# 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 1.40 2010/01/03 14:23:29 pacho Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/t-coffee/ChangeLog,v 1.41 2010/06/15 13:47:35 jlec Exp $
+
+*t-coffee-8.69 (15 Jun 2010)
+
+ 15 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/8.69-flags.patch,
+ +t-coffee-8.69.ebuild, +files/8.69-test.patch:
+ Version bump, included test, respecting LDFLAGS and keyworded for linux
+ prefix
03 Jan 2010; Pacho Ramos <pacho@gentoo.org> t-coffee-8.14.ebuild:
amd64 stable, bug 298765
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Hash: SHA1
+AUX 8.69-flags.patch 3118 RMD160 f79da4565606b5ae9a7d6d4fb949092ce4199d1b SHA1 a6c08ad84553500e3c8667a636fc0f191923462c SHA256 44449539bda6d4a84f6ba156f524b91bb2b34d12a530834256c414588228dc51
+AUX 8.69-test.patch 524 RMD160 21970ae93e40f630db15b3aaa267807e1d0cdd38 SHA1 bf27dc682ebbf4ba2a4df507f5b7e22197e9f38f SHA256 05ad8d6a9bce520d49ed7de18143067858346b18766f42e597cc0974d4d8957a
DIST T-COFFEE_distribution_Version_5.65.tar.gz 2892013 RMD160 50c04dfbda649ebbf0e691a74bd62433bb1dbd14 SHA1 a8dc4bcc37eaa8237670c9daf1b260c8452fab89 SHA256 536cfe25648fbaf4d96baf36b3c8d4d2d81e97b2939e09e89880cae39893d0c6
DIST T-COFFEE_distribution_Version_7.54.tar.gz 3968725 RMD160 d11964db5232d137bf0db8101dfb75b1fde25936 SHA1 a302954a10860455bc23f924628598757c39eb12 SHA256 9d7d56abc000b61b48908fa4f93fb382a35df11c883966a0119605cd16aa668e
DIST T-COFFEE_distribution_Version_8.14.tar.gz 4202237 RMD160 b292e4d4dd6576ad10dacafbb19eaa4f9154b85c SHA1 0286f719569f6717f879b38af520939f4399ab07 SHA256 ffc527e65e81cabc912a2816895efd46fb28bbd45e50327cd7e5d01ba88bcb03
+DIST T-COFFEE_distribution_Version_8.69.tar.gz 4112765 RMD160 5a2e7e089a5d2cc536247b9b26c7b6c216d7ef03 SHA1 3db6557c40587dba005179c98cc5b63b6dca9e44 SHA256 f346376bf341ce30f30f8c077820da466bed3e560c02d0ddd1a992381855d0f5
EBUILD t-coffee-5.65.ebuild 1999 RMD160 7ae18da2d689343547258b54f1de66f289f47114 SHA1 6518aae4c5e8b9bc55eaff6c0e763ae22995c393 SHA256 25d353182a9e946df52ad7dea404800a169067c77441c8d2456042b0cbea4d25
EBUILD t-coffee-7.54.ebuild 1857 RMD160 ee23165c9f4e40b608c960d6c14886b1a680a4e6 SHA1 eb77681d7a1facb7fdab7c0ca45fe6dc02b99e61 SHA256 3da47ef23cf41088177fe5c8b90f96627c0f29f777145e79bf28b7aab618f372
EBUILD t-coffee-8.14.ebuild 1863 RMD160 9dcfe5c6bbd1cf21d9f0ed0c9bae2ffab4816b02 SHA1 67cfd906a72e472fbf83156d0d3ee5371ad8b6b1 SHA256 75e3382c765661e1aca0900fc389a04999b72c08ee650950d5c3c98d3d21378f
-MISC ChangeLog 5344 RMD160 ae7f8fd1299c228e0af17a2127d5d95f9684b852 SHA1 6693fab43e94833ae8be62c5cfcbf739d4a51f9c SHA256 7de20c20c6b451f3e8d5c6f1d11fd889906dc7760540f15b38893082918efbcb
+EBUILD t-coffee-8.69.ebuild 2054 RMD160 b3356175d2bee3f6fd1462382a56318ef761a0f5 SHA1 14d55744c4da0a41a131bd9aa8d5dd0214c824e6 SHA256 396a8047dda0d3bc881332be6f92410bf8cbe19833c5758cad5343c9fc746151
+MISC ChangeLog 5578 RMD160 76be18d2a71acb3a2459c19597bf2bec24b08d54 SHA1 2115db9be417cf05b42a6af58c68888469fb320c SHA256 9d59f96ce6fdfe2c5708d8053c433eb0ec5216b2fe927b805d0caeb2b8927bdc
MISC metadata.xml 760 RMD160 b9b95d31917ca092fbc88aaf871ffc6c22746860 SHA1 ee9d60b1947e1fb1542488003713ec1bcf3f3b71 SHA256 9d60cbec2e12219f15e311a1e8cb694b77fd7897c98186be3012f815c0f7bd12
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--- /dev/null
+diff --git a/t_coffee_source/makefile b/t_coffee_source/makefile
+index d2d00da..2357c44 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 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 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 t_coffee.o -lm
+
+ all: t_coffee TMalign
+
+@@ -8,4 +8,4 @@ clean:
+ rm *.o
+
+ TMalign:
+- $(FCC) TMalign.f -o TMalign
++ $(FCC) $(FFLAGS) ${LDFLAGS} TMalign.f -o TMalign
--- /dev/null
+diff --git a/bin/test.pl b/bin/test.pl
+index 145be47..81c50bd 100755
+--- a/bin/test.pl
++++ b/bin/test.pl
+@@ -1,5 +1,5 @@
+ #!/usr/bin/env perl
+ chdir "./test";
+-$r=system "../bin/t_coffee test.pep -method fast_pair -outfile=new_reference_test.aln -outorder=input>/dev/null";
++$r=system "../t_coffee_source/t_coffee test.pep -method fast_pair -outfile=new_reference_test.aln -outorder=input>/dev/null";
+ if ($r==0){print "\nInstallation of t_coffee Successful\n";}
+ else {print "\nInstallation of t_coffee Not Successful\n";}
--- /dev/null
+# Copyright 1999-2010 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 1.1 2010/06/15 13:47:35 jlec Exp $
+
+EAPI="2"
+
+inherit flag-o-matic toolchain-funcs
+
+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/T-COFFEE_distribution_Version_${PV}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="sci-biology/clustalw"
+DEPEND="${DEPEND}
+ test? ( dev-lang/perl )"
+
+S="${WORKDIR}/T-COFFEE_distribution_Version_${PV}"
+
+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 "${FILESDIR}"/${PV}-flags.patch
+ epatch "${FILESDIR}"/${PV}-test.patch
+}
+
+src_compile() {
+ [[ $(gcc-version) == "3.4" ]] && append-flags -fno-unit-at-a-time
+ [[ $(gcc-version) == "4.1" ]] && append-flags -fno-unit-at-a-time
+ emake \
+ CC="$(tc-getCC)" CFLAGS="${CFLAGS}" \
+ -C t_coffee_source || die_compile
+}
+
+src_test() {
+ cd "${TCDIR}"
+ perl bin/test.pl || die
+}
+
+src_install() {
+ dobin t_coffee || die "Failed to install program."
+
+ insinto /usr/share/${PN}/lib/html
+ doins "${TCDIR}"/html/* \
+ || die "Failed to install Web interface files."
+
+ cd "${TCDIR}"/doc
+ dodoc aln_compare.doc.txt seq_reformat.doc.txt \
+ t_coffee_technical.txt t_coffee_tutorial.txt \
+ || die "Failed to install text documentation."
+
+ dohtml t_coffee_technical.htm t_coffee_tutorial.htm \
+ || die "Failed to install HTML documentation."
+
+ insinto /usr/share/doc/${PF}
+ doins t_coffee_technical.doc t_coffee_tutorial.doc \
+ || die "Failed to install DOC documentation."
+
+ insinto /usr/share/${PN}
+ doins -r "${TCDIR}"/example \
+ || die "Failed to install example files."
+}
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