reinit the tree, so we can have metadata

6 files changed, 421 insertions, 0 deletions

diff --git a/sci-biology/trnascan-se/Manifest b/sci-biology/trnascan-se/Manifest
new file mode 100644
index 000000000000..d5df13d2c367
--- /dev/null
+++ b/sci-biology/trnascan-se/Manifest
@@ -0,0 +1,8 @@
+AUX trnascan-se-1.23-glibc-2.10.patch 6702 SHA256 16c6083f8a2991d22252a23184a45c74e0fd75b5a45085c3dcea7d1cd503cf42 SHA512 2df0a5d6bf633b9b1c1ccce002c5a751a3f5c5eedf755b24a3af1a6d07a93816b6be4195aa3142ebcbd16ad9b373223f398fbac1d91769b26be1d295f080f181 WHIRLPOOL d8bc3d22d50446ffc628276261d091cb0552e564c0d80c9c6fe6e4108c3c036a11fadd48c45a115fef56ac01a49df0b7a0cebb026fcff05344822c29b074f971
+AUX trnascan-se-1.23-ldflags.patch 971 SHA256 6013162268bc78f6752ce8703d9fd1810f634a9176b55dac67155b8decb8e6e9 SHA512 bcfdc71dc8454e110d45f44bf9c4a0b4e77ca85bcf0b501dd2de60c47418bc5d442b1ac976c6a333eb4398a12e4478b8817436246a1f872df208d5eaf64c3ac2 WHIRLPOOL f1afc811efcc061a114ab6b14ac2ef4ce8c7091bdfa6a392ac55dd6f1e38f1d1ded94f218309e2e3abd515ef80bffbefd7e4ed30d993e16603c0477b988f48b3
+AUX trnascan-se-1.31-ldflags.patch 973 SHA256 e103841dfe3f289493c80fc938a3c9318a550e160b3269b9856405ee48dc648a SHA512 ff677ce9ac3ed9299f6a3bf977642e2a6c300a1b801436bb5d3787968cfe28357a0ec23d0438f0b15c06324cd7e1bbbda590c8fb5574577a3f653779316931df WHIRLPOOL 2ba11012cd414d2dc9a523109bfebe726a347558cf1098f52410fc88c652665e6babeaef5581dce12fdd1a83af8ed417d8040ef481d5036a9632838f997333c2
+DIST trnascan-se-1.31.tar.gz 740960 SHA256 862924d869453d1c111ba02f47d4cd86c7d6896ff5ec9e975f1858682282f316 SHA512 ba55bc8dfa7e5aee9c9a86c135a55b767cda083b74668bd9af4aaaeb693f9c3a17dc8bade5793de12b775564f09fbb861b0ab4f25bf83ccb0954fecd01bb328d WHIRLPOOL aef8b9f8d44799bac134a36af45374cdaba4b30c041e71e3095252aa8272fe9bd0aa76091211ac270ad609f67f388d577a83ec2ed2433997963fd5708c5b6665
+EBUILD trnascan-se-1.31.ebuild 1191 SHA256 f70623b4b41a9efe071bb98865a3eb1ecc67293f42371d32ed118c47c3fb6ebb SHA512 d79fa9d244d4f3ab98fff94aca074bd23cc953c0b812a270daca2e80c440fcdcfd38e92cba2eea6ccd2ad9873c8fb898f46b9f4356c638d01fa0f2b21e23c55b WHIRLPOOL 564cd24e354568dfcedf143fe6a60746ee282c334e6ee20fde196803cf57a237c52913be7be1ef559b0403bdb8676cc9bb3429e4f9f27dcd4b71b6c5c8f4527b
+MISC ChangeLog 2630 SHA256 c56279b0e6cc8f7d84de536b5b3c6a8b152ead15a41f8a2927ef13a0691251e3 SHA512 d1a2dd013269faa1608f1015ff965ffe35c56df2001a6be7a64d6e5589c20dbf4e3b3732d3696e06ac08c78eb7933dd2736c293f5a591854375db76967524c2e WHIRLPOOL e25bad73167056904784b8b236615c58f1f2e107727265139147950600daf703ba2bd55453977f4cba2ae9fb416ef392625fa07ac25868664ccaefcf303b5673
+MISC ChangeLog-2015 2136 SHA256 c029d5251ef50292b150acebe84c985fc78797e026570389855ec6f5d48243a9 SHA512 5163d5de7b8962b0b744bf632db8cc3614970ae792c04d423f8a016c6757a8583053e05836fabb8dfb7bf2e78cba2d872fa18438689d2bcbbcaaedd9d7009472 WHIRLPOOL 90cc0c3fc4dcecb496558acb97b0e1c5f529c9dc4d1b05a2533991560b4d448927f945226b12f581b39bfbe05b86f068b3430368bfcb384e3384b499091a3b11
+MISC metadata.xml 608 SHA256 f64eaf62ed800ea168869df240fc649a3141d18509ca545d46577656a74d83cf SHA512 d94549c3878aa8a32f107bfe2cebb07e9965b61fe2cfa030211b98db2e98b2aad71e5e4e7fbeb97ba2767f6a0dc244992045da13560c2e3f3cad3044a86ef826 WHIRLPOOL d7bf3b4559c5082f7c5963c9b71fb4ca746fb5cf107b5f550478cd4fbeba763f1db2dd5fb645e5d18fe7ebd38e72fb66a26e9f43e25b6fb8052da7b74f59ca43
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
new file mode 100644
index 000000000000..e21da6e58db0
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-glibc-2.10.patch
@@ -0,0 +1,292 @@
+diff -ur trnascan-se-1.23.orig/sqio.c trnascan-se-1.23/sqio.c
+--- trnascan-se-1.23.orig/sqio.c	2002-04-12 23:12:04.000000000 +0300
++++ trnascan-se-1.23/sqio.c	2009-08-05 21:45:53.000000000 +0300
+@@ -235,7 +235,7 @@
+ }
+ 
+ static void 
+-getline(struct ReadSeqVars *V)
++get_line(struct ReadSeqVars *V)
+ {
+   readline(V->f, V->sbuffer);
+ }
+@@ -306,7 +306,7 @@
+   V->seqlen = 0;
+   if (addfirst) addseq(V->sbuffer, V);
+   do {
+-    getline(V);
++    get_line(V);
+     done = feof(V->f);
+     done |= (*endTest)(V->sbuffer, &addend);
+     if (addend || !done)
+@@ -332,7 +332,7 @@
+   char *sptr;
+ 				/* load first line of entry  */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    get_line(V);
+   if (feof(V->f)) return;
+ 
+   if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL)
+@@ -341,7 +341,7 @@
+       SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID);
+     }
+   do {
+-    getline(V);
++    get_line(V);
+     if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0)
+       SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC);
+     else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0)
+@@ -350,7 +350,7 @@
+ 	  SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC);
+       }
+   } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0));
+-  getline(V);			/* skip next line, coords */
++  get_line(V);			/* skip next line, coords */
+ 
+   readLoop(0, endPIR, V);
+ 
+@@ -364,7 +364,7 @@
+   /* get next line
+    */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -382,7 +382,7 @@
+   char *nm;
+ 				/* position past ';' comments */
+   do {
+-    getline(V);
++    get_line(V);
+   } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) ));
+ 
+   if (!feof(V->f))
+@@ -394,7 +394,7 @@
+     }
+   
+   while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int 
+@@ -416,7 +416,7 @@
+ 	  if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL)
+ 	    SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME);
+ 	}
+-      getline(V);
++      get_line(V);
+     }
+ 
+   if (! feof(V->f))
+@@ -425,7 +425,7 @@
+   /* load next line
+    */
+   while ((!feof(V->f)) && (*V->sbuffer != ';')) 
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -443,7 +443,7 @@
+   int   in_definition;
+ 
+   while (strncmp(V->sbuffer, "LOCUS", 5) != 0)
+-    getline(V);
++    get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL)
+     {
+@@ -454,7 +454,7 @@
+   in_definition = FALSE;
+   while (! feof(V->f))
+     {
+-      getline(V);
++      get_line(V);
+       if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer)
+ 	{
+ 	  if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL)
+@@ -487,11 +487,11 @@
+ 
+ 
+   while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer))))
+-    getline(V);
++    get_line(V);
+ 				/* SRE: V->s now holds "//", so sequential
+ 				   reads are wedged: fixed Tue Jul 13 1993 */
+   while (!feof(V->f) && strstr(V->sbuffer, "LOCUS  ") != V->sbuffer)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int
+@@ -521,12 +521,12 @@
+   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+ 
+-  getline(V);   /*skip title-junk line*/
++  get_line(V);   /*skip title-junk line*/
+ 
+   readLoop(0, endNBRF, V);
+ 
+   while (!(feof(V->f) || (*V->sbuffer != 0 && *V->sbuffer == '>')))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -559,7 +559,7 @@
+   } else Die("bogus GCGdata format? %s", V->sbuffer);
+ 
+ 				/* second line contains free text description */
+-  getline(V);
++  get_line(V);
+   SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC);
+ 
+   if (binary) {
+@@ -579,7 +579,7 @@
+   else readLoop(0, endGCGdata, V);
+   
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static int
+@@ -625,7 +625,7 @@
+     readLoop(0, endPearson, V);
+ 
+   while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>'))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -652,7 +652,7 @@
+ 
+ 				/* make sure we have first line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL)
+     {
+@@ -661,7 +661,7 @@
+     }
+ 
+   do {
+-    getline(V);
++    get_line(V);
+     if (!feof(V->f) && strstr(V->sbuffer, "AC  ") == V->sbuffer)
+       {
+ 	if ((sptr = strtok(V->sbuffer+5, ";  \t\n")) != NULL)
+@@ -685,7 +685,7 @@
+ 
+ 				/* load next record's ID line */
+   while (!feof(V->f) && strncmp(V->sbuffer, "ID  ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -701,7 +701,7 @@
+ {
+   char *sptr;
+ 
+-  getline(V);  /*s == "seqLen seqid string..."*/
++  get_line(V);  /*s == "seqLen seqid string..."*/
+ 
+   if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -712,7 +712,7 @@
+   readLoop(0, endZuker, V);
+ 
+   while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '('))))
+-    getline(V);
++    get_line(V);
+ }
+ 
+ static void 
+@@ -734,7 +734,7 @@
+ 
+   do {
+     done = feof(V->f);
+-    getline(V);
++    get_line(V);
+     if (! done) addseq(V->sbuffer, V);
+   } while (!done);
+ }
+@@ -746,7 +746,7 @@
+   char *sptr;
+   int   dostruc = FALSE;
+ 
+-  while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V);
++  while (strncmp(V->sbuffer, "NAM ", 4) != 0) get_line(V);
+ 
+   if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL)
+     SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME);
+@@ -754,7 +754,7 @@
+   /*CONSTCOND*/
+   while (1)
+     {
+-      getline(V);
++      get_line(V);
+       if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; }
+ 
+       if (strncmp(V->sbuffer, "SRC ", 4) == 0)
+@@ -786,14 +786,14 @@
+   while (1)
+     {
+ 				/* sequence line */
+-      getline(V);
++      get_line(V);
+       if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) 
+ 	break;
+       addseq(V->sbuffer, V);
+ 				/* structure line */
+       if (dostruc)
+ 	{
+-	  getline(V);
++	  get_line(V);
+ 	  if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; }
+ 	  addstruc(V->sbuffer, V);
+ 	}
+@@ -801,7 +801,7 @@
+ 
+ 
+   while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0)
+-    getline(V);
++    get_line(V);
+ }
+ 
+ 
+@@ -848,7 +848,7 @@
+ 
+   /* Load the first line.
+    */
+-  getline(dbfp);
++  get_line(dbfp);
+ 
+   return dbfp;
+ }
+@@ -862,7 +862,7 @@
+ SeqfilePosition(SQFILE *sqfp, long offset)
+ {
+   fseek(sqfp->f, offset, SEEK_SET);
+-  getline(sqfp);
++  get_line(sqfp);
+ }
+ 
+ 
+@@ -954,7 +954,7 @@
+ 	do {			/* skip leading comments on GCG file */
+ 	  gotuw = (strstr(V->sbuffer,"..") != NULL);
+ 	  if (gotuw) readUWGCG(V);
+-	  getline(V);
++	  get_line(V);
+ 	} while (! feof(V->f));
+ 	break;
+ 
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
new file mode 100644
index 000000000000..783e4340823d
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.23-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 53e5c5b..a2d3feb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
+ all: 	$(PROGS) tRNAscanSE setpaths
+ 
+ covels-SE:  $(OBJ) scan_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+ 
+ coves-SE: $(OBJ) score_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+ 
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+-	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o eufindtRNA eufind_main.o \
+ 	pavesi.o $(SQUIDOBJ) $(LIBS)
+ 
+ trnascan-1.4: trnascan.o
+-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
+ 
+ tRNAscanSE:
+ 	$(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
new file mode 100644
index 000000000000..f28b1e8f6bb0
--- /dev/null
+++ b/sci-biology/trnascan-se/files/trnascan-se-1.31-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/Makefile b/Makefile
+index 53e5c5b..a2d3feb 100644
+--- a/Makefile
++++ b/Makefile
+@@ -109,17 +109,17 @@ MPOBJ = mpviterbi.o mp-dbviterbi.o
+ all: 	$(PROGS) tRNAscan-SE setpaths
+ 
+ covels-SE:  $(OBJ) scan_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS)
+ 
+ coves-SE: $(OBJ) score_main.o
+-	$(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
++	$(CC) $(CFLAGS) $(RFLAGS) $(LDFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS)
+ 
+ eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o
+-	$(CC) $(CFLAGS)  -o eufindtRNA eufind_main.o \
++	$(CC) $(CFLAGS)  $(LDFLAGS) -o eufindtRNA eufind_main.o \
+ 	pavesi.o $(SQUIDOBJ) $(LIBS)
+ 
+ trnascan-1.4: trnascan.o
+-	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c
++	$(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" $(LDFLAGS) -o trnascan-1.4 trnascan.c
+ 
+ tRNAscan-SE:
+ 	$(PERLDIR)/$(PERLBIN) checkversion.pl
diff --git a/sci-biology/trnascan-se/metadata.xml b/sci-biology/trnascan-se/metadata.xml
new file mode 100644
index 000000000000..ab96459c84db
--- /dev/null
+++ b/sci-biology/trnascan-se/metadata.xml
@@ -0,0 +1,15 @@
+<?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>
+		tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA
+		genes, with a false positive rate of less than one per 15 gigabases,
+		and with a search speed of about 30 kb/second. It was implemented for
+		large-scale human genome sequence analysis, but is applicable to
+		other DNAs as well.
+	</longdescription>
+</pkgmetadata>
diff --git a/sci-biology/trnascan-se/trnascan-se-1.31.ebuild b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
new file mode 100644
index 000000000000..cd8dc152d6d2
--- /dev/null
+++ b/sci-biology/trnascan-se/trnascan-se-1.31.ebuild
@@ -0,0 +1,54 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit perl-functions toolchain-funcs
+
+DESCRIPTION="tRNA detection in large-scale genome sequences"
+HOMEPAGE="http://lowelab.ucsc.edu/tRNAscan-SE/"
+SRC_URI="http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+S="${WORKDIR}"/tRNAscan-SE-1.3.1/
+
+PATCHES=(
+	"${FILESDIR}"/${P}-ldflags.patch
+)
+
+src_prepare() {
+	default
+	sed \
+		-e "s:BINDIR  = \$(HOME)/bin:BINDIR = ${EPREFIX}/usr/bin:" \
+		-e "s:LIBDIR  = \$(HOME)/lib/tRNAscan-SE:LIBDIR = ${EPRFIX}/usr/share/${PN}:" \
+		-e "s:MANDIR  = \$(HOME)/man:MANDIR = ${EPREFIX}/usr/share/man:" \
+		-e "s:CC = gcc:CC = $(tc-getCC):" \
+		-e "s:CFLAGS = -O:CFLAGS = ${CFLAGS}:" \
+		-i Makefile || die
+
+	perl_set_version
+}
+
+src_test() {
+	emake PATH="${S}:${PATH}" testrun
+}
+
+src_install() {
+	dobin covels-SE coves-SE eufindtRNA tRNAscan-SE trnascan-1.4
+
+	newman tRNAscan-SE.man tRNAscan-SE.man.1
+
+	dodoc MANUAL README Release.history
+
+	insinto /usr/share/${PN}/
+	doins *.cm gcode.* Dsignal TPCsignal
+
+	dodoc Manual.ps
+
+	insinto ${VENDOR_LIB}
+	doins -r tRNAscanSE
+}