removed PHRED_PARAMETER_FILE env, #253451

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 94 insertions, 7 deletions

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index 26f4f2b2ad8a..89c1839cd206 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/consed
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.2 2009/03/15 16:58:21 weaver Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.3 2010/05/22 08:53:37 jlec Exp $
+
+*consed-19-r2 (22 May 2010)
+
+  22 May 2010; Justin Lecher <jlec@gentoo.org> consed-19-r1.ebuild,
+  +consed-19-r2.ebuild:
+  removed PHRED_PARAMETER_FILE env, #253451, some QA
 
 *consed-19-r1 (15 Mar 2009)
 
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
index aae40fabcc0b..832f59678abb 100644
--- a/sci-biology/consed/Manifest
+++ b/sci-biology/consed/Manifest
@@ -1,5 +1,16 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 DIST consed-19-linux.tar.gz 29835559 RMD160 06765fe4beee2bb8f1f72b7cb9522acadf8df1d3 SHA1 7b01affde92cda6ff0bcb49199ed6c7e60b044d5 SHA256 27501d714e4cd7ea04def6a7f985b674bc454ed8bd7d1e86b41b0283e2b9e089
 DIST consed-19-sources.tar.gz 6867357 RMD160 52bb03197a75827214b30c8ce833d9479fc9aa63 SHA1 ee40c48b887fc457c869b0d997ca650a0a7864af SHA256 1db37b17608e49470926dae261c76d400cf3f9eb5feea52cd732e0bfa4cadee3
-EBUILD consed-19-r1.ebuild 2293 RMD160 4c854f458baf43e9eb2928fc3a9076a5a4b6f42c SHA1 2a2e523f5d8ce67d82752d7a433ce93fbd352f42 SHA256 e521dd9ab4a1ac067f28e4201522be60a2ca0e71a12c7b108b22a1a3bfffc634
-MISC ChangeLog 634 RMD160 c1a3f3f391aca73a02f7762e458993fb6b8acd29 SHA1 f0c505ecf73f87fb1bd241af53d48c2575070a84 SHA256 6351b7699ebd3ce54c45a00cec56bd09a266fffb07306427c0285a49f37056f1
+EBUILD consed-19-r1.ebuild 2213 RMD160 22462f142edffba2e52f5d32d4874b4c4bad8cc5 SHA1 2de25216c0fd2303d0f12c82e4f28de0c4cdb28e SHA256 45bca05c8bf86c1d980bfa586fe31614de19de2d63cb7f0ff4b941c8a7d49794
+EBUILD consed-19-r2.ebuild 2239 RMD160 b2a80d059e24a8ef76103e9876af237ff00df7bc SHA1 74a60f4de97af82c11e97ab4016233d004adf44e SHA256 3b4f95d7cfb8aab435893ba31052f4626cfdb86231dd3c13213db2b6ab7305a5
+MISC ChangeLog 807 RMD160 45b8e3cddd13d03bce7caa6c72dedfc11668cbfe SHA1 6921a9537ed411a09e816dd90b899b36b74ced10 SHA256 a87218a7a02b9ed4e931a42ee478a957a7a64f6e1b9de0998bafcde59f9f4f31
 MISC metadata.xml 259 RMD160 d9d81b67d635fabd81aef8ae0edf971211ae9072 SHA1 8e32f751c67ff891fa35405a2cf6fb33752d6eb1 SHA256 541c3fbcf299d9a8ccf4132ee61f9e53a5d737cefdaa6fdc77764d8d4c7f3110
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.14 (GNU/Linux)
+
+iEYEARECAAYFAkv3m5cACgkQgAnW8HDreRaYXQCgwALXfjbM3587Szfmdmjr6jhV
+Qw0AoKQLNmqKi3wjTwFL82yWh8MDqE/3
+=vrsW
+-----END PGP SIGNATURE-----
diff --git a/sci-biology/consed/consed-19-r1.ebuild b/sci-biology/consed/consed-19-r1.ebuild
index 168e97a9fe72..cb85bd73368d 100644
--- a/sci-biology/consed/consed-19-r1.ebuild
+++ b/sci-biology/consed/consed-19-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.1 2009/03/15 16:58:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.2 2010/05/22 08:53:37 jlec Exp $
 
 inherit toolchain-funcs
 
@@ -59,7 +59,6 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME=/usr' > "${S}/99consed"
-	echo 'PHRED_PARAMETER_FILE=/usr/share/phred/phredpar.dat' >> "${S}/99consed"
 	doenvd "${S}/99consed" || die
 	dodoc README.txt *_announcement.txt
 }
diff --git a/sci-biology/consed/consed-19-r2.ebuild b/sci-biology/consed/consed-19-r2.ebuild
new file mode 100644
index 000000000000..32b281e0cf99
--- /dev/null
+++ b/sci-biology/consed/consed-19-r2.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.1 2010/05/22 08:53:37 jlec Exp $
+
+EAPI=3
+
+inherit toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="x11-libs/openmotif"
+RDEPEND="${DEPEND}
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
+	einfo "and place it in ${DISTDIR},"
+	einfo "obtain the file"
+	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
+	sed -i \
+		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
+	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
+	sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "${EPREFIX}/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
+}
+
+src_compile() {
+	emake || die
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${PN}/examples
+	doins -r standard polyphred autofinish assembly_view 454_newbler \
+		align454reads align454reads_answer solexa_example \
+		solexa_example_answer selectRegions selectRegionsAnswer || die
+	echo 'CONSED_HOME=${EPREFIX}/usr' > "${S}/99consed"
+	doenvd "${S}/99consed" || die
+	dodoc README.txt *_announcement.txt || die
+}
+
+pkg_postinst() {
+	einfo "Package documentation is available at"
+	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
+}