sci-biology/t-coffee: Version Bump

(Portage version: 2.2.0_alpha147/cvs/Linux x86_64, signed Manifest commit with key 70EB7916)

5 files changed, 91 insertions, 8 deletions

diff --git a/sci-biology/t-coffee/ChangeLog b/sci-biology/t-coffee/ChangeLog
index 237e917dfa71..c42c551b9366 100644
--- a/sci-biology/t-coffee/ChangeLog
+++ b/sci-biology/t-coffee/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/t-coffee
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.48 2010/10/15 19:02:28 jlec Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.49 2012/12/11 14:39:22 jlec Exp $
+
+*t-coffee-9.03.1318 (11 Dec 2012)
+
+  11 Dec 2012; Justin Lecher <jlec@gentoo.org> t-coffee-8.69.ebuild,
+  t-coffee-8.93.ebuild, +t-coffee-9.03.1318.ebuild,
+  +files/t-coffee-9.03.1318-flags.patch:
+  Version Bump
 
   15 Oct 2010; Justin Lecher <jlec@gentoo.org> -t-coffee-5.65.ebuild,
   -t-coffee-8.14.ebuild:
diff --git a/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch
new file mode 100644
index 000000000000..5b15108b3bfa
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-9.03.1318-flags.patch
@@ -0,0 +1,21 @@
+ t_coffee_source/makefile | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile
+index 9e01ba0..026b714 100644
+--- a/t_coffee_source/makefile
++++ b/t_coffee_source/makefile
+@@ -1,6 +1,6 @@
+  
+ t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o 
+-	$(CC) $(CFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o  -lm
++	$(CC) $(CFLAGS) $(LDFLAGS) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o  -lm
+ 
+ all:  t_coffee TMalign
+ 
+@@ -8,4 +8,4 @@ clean:
+ 	rm *.o
+ 
+ TMalign:
+-	 $(FCC) TMalign.f -o TMalign
++	 $(FC) $(FCLAGS) $(LDFLAGS) TMalign.f -o TMalign
diff --git a/sci-biology/t-coffee/t-coffee-8.69.ebuild b/sci-biology/t-coffee/t-coffee-8.69.ebuild
index fad274e4072b..67c2c3e4cc05 100644
--- a/sci-biology/t-coffee/t-coffee-8.69.ebuild
+++ b/sci-biology/t-coffee/t-coffee-8.69.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-8.69.ebuild,v 1.5 2010/10/15 18:51:43 ranger Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-8.69.ebuild,v 1.6 2012/12/11 14:39:22 jlec Exp $
 
 EAPI="2"
 
-inherit flag-o-matic toolchain-funcs
+inherit eutils flag-o-matic toolchain-funcs
 
 DESCRIPTION="A multiple sequence alignment package"
 HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
diff --git a/sci-biology/t-coffee/t-coffee-8.93.ebuild b/sci-biology/t-coffee/t-coffee-8.93.ebuild
index 90a0f33bc8c9..e128906e764f 100644
--- a/sci-biology/t-coffee/t-coffee-8.93.ebuild
+++ b/sci-biology/t-coffee/t-coffee-8.93.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-8.93.ebuild,v 1.1 2010/10/03 11:11:56 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-8.93.ebuild,v 1.2 2012/12/11 14:39:22 jlec Exp $
 
 EAPI="2"
 
-inherit flag-o-matic toolchain-funcs
+inherit eutils flag-o-matic toolchain-funcs
 
 DESCRIPTION="A multiple sequence alignment package"
 HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318.ebuild
new file mode 100644
index 000000000000..d4325f1ffae8
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-9.03.1318.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/t-coffee-9.03.1318.ebuild,v 1.1 2012/12/11 14:39:22 jlec Exp $
+
+EAPI=5
+
+inherit eutils flag-o-matic fortran-2 toolchain-funcs versionator
+
+MY_PV="$(replace_version_separator 2 .r)"
+MY_P="T-COFFEE_distribution_Version_${MY_PV}"
+
+DESCRIPTION="A multiple sequence alignment package"
+HOMEPAGE="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"
+SRC_URI="http://www.tcoffee.org/Packages/Stable/Version_${MY_PV}/${MY_P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="sci-biology/clustalw"
+DEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+die_compile() {
+	echo
+	eerror "If you experience an internal compiler error (consult the above"
+	eerror "messages), try compiling t-coffee using very modest compiler flags."
+	eerror "See bug #114745 on the Gentoo Bugzilla for more details."
+	die "Compilation failed"
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-flags.patch
+}
+
+src_compile() {
+	[[ $(gcc-version) == "3.4" ]] || \
+		[[ $(gcc-version) == "4.1" ]] && \
+		append-flags -fno-unit-at-a-time
+	emake \
+		CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		-C t_coffee_source all
+}
+
+src_install() {
+	dobin t_coffee_source/{t_coffee,TMalign}
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r example
+	fi
+}