1 63
 MD5 d652b16d7ec999abd36a1e222a7b0ca9 files/digest-rebase-602 63
-RMD160 b41adf63e5de4f2c66e32bf1d65ea0e9d2e2d736 files/digest-rebase-602 63
-SHA256 cb89e9c7f5bdf4438d4e35b0e5c6c3a1e42a8182607080b3116fcb977ef07610 files/digest-rebase-602 63
+MD5 5bd3ee69a92fe75245399d6d3ba20f42 files/digest-rebase-603 63
 MD5 550f8d428f3e75690b43d32df6aa60cd metadata.xml 900
-RMD160 6124f8e0fba32951daaba2f52d7f6f0f00233b2d metadata.xml 900
-SHA256 e947dfc382096458c2183dc90fe7add203f8a6d86ccdfea668176451d58e2e7d metadata.xml 900
 MD5 292928f0068bac8ab37a29c223af581e rebase-512.ebuild 1238
-RMD160 4dc23297f81069f315445fb30e652878c0722a97 rebase-512.ebuild 1238
-SHA256 ffcf6a7746df03153fe059d7ae827c61d48954905ed27d9f6bde28e1ef32bb38 rebase-512.ebuild 1238
 MD5 0548120df1780978e8f3f0d6d45ed7a4 rebase-601-r1.ebuild 1358
-RMD160 5282654ca69342935bad8e46033887c4fca5ac74 rebase-601-r1.ebuild 1358
-SHA256 dae5a787f50988f7e291b37c0a677fdc73ae2864f9db2be88aa2a6f2e2a5a57d rebase-601-r1.ebuild 1358
 MD5 9383effacdb187a2360dbb1112eb3ba7 rebase-602.ebuild 1360
-RMD160 61a278486d31734cb0cd0b0faa0f9b096cce90c7 rebase-602.ebuild 1360
-SHA256 f088d3941d71b53f5c1493caf6c8d9907c31e7bc976436bf62af448379f6001e rebase-602.ebuild 1360
+MD5 9383effacdb187a2360dbb1112eb3ba7 rebase-603.ebuild 1360

diff --git a/sci-biology/rebase/files/digest-rebase-603 b/sci-biology/rebase/files/digest-rebase-603
new file mode 100644 (file)
index 0000000..2079feb
--- /dev/null
+++ b/sci-biology/rebase/files/digest-rebase-603
@@ -0,0 +1 @@
+MD5 2b207277228f7ee9b5f7231bac809ec2 rebase-603.tar.bz2 182746

diff --git a/sci-biology/rebase/rebase-603.ebuild b/sci-biology/rebase/rebase-603.ebuild
new file mode 100644 (file)
index 0000000..0130934
--- /dev/null
+++ b/sci-biology/rebase/rebase-603.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/rebase/rebase-603.ebuild,v 1.1 2006/03/15 14:34:54 ribosome Exp $
+
+DESCRIPTION="A restriction enzyme database"
+LICENSE="public-domain"
+HOMEPAGE="http://rebase.neb.com"
+SRC_URI="mirror://gentoo/${P}.tar.bz2"
+
+SLOT="0"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="~x86 ~ppc ~amd64 ~ppc-macos ~ppc64"
+
+DEPEND="emboss? ( >=sci-biology/emboss-3.0.0-r1 )"
+
+src_compile() {
+       if use emboss; then
+               echo
+               einfo "Indexing ${PN} for usage with EMBOSS."
+               mkdir REBASE
+               EMBOSS_DATA=. rebaseextract -auto -infile withrefm.${PV} \
+                       -protofile proto.${PV} || die "Indexing ${PN} failed."
+               echo
+       fi
+}
+
+src_install() {
+       if ! use minimal; then
+               insinto /usr/share/${PN}
+               doins withrefm.${PV} proto.${PV} || die \
+                       "Failed to install raw database."
+       fi
+       newdoc REBASE.DOC README || die "Failed to install documentation."
+       if use emboss; then
+               insinto /usr/share/EMBOSS/data/REBASE
+               doins REBASE/{embossre.enz,embossre.ref,embossre.sup} || die \
+                       "Failed to install EMBOSS data files."
+               insinto /usr/share/EMBOSS/data
+               doins embossre.equ || die "Failed to install enzyme prototypes file."
+       fi
+}