Bump to EAPI=5 and host tarball instead of just mirror it

Package-Manager: portage-2.2.18/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

diff --git a/sci-biology/cutg/ChangeLog b/sci-biology/cutg/ChangeLog
index de848c97d586b0c7b471fffcf629d89f45a405b8..147db5682017b81fdbc928ffd08d717eb4b86b7f 100644 (file)
--- a/sci-biology/cutg/ChangeLog
+++ b/sci-biology/cutg/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/cutg
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.56 2011/08/09 15:36:17 xarthisius Exp $
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/ChangeLog,v 1.57 2015/03/05 10:14:41 jlec Exp $
+
+*cutg-160-r1 (05 Mar 2015)
+
+  05 Mar 2015; Justin Lecher <jlec@gentoo.org> +cutg-160-r1.ebuild,
+  metadata.xml:
+  Bump to EAPI=5 and host tarball instead of just mirror it
 
   09 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> cutg-151.ebuild,
   cutg-160.ebuild:
@@ -231,4 +237,3 @@
   cutg-141.0.ebuild, metadata.xml :
   Initial import.  Ebuild submitted by Olivier Fisette <ribosome@gentoo.org>.
   Reference: Gentoo Bugzilla, bug #54322
-

diff --git a/sci-biology/cutg/Manifest b/sci-biology/cutg/Manifest
index ed96155677724c79f5a8b78a4d97abe652d5e8bc..446b83ead8e2c6edfc0643b3e6c8ab621fd059cc 100644 (file)
--- a/sci-biology/cutg/Manifest
+++ b/sci-biology/cutg/Manifest
@@ -1,18 +1,30 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
+Hash: SHA512
 
-DIST CUTG.151.tar.gz 165813396 RMD160 77a304321f1535af8bb6eff1ce5c8e559a64535c SHA1 0327ccf522d9e38ab6e261bb0e2077533bf1892b SHA256 8184ac1a99ba54791d4ca672d514daeafd7e6736e76524fbbd7b3930d7d8534f
-DIST cutg-160.tar.bz2 204801251 RMD160 fd942323dc92d456498f2f12abfaef5ee511723d SHA1 132b339a47f415c21b0a46eee4b83c9fcfbdd2e7 SHA256 8d5139a5f1441535296f2d5625b90863be0c26fabe703a01c290b1d91bae936f
-EBUILD cutg-151.ebuild 1336 RMD160 b3c4c45f3677ca527d48667f05f0473a565acccd SHA1 474712436ab4b66e90f314cd4e71253780584413 SHA256 ea1ee12ccb126955e9121a86886a65aa956a00ccb1afee4a5c174e9aa7507da3
-EBUILD cutg-160.ebuild 1414 RMD160 77793282db99778e9bb7cfc8232337a902fbe716 SHA1 82faae6df8ef85066948e930a54db748288b3ad2 SHA256 bfe2694fef33b8f7568d487e6491259e51e4b4fc8855e4c186ec2be49f622ce1
-MISC ChangeLog 7059 RMD160 b34cf1c833a734f388c3c4a95c470b6c8de54301 SHA1 52398eb9a212a40fcccbdf99aa44c98486b351bb SHA256 0f3b9081906f264d6c3cd07b203f27739e7e8dd9de2503c2247c88cb735f3bda
-MISC metadata.xml 505 RMD160 8ede6f228f19c43d1a31b23742379ecfab5551dc SHA1 5145ff8f88e2abe468f4b52bb779fa216b702f4c SHA256 f3e78190afd16c11177dc9597736cf541fe5024ab1d48d7e2b46c351539e416d
+DIST CUTG.151.tar.gz 165813396 SHA256 8184ac1a99ba54791d4ca672d514daeafd7e6736e76524fbbd7b3930d7d8534f
+DIST cutg-160.tar.bz2 204801251 SHA256 8d5139a5f1441535296f2d5625b90863be0c26fabe703a01c290b1d91bae936f SHA512 3f52e39b8ab97289d6d7b401046f75f8a93b3e54d97ad6f3e11faa2bbb6591608693ac57ecbda901b6586c1d6a1d833cfbe23777b45873b3fb20c46af65a8e65 WHIRLPOOL ce62b45d042c48ec27e86d764c9cd081752b2806ec57ad7e773aaa5a3016e65996c920db4ed04872da74a76d1f09e48a791f046f988567599690dde210a4a209
+DIST cutg-160.tar.xz 178015420 SHA256 faa2e5e4417e5cadd67bfff0c011f2f3e2e0c5d8b324fc441f9346808f6ed1fa SHA512 9b72283f311fb805b7b22f59f3ca8fed2ab0af72b82247900922999792c1b112dcaca9b29b265a1e0e7b9eaf9ff846a1dc4c196fb95ddbfb3ee5175755ffb8e7 WHIRLPOOL 540f9ba9f2f69718688531c85729c567cd6ba260f12d23b5f3c00d9689da93aefab588fe3dd926defacf4a21982406055ebee413e39ce53a2916e5e571037e93
+EBUILD cutg-151.ebuild 1336 SHA256 ea1ee12ccb126955e9121a86886a65aa956a00ccb1afee4a5c174e9aa7507da3 SHA512 12173f73920d39b92c3e9614c77e0c185de63430f09b2b9be34a43296559000dc88403c7c6355fc3b0c26acc23a692300238e705e9299c468330d26524557afc WHIRLPOOL ad9363efffc338754a048e1e49d07e60b05aaeb3887c24b1ba8d9e8bd9ad45bd239a84432da1fefa21ab94e62567df64123c47ef66f7defa2672673e15bc1805
+EBUILD cutg-160-r1.ebuild 1389 SHA256 c42478c2db1aa72d2e40a03fec65df56ad5c17df043c4a511c176e987b9a9879 SHA512 3f9586e1f24dc6bfbf523016b40d3496a8a3ae43f5871901c0b7962b991c4d7cf3ad229cbb83a036959b30a993b94ddd85c0abe92324162683e21beb760e5549 WHIRLPOOL 7a2f0e54ddf59afdb5558374cdd13a49d2dce569788e1ecd3d4ca99b9e38bcb2656805f1336b259071ca0a6e4b532ea6906fab5ce8ec77b83650b8241a25a03d
+EBUILD cutg-160.ebuild 1414 SHA256 bfe2694fef33b8f7568d487e6491259e51e4b4fc8855e4c186ec2be49f622ce1 SHA512 9b8ed300839a2798da0204d78f62aefabbc0c6e394375d8e17a80902690e6968808f6fdcf0e3821114073063c9b0295fac1d248302892847a758916a7b67a8d1 WHIRLPOOL 76559a63ed6ed406d1f36a93478a5acf7f43f6397af2174fd665b90dc2167fca34f751d27fd55460f97e50b2b617bdbaf0e4792b3844ff1ba7393ac7b08aaf60
+MISC ChangeLog 7225 SHA256 524e33e8aaa96231329f0c22bcf604f96700da6dc44a3640f9747bddfd22f117 SHA512 2a3dec0aee15b5b86d9859bfea881350a3d993f9b85d7bd1689212e462caee85bcc36c129aa2a4c5f4fdf2558bb512ba1d8937cb205c3927cf8127e3861e5155 WHIRLPOOL 37a97eb6aca51d2838a33cca2b801024305c7577bc6120aad1682281882bc70e1c70c19ba428a5279afda77e904079a4010c0bf4d4b5322981f6f1086f2c7512
+MISC metadata.xml 507 SHA256 70c2bfb0dece5d434c19995ad254bd05045717b30c84c806d9d8253209154c22 SHA512 beca673e58112943bd3e84b5962a1c732fe539f83fb3b4a3a5e3bd8129b4a557d3d3dae29589c8468487b3f04622c6d99aa52379d164561e00bbfaf749a14a24 WHIRLPOOL acc2121d7036206d0868ed607aed32d248517427112ce265eb85e7660f43490f9a00a5224e3d281e65b0ac6b7938328d87c5290f88dcfef7b9da0780645ef82a
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diff --git a/sci-biology/cutg/cutg-160-r1.ebuild b/sci-biology/cutg/cutg-160-r1.ebuild
new file mode 100644 (file)
index 0000000..4e576d2
--- /dev/null
+++ b/sci-biology/cutg/cutg-160-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/cutg/cutg-160-r1.ebuild,v 1.1 2015/03/05 10:14:41 jlec Exp $
+
+EAPI=5
+
+DESCRIPTION="Codon usage tables calculated from GenBank"
+HOMEPAGE="http://www.kazusa.or.jp/codon/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"
+
+SLOT="0"
+LICENSE="public-domain"
+# Minimal build keeps only the indexed files (if applicable) and the
+# documentation. The non-indexed database is not installed.
+IUSE="emboss minimal"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="emboss? ( sci-biology/emboss )"
+RDEPEND="${DEPEND}"
+
+RESTRICT="binchecks strip"
+
+src_compile() {
+       if use emboss; then
+               mkdir CODONS || die
+               ebegin "Indexing CUTG for usage with EMBOSS."
+               EMBOSS_DATA="." cutgextract -auto -directory "${S}" || die \
+                       "Indexing CUTG failed."
+               eend
+       fi
+}
+
+src_install() {
+       local file
+       if ! use minimal; then
+               dodir /usr/share/${PN}
+               mv *.codon *.spsum "${ED}"/usr/share/${PN} || die \
+                       "Installing raw CUTG database failed."
+       fi
+
+       if use emboss; then
+               dodir /usr/share/EMBOSS/data/CODONS
+               cd CODONS || die
+               for file in *; do
+                       mv ${file} "${ED}"/usr/share/EMBOSS/data/CODONS/ || die \
+                               "Installing the EMBOSS-indexed database failed."
+               done
+       fi
+
+       dodoc README CODON_LABEL SPSUM_LABEL
+}

diff --git a/sci-biology/cutg/metadata.xml b/sci-biology/cutg/metadata.xml
index 9cd5324b71ca3dd6a736a850be5ddeeb282cfa3f..59b110912ca65db905fd72108367ffd896edd1ab 100644 (file)
--- a/sci-biology/cutg/metadata.xml
+++ b/sci-biology/cutg/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-       <herd>sci-biology</herd>
-       <longdescription>
+  <herd>sci-biology</herd>
+  <longdescription>
                Codon usage tables maintained at the Kazusa DNA Research Institute.
                Codon usage in individual genes has been calculated using the
                nucleotide sequence data obtained from the GenBank Genetic Sequence