reinit the tree, so we can have metadata

7 files changed, 220 insertions, 0 deletions

diff --git a/sci-biology/t-coffee/Manifest b/sci-biology/t-coffee/Manifest
new file mode 100644
index 000000000000..297927345e87
--- /dev/null
+++ b/sci-biology/t-coffee/Manifest
@@ -0,0 +1,10 @@
+AUX t-coffee-11.00-mayhem.patch 1230 SHA256 591a68129f5f62a1e7bf03b219bf98c9e2b0534a9abb0b9657fe81288bc94f13 SHA512 b2c232f3e517c9c944c3d13a96b8383f8875e2e968ed16df25e37c6bfeee106cf82f9107187081753fbcaba6e27713fe5f4ca51d2f859ea7e8744f3b2b41f035 WHIRLPOOL 5d66e781920835c6b7e283a380fe166a38f6a9ed250f808634b491fd5f4634c2f3bce4f77396e94113b10af8fc290ab04daf9076d5ab9bf75d8352b178025281
+AUX t-coffee-11.00-set_proper_dir_permissions.patch 1203 SHA256 df138a69c325fbd0f1beb12adaa2a1fc33bf38174dea128f036c2fe42e2d339f SHA512 fb19aae00ccc0824bcb757d32ee921159e9ece9c0336b3d663e0140ccfca77bf3fcce0eeb304517e41dc1dd4c9469c345c0c35fe8e7fdf120c6fddba4a4e1524 WHIRLPOOL eadcd416d579f3ae69d82d0c49ff1c87d7a540a2fa8e246af5ae89eedf47d64e76db5a39d692a82e6bf3a5ffa5013007937ecf7214c0985621f7e571e2e743c2
+AUX t-coffee-9.03.1318-flags.patch 3376 SHA256 a6519f65d456bd62860444960f2978de884a1a9a83c4558904277629cbfc8b32 SHA512 db1d4463280a95ce644065c64a653d31d57d144c45afba5ff1dd03911ce3c3c1afb15a29c09b4089558acc364385e3eeddbf9179c662191d730d34e09675243c WHIRLPOOL 3f362b8437f1351b6f33eb25761189c783312e397228bbd70a58ff188ded2c5abbed980fb23231cbce240272872edcbc24d3b5556934f148dbeb6f1c74fee1d8
+DIST T-COFFEE_distribution_Version_11.00.8cbe486.tar.gz 3526354 SHA256 b8018433574ff7705c49cd974bebb06a48eb8bc5e38aaa9eb4f53f2e7778e72c SHA512 5c486411bae430cfca6f4623f4dff348e2d9ab7c2eb0edef8059c6cb9c01ee48347e06be0c5d19ee1ace4b9f597f19beee8da2d7eecba29c5a78c2aec800be92 WHIRLPOOL 205eb1b416b38c4d86722ec501d815cc3f9f974a79e07f6fff32855972a9d3a9849585ca345fa66bbcbe15dca8f16930e7bafe44ce5d39e23f9f73023da13b7c
+DIST T-COFFEE_distribution_Version_9.03.r1318.tar.gz 3455629 SHA256 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c SHA512 40220c9fca5bee59b66757162ff2279c2ab221cca07532c64ed3606a95a787080cd4d6bf301ca6d20d8ba4f0c2166e5785fc0ad81ed6528eb527f24d59e79cc8 WHIRLPOOL a9d6b5abdf9851289d1de985fe0eda16f40d72ad23c74ee80ec7a365d9e6124ba12b4dc17894b98bd8d886f4dd0a25bce96cd4e2ec1bc7c2177d6ab8aa00bb65
+EBUILD t-coffee-11.00-r1.ebuild 1279 SHA256 cb2f6c279a6728135d09de8e0e0072bdedfdeaff023c5e05b1cda50ed9cd7e6a SHA512 e2e5c6027efc490de8f83bcfdd32fa67ad1b1e40539ccf3e8e2523a7242cdd24621877afaa5f6ed8998e68919faaa439ae8a010638c60c2123b6423cec2a1a3b WHIRLPOOL dc70ec60dae9c3339c3bc33b02bb74135c07b208763321519289a8e70c29770762a5c23cc0c7e7527c403c27eda4ab10f713b9a9383c3fcab8fd58ace4a49790
+EBUILD t-coffee-9.03.1318-r1.ebuild 1335 SHA256 6505cb1df112a38868a971295400fcf36fbc669918933bae97d88772308cf9b8 SHA512 92e0607a498f4d84b297d492bf3e12b6565e25ded94e77e6703ea3b5d9745fb1c6cd7d4f8914fd859cf4ccea8c595069669dd47a607901054a344f6c564ab8a2 WHIRLPOOL f6589ba9543e60b4775d8a0f69c0022a0dd9310da5bad37542edce52f8d4be5030980dbc6166f8bbb8a8a6b3c0c76fc4529743a27c82623a2824b4c007b14e95
+MISC ChangeLog 2950 SHA256 69d9018b2fbf47a2989ec1e2bb2b544f5848b7357d326911fb81950af229974c SHA512 24bd756af677fb4c158e5bbb9392d7812f8c8b02354d038c0e144a2fdacb9c1431ffc9e8f7a42f0c3ad7256773ae622d9290fef6802a6f163e880fc5e83e05ba WHIRLPOOL 70378657dfd49d902bf449890ee8908c8abaaf401deb9f90f3f9f7659d8492cd65c049229ea76208916c1c15207ac7f6071ad19fd07d40e472e209e51cf6496a
+MISC ChangeLog-2015 7815 SHA256 133b325ff75dc47a24b53ee303328acdebfc5a28b7634011fc6668c7ea648441 SHA512 edaccc55b78bd5676b6bc6fd6fb5bca2f5030cb1b114af70f87529758f9359f6f9fef8505245a9e8d5d9a193cd26469b1cfdd53f71ef98c956c7c468921ae396 WHIRLPOOL 00ca5b9ac841ead18bb4c147cfd63db72b4b8f37a74b21138c4a44a6e2aa039e9c460ee0edd1ba4d009da386bd7f845a0cd8d1c0cb562262602a3088bdf8f8c9
+MISC metadata.xml 769 SHA256 d80d159fbc721007d2dce6ffcd0f8ae345f5d3934f3c454f0b85a814ea6849ac SHA512 33c84555d372ac808c763161ba35fc0c04b1aaaf400fe08b0d182c7dcb1f1c8d4f4e247bd0b51b744e1debc0e4805402d2195ca7b83be59d5001bcac0a5dbc6f WHIRLPOOL 3563ebc92c047fa51a9d23426428fcb495291695c53a1b3ee8663ccf14c265cde43c6069128a069f3b10264946b0e794e0b823713cfd1367b3cc2ef1c6105640
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch
new file mode 100644
index 000000000000..cbfeeabc181b
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-mayhem.patch
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
+Bug-Debian: https://bugs.debian.org/716373
+Description: Fix Mayhem issue
+ The idea behind this patch is that if there is a problem to set the HOME
+ directories no additional processes can exist and so we should *really*
+ exit.  Somehow the printf_exit() function does some logic which ends up
+ in an endless loop and thus forcing the exit will help here.
+ .
+ Unfortunately this does not solve the issue completely since inside the
+ Exit call a "Segmentation fault" happens - so some broken pointer handling
+ seems to happen somewhere before.
+
+--- a/t_coffee_source/util_lib/util.c
++++ b/t_coffee_source/util_lib/util.c
+@@ -4642,7 +4642,8 @@ char *get_home_4_tcoffee ()
+     }
+   else
+     {
+-      printf_exit (EXIT_FAILURE, stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
++      fprintf(stderr, "ERROR: Could not set a HOME directory.\nSet any of the following environement variables to some suitable location: HOME, HOME_4_TCOFFEE, TMP or TEMP [FATAL:%s]\n", PROGRAM);
++      exit(EXIT_FAILURE);
+     }
+ 
+ 
diff --git a/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch
new file mode 100644
index 000000000000..a3f47cd9fce2
--- /dev/null
+++ b/sci-biology/t-coffee/files/t-coffee-11.00-set_proper_dir_permissions.patch
@@ -0,0 +1,35 @@
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 21 Dec 2015 21:30:36 +0100
+Bug-Debian: https://bugs.debian.org/751579
+Description: When creating subdirectories in $HOME do not
+ make these world writable but keep users umask
+
+--- a/t_coffee_source/util_lib/util.c
++++ b/t_coffee_source/util_lib/util.c
+@@ -7714,6 +7714,10 @@ int my_mkdir ( char *dir_in)
+   int a, buf;
+   char *dir;
+ 
++  static char *home = getenv ("HOME");
++  static mode_t oldmask = umask(0);
++  int change_umask = 0;
++  if (strncmp (dir_in, home, strlen(home))==0) change_umask = 1;
+ 
+   dir=(char*)vcalloc ( strlen (dir_in)+strlen (get_home_4_tcoffee())+100, sizeof (char));
+   sprintf ( dir, "%s", dir_in);
+@@ -7733,10 +7737,11 @@ int my_mkdir ( char *dir_in)
+ 
+ 	  if (access(dir, F_OK)==-1)
+ 	    {
+-		  mode_t oldmask = umask(0);
+-	      mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
+-	      umask(oldmask);
+-
++	      if ( change_umask == 1 ) mkdir (dir, 0777-oldmask);
++	      else {
++	        mkdir (dir, S_IRWXU | S_IRWXG | S_IRWXO);
++	        umask(oldmask);
++	      }
+ 	      if ( access (dir, F_OK)==-1)
+ 		{
+ 		  myexit(fprintf_error ( stderr, "\nERROR: Could Not Create Directory %s [FATAL:%s]", dir, PROGRAM));	}
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) $(LDFLAGS) TMalign.f -o TMalign
diff --git a/sci-biology/t-coffee/metadata.xml b/sci-biology/t-coffee/metadata.xml
new file mode 100644
index 000000000000..d0787617064b
--- /dev/null
+++ b/sci-biology/t-coffee/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <longdescription>
+		T-Coffee is a multiple sequence alignment package. Given a set of
+		sequences (Proteins or DNA), T-Coffee generates a multiple sequence
+		alignment. Version 2.00 and higher can mix sequences and structures.
+		T-Coffee allows the combination of a collection of multiple/pairwise,
+		global or local alignments into a single model. It also allows to
+		estimate the level of consistency of each position within the new
+		alignment with the rest of the alignments.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
new file mode 100644
index 000000000000..919287c790f8
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-11.00-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+MY_HASH="8cbe486"
+MY_PV="${PV}.${MY_HASH}"
+MY_P="T-COFFEE_distribution_Version_${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 ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-biology/clustalw
+	sci-chemistry/tm-align"
+DEPEND=""
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+	sed \
+		-e '/@/s:.*;:\t:g' \
+		-e '/Linking/s:$(CC):$(CC) $(CFLAGS) $(LDFLAGS):g' \
+		-i t_coffee_source/makefile || die
+	epatch \
+		"${FILESDIR}"/${P}-mayhem.patch \
+		"${FILESDIR}"/${P}-set_proper_dir_permissions.patch
+}
+
+src_compile() {
+	[[ $(gcc-version) == "3.4" ]] || \
+		[[ $(gcc-version) == "4.1" ]] && \
+		append-flags -fno-unit-at-a-time
+	emake \
+		V=1 \
+		CC="$(tc-getCXX)" \
+		CFLAGS="${CXXFLAGS} -Wno-write-strings -Wno-unused-result" \
+		-C t_coffee_source t_coffee
+}
+
+src_install() {
+	dobin t_coffee_source/t_coffee
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r example
+	fi
+}
diff --git a/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild
new file mode 100644
index 000000000000..9f32c135fb78
--- /dev/null
+++ b/sci-biology/t-coffee/t-coffee-9.03.1318-r1.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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 ~ppc64 x86 ~amd64-linux ~x86-linux"
+IUSE="examples"
+
+RDEPEND="
+	sci-biology/clustalw
+	sci-chemistry/tm-align"
+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="${CFLAGS}" \
+		-C t_coffee_source t_coffee
+}
+
+src_install() {
+	dobin t_coffee_source/t_coffee
+
+	if use examples; then
+		insinto /usr/share/${PN}
+		doins -r example
+	fi
+}