reinit the tree, so we can have metadata

5 files changed, 207 insertions, 0 deletions

diff --git a/sci-biology/dialign-tx/Manifest b/sci-biology/dialign-tx/Manifest
new file mode 100644
index 000000000000..4c873ae49621
--- /dev/null
+++ b/sci-biology/dialign-tx/Manifest
@@ -0,0 +1,7 @@
+AUX dialign-tx-1.0.2-implicits.patch 776 SHA256 c13bfae6c2ffa4a676fc92a1dbe7f82d08578e5f36add057d0ad84a955aa7ca5 SHA512 632da19c24834f011778e1be23a8b19f64da4e52386c99838393f678e927174bd8d3d9d175716e2651fcb884673123136166c401d3e687b882e5eaf69d597a1b WHIRLPOOL d5fd29ad957ffc734d4ef24811e3f131f86bfa2ffd4bd41da4353fd10f1a3a370e6ac531a943ded7fe908b89373e32e857d478e80453889e41aa1d102db272ea
+AUX dialign-tx-1.0.2-modernize.patch 6149 SHA256 9556d6429018450214d2f49b0f148b380fde11575bcbc3f465e495fa130d9903 SHA512 cf1c1200500eb3e5f159468fe52536e8ffff60de21e09bb81e585270224ac4ce93d59fe80bd5a8212a4154ad90b23ec415be11b42792440c7fd53f75762d047a WHIRLPOOL 56d6ddaa0e2c62afdae05f11fcf8323bdb6b9b75a8e3a34c3e409395a8447de5c18e418dfae541fed2df7b045785ac81459f16ced912cfb0422839b2e2eda202
+DIST DIALIGN-TX_1.0.2.tar.gz 1765296 SHA256 fb3940a48a12875332752a298f619f0da62593189cd257d28932463c7cebcb8f SHA512 ff43f1f2900bdd12b7a8ba382a4d6ad68e6c2e6d7ceb1a65f0e571bb891cc2dc2661fb6ce698aaabf0e20c14565b5927ae0076a7170c8611679f936851a00c43 WHIRLPOOL 70565aa507f23a4f79affd8bda64e1b2698680e2288718c7518bd1d3782ca51ab747f8860e5513e7b1d480efd065702cc407c8137e96c47c3aad28ecdd345277
+EBUILD dialign-tx-1.0.2-r1.ebuild 998 SHA256 83df32036d359ea01946b576ddb43a7dc0bd748387a410dcd8c147494ef9ac6b SHA512 7baa791bc863006cf66828bf3a08ec87afe03f72ba181280f5e26cf826a939bcc854bb94b40551f11a818006dae3a229db15f61b09f11438dece536e150b0ad0 WHIRLPOOL c140d4c566db4ae8b8375de58191031ee9d85d2ef3a1923df198d812c3782dc956c879dd6593653d4ce628e73aba90063fea28f676ccf55905b9366064160464
+MISC ChangeLog 2711 SHA256 ea9068d9b980f212b36e963cfb776cb7cf1aa819cb084833b92eff4a4d8f5b96 SHA512 f96f8e77c48085ab00ab16ef442db74808d5088b8626e08ad02ef2c292c9500fd2a9c8bfcd8c13bda264c36d5609e60afea0f9e270e9dcf685dd897362082bf9 WHIRLPOOL e3aff32f3dbe71b1e769bb251d761371d2d60ad39fc3523e36fadac6f378037e412aeae21a6e72ceec6e171a77cc51ad22a5370a6ec9137059d39d19926cac14
+MISC ChangeLog-2015 2455 SHA256 826243159ec72a293d7fdd92561bfa034991227eb8cff363a272dec0211c2986 SHA512 f36fbf5567d04ed9b3880480136a1524a562160d4cd8c6092c4df7a0ef05d3ddde9e483016dbc32f60ca2de5706f9bd2c0a77464c1ffe767d7f4a9e636533dd8 WHIRLPOOL 873a2d1aa9ff64633684ef3195909e92ef0a2d3d6ff4dcb4c1a828c4d0511eea82e93f03c5e660e4116e83135eaca59f369d88c0344831c871319ad8c2f1081f
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
new file mode 100644
index 000000000000..2f63ea80bb45
--- /dev/null
+++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils multilib toolchain-funcs
+
+MY_P=DIALIGN-TX_${PV}
+
+DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment"
+HOMEPAGE="http://dialign-tx.gobics.de/"
+SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz"
+
+LICENSE="LGPL-2.1"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+S=${WORKDIR}/${MY_P}
+
+src_prepare() {
+	sed -e "s/\$(CC) -o/\$(CC) \$(LDFLAGS) -o/" \
+		-i source/Makefile || die #336533
+	epatch	"${FILESDIR}"/${P}-implicits.patch \
+		"${FILESDIR}"/${P}-modernize.patch
+}
+
+src_compile() {
+	emake -C source clean
+	emake -C source CC="$(tc-getCC)" \
+		CPPFLAGS=""
+}
+
+src_install() {
+	dobin "${S}"/source/dialign-tx
+	insinto /usr/$(get_libdir)/${PN}/conf
+	doins "${S}"/conf/*
+}
+
+pkg_postinst() {
+	einfo "The configuration directory is"
+	einfo "${ROOT}usr/$(get_libdir)/${PN}/conf"
+	einfo "You will need to pass this to ${PN} on every run."
+}
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
new file mode 100644
index 000000000000..a8388d03232f
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch
@@ -0,0 +1,18 @@
+--- source/museq.c
++++ source/museq.c
+@@ -38,6 +38,7 @@
+ //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
+ //		 struct prob_dist *pdist);
+ //extern struct diag_col *create_diag_col(int seq_amount);
++extern void free_diag(struct diag* dg);
+ extern void free_diag_col(struct diag_col* dcol);
+ extern struct diag_col *find_all_diags(struct scr_matrix *smatrix, 
+ 				struct prob_dist *pdist, 
+@@ -52,6 +53,7 @@
+ 
+ // alig.c
+ extern struct alignment* create_empty_alignment(struct seq_col *scol);
++extern void free_alignment(struct alignment *algn);
+ //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+ extern int  simple_aligner(struct seq_col *scol, struct diag_col *dcol, 
+ 			    struct scr_matrix* smatrix, 
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch
new file mode 100644
index 000000000000..b732e34da81c
--- /dev/null
+++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-modernize.patch
@@ -0,0 +1,130 @@
+Fix changed gnu89->gnu11 inline semantics with GCC-5, Gentoo Bug #570252
+https://bugs.gentoo.org/show_bug.cgi?id=570252
+
+In addition, fixed multiple -Wformat= warnings, such as
+
+io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 3 has type ‘int *’ [-Wformat=]
+   while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
+                    ^
+io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 4 has type ‘int *’ [-Wformat=]
+io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 5 has type ‘int *’ [-Wformat=]
+io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 6 has type ‘int *’ [-Wformat=]
+io.c:535:20: warning: format ‘%li’ expects argument of type ‘long int *’, but argument 7 has type ‘int *’ [-Wformat=]
+
+--- DIALIGN-TX_1.0.2/source/alig.c
++++ DIALIGN-TX_1.0.2/source/alig.c
+@@ -10,9 +10,9 @@
+ 
+ extern void error(char *message);
+ extern void merror(char *msg1, char *msg2);
+-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
++extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
+ 			struct prob_dist *pdist);
+-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
++extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
+ 		    struct prob_dist *pdist);
+ //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
+ extern struct diag* create_diag(struct seq_part* part1, struct seq_part* part2, 
+@@ -520,7 +520,7 @@
+  * datastructure (i.e. frontiers). The given diag must be consistent
+  * to the given alignment !
+  */
+-inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
++char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg) {
+ 
+   char alignedSomething = 0;
+   int i,j,k;
+--- DIALIGN-TX_1.0.2/source/assemble.c
++++ DIALIGN-TX_1.0.2/source/assemble.c
+@@ -10,9 +10,9 @@
+ 
+ extern void error(char *message);
+ extern void merror(char *msg1, char *msg2);
+-extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
++extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, 
+ 			struct prob_dist *pdist);
+-extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
++extern void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix, 
+ 		    struct prob_dist *pdist);
+ //extern struct seq_part* create_seq_part(int num, struct seq* aSeq, unsigned int startpos);
+ extern long double** create_tmp_pdist(struct prob_dist *pdist);
+@@ -22,7 +22,7 @@
+                          int n2, struct seq* sq2, unsigned int sp2,
+                          int dlength);
+ extern void free_diag(struct diag* dg);
+-extern inline struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,  
++extern struct simple_diag_col* find_diags_guided(struct scr_matrix *smatrix,  
+ 							struct prob_dist *pdist, 
+ 							struct gt_node* n1,  
+ 							struct gt_node* n2, 
+@@ -34,10 +34,10 @@
+ 
+ extern struct alignment* create_empty_alignment(struct seq_col *scol);
+ extern void free_alignment(struct alignment *algn);
+-extern inline struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
++extern struct algn_pos *find_eqc(struct algn_pos **ap, int seqnum, int pos);
+ extern struct alignment* copy_alignment( struct alignment *o_algn, struct alignment *algn, char doDgc);
+ //extern char adapt_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+-extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
++extern char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
+ //extern inline struct diag_cont* enter_sorted(struct diag_cont* backlog_diags, struct diag_cont *cand);
+ //extern inline char fit_fpos_diag(struct alignment *algn, struct diag* dg);
+ 
+--- DIALIGN-TX_1.0.2/source/diag.c
++++ DIALIGN-TX_1.0.2/source/diag.c
+@@ -183,7 +183,7 @@
+  * omitScore = 0:  normal 
+  * omitScore = 1:  no score calculation 
+  */ 
+-inline void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
++void real_calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
+ 		 struct prob_dist *pdist, char omitScore, long double **tmp_dist, struct alignment *algn ) { 
+    
+   if(dg->multi_dg) {
+@@ -302,7 +302,7 @@
+   } 
+ } 
+  
+-inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
++void calc_weight(struct diag* dg, struct scr_matrix* smatrix,  
+ 		 struct prob_dist *pdist) { 
+   real_calc_weight(dg, smatrix, pdist, 0,NULL,NULL); 
+ } 
+--- DIALIGN-TX_1.0.2/source/io.c
++++ DIALIGN-TX_1.0.2/source/io.c
+@@ -267,7 +267,7 @@
+     for( c=r; c<length; c++) {
+       // check whether it is a regular acid or a special character like '$',...
+       if( (r<length-additional) && (c<length-additional)) {
+-		fscanf( fp, "%i", &is);
++		if( fscanf( fp, "%i", &is) ){};
+       } else {
+ 		is = 0;
+       }
+@@ -279,7 +279,7 @@
+       // ensure symmetry of the weight matrix
+       data[length*c+r] = is;
+     }
+-    fscanf(fp, "%s\n", rline);
++    if( fscanf(fp, "%s\n", rline) ){};
+   }
+   fclose(fp);
+ 
+@@ -368,7 +368,7 @@
+     }
+     for(scr=0;scr<=mxscr;scr++) {
+       dist[i][scr]=1.0;
+-      fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
++      if( fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight ) ){};
+       //if(i!=ti || tscr!=scr) merror("read_scr_matrix(): (4) Invalid format of file ",filename);
+       scr = tscr;
+       if(weight==0.0) weight = 1.0;
+@@ -532,7 +532,7 @@
+   sdcol->data = malloc(sizeof (struct diag*)*alloc_size);
+   sdcol->length=0;
+ 
+-  while( fscanf(fp,"%li %li %li %li %li %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
++  while( fscanf(fp,"%i %i %i %i %i %le\n",&s1,&s2,&sp1,&sp2,&len,&score ) == 6) {
+     if(sdcol->length >= alloc_size) {
+       alloc_size+=16;
+       sdcol->data = realloc(sdcol->data,sizeof (struct diag*)*alloc_size);
diff --git a/sci-biology/dialign-tx/metadata.xml b/sci-biology/dialign-tx/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/dialign-tx/metadata.xml
@@ -0,0 +1,8 @@
+<?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>
+</pkgmetadata>