Moving to sci-biology/elph

6 files changed, 0 insertions, 209 deletions

diff --git a/app-sci/elph/ChangeLog b/app-sci/elph/ChangeLog
deleted file mode 100644
index e38981a9952b..000000000000
--- a/app-sci/elph/ChangeLog
+++ /dev/null
@@ -1,18 +0,0 @@
-# ChangeLog for app-sci/elph
-# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/elph/ChangeLog,v 1.4 2004/11/07 20:36:06 ribosome Exp $
-
-  07 Nov 2004; Olivier Fisette <ribosome@gentoo.org> metadata.xml,
-  -elph-0.1.2.ebuild, elph-0.1.4.ebuild:
-  Removed buggy version (0.1.2). Added 0.1.4 to x86. Set myself as
-  maintainer. Added long description.
-
-  30 Oct 2004; Olivier Fisette <ribosome@gentoo.org> +elph-0.1.4.ebuild
-  +files/elph-0.1.4-usage.patch :
-  New version.
-
-*elph-0.1.2 (22 May 2003)
-
-  22 May 2003; Jon Portnoy <avenj@gentoo.org> elph-0.1.2.ebuild :
-  Initial import. Ebuild submitted by Stephen Diener in bug
-  #21308.
diff --git a/app-sci/elph/Manifest b/app-sci/elph/Manifest
deleted file mode 100644
index de153bfcce16..000000000000
--- a/app-sci/elph/Manifest
+++ /dev/null
@@ -1,5 +0,0 @@
-MD5 949ade389190d12523f5edb5b7d1d16b elph-0.1.4.ebuild 936
-MD5 28f225644d3a653732d38a2b99b2277a ChangeLog 698
-MD5 13040a191bb49af836a11a1727f7841c metadata.xml 610
-MD5 75fe098a9b1df66ed55f16b4cfde3922 files/elph-0.1.4-usage.patch 3909
-MD5 170bc1e9213d1c70d75ae92411a3567c files/digest-elph-0.1.4 61
diff --git a/app-sci/elph/elph-0.1.4.ebuild b/app-sci/elph/elph-0.1.4.ebuild
deleted file mode 100644
index 721d228383af..000000000000
--- a/app-sci/elph/elph-0.1.4.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/elph/elph-0.1.4.ebuild,v 1.2 2004/11/07 20:36:06 ribosome Exp $
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
-HOMEPAGE="http://www.tigr.org/software/ELPH/index.shtml"
-SRC_URI="ftp://ftp.tigr.org/pub/software/ELPH/ELPH-${PV}.tar.gz"
-LICENSE="Artistic"
-
-SLOT="0"
-KEYWORDS="x86"
-IUSE=""
-
-S="${WORKDIR}/ELPH/sources"
-
-src_unpack() {
-	unpack ${A}
-	cd ${S}
-	epatch ${FILESDIR}/${P}-usage.patch
-	sed -i -e "s/CC      := g++/CC      := $(tc-getCXX)/" Makefile
-	sed -i -e "s/-fno-exceptions -fno-rtti -D_REENTRANT -g/${CXXFLAGS}/" Makefile
-	sed -i -e "s/LINKER    := g++/LINKER    := $(tc-getCXX)/" Makefile
-}
-
-src_compile() {
-	make || die
-}
-
-src_install() {
-	dobin elph
-	cd ${WORKDIR}/ELPH
-	dodoc VERSION
-	newdoc Readme.ELPH README
-}
diff --git a/app-sci/elph/files/digest-elph-0.1.4 b/app-sci/elph/files/digest-elph-0.1.4
deleted file mode 100644
index 623e842d2d74..000000000000
--- a/app-sci/elph/files/digest-elph-0.1.4
+++ /dev/null
@@ -1 +0,0 @@
-MD5 5065b4d6062d8654fae5337cf0ea0e01 ELPH-0.1.4.tar.gz 40181
diff --git a/app-sci/elph/files/elph-0.1.4-usage.patch b/app-sci/elph/files/elph-0.1.4-usage.patch
deleted file mode 100644
index be49e2d1ebb8..000000000000
--- a/app-sci/elph/files/elph-0.1.4-usage.patch
+++ /dev/null
@@ -1,133 +0,0 @@
---- elph.cc~	2003-06-03 14:45:22.000000000 -0400
-+++ elph.cc	2004-10-30 10:14:49.220415168 -0400
-@@ -26,11 +26,11 @@
-                    period variable\n\
-   -x             : print maximum positions within sequences\n\
-   -g             : find significance of motif\n\
--  -t <matrix>    : test if there is significant difference between the two 
--                   input files for a given motif matrix; <matrix> is the file
-+  -t <matrix>    : test if there is significant difference between the two\n\
-+                   input files for a given motif matrix; <matrix> is the file\n\
-                    containing the motif matrix\n\
--  -l             : compute Least Likely Consensus (LLC) for given motif 
--  -c             : in conjunction with -m option: motif is not necessarily in 
-+  -l             : compute Least Likely Consensus (LLC) for given motif\n\
-+  -c             : in conjunction with -m option: motif is not necessarily in\n\
-                    the closest edit distance from input motif\n\
-   LEN=n          : n = length of motif\n\
-   ITERNO=n       : n = no of iterations to compute the global maximum;\n\
-@@ -41,7 +41,7 @@
-                    default = 1000\n\
-  "
- 
--// global variables: 
-+// global variables:
- int ITER_NO=10;
- int MAX_LOOP=500;
- int printmax=0;
-@@ -66,7 +66,7 @@
-   seqType t;
- 
-   GArgs args(argc, argv, "ho:abglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO=");
--  
-+
-   // == Process arguments.
- 
-   int e;
-@@ -83,7 +83,7 @@
- 
-   if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files
- 
--    M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);    
-+    M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
-     M->twofilesignif(gdet,testfile,SignifNo,print,pattern);
- 
-   }
-@@ -93,11 +93,11 @@
-                             // given motif
- 
-       M = new Motif(infile,outf,t,pattern);
--      if(defLLC) { 
-+      if(defLLC) {
- 	double llc=M->computeLLC(pattern,print);
- 	fprintf(outf,"LLC = %f\n",llc);
-       }
--      
-+
-     }
-     else {
- 
-@@ -108,7 +108,7 @@
-     }
- 
-     double globAlignProb;
--    
-+
-     globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet);
- 
- 
-@@ -116,13 +116,13 @@
-     /*info=M->InfoPar(globAlignProb);
-       fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info);
-       M->printMotif();*/
--    
-+
-     // optimizing
-     fprintf(stderr,"Optimizing...\n");
-     globAlignProb=M->optimize(globAlignProb,info,closest);
-     fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n");
-     fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb));
--    
-+
-     if(runsignif) {
-       M->runforsignif(SignifNo,print,gdet,pattern);
-     }
-@@ -134,17 +134,17 @@
- 
- seqType Process_Options(GArgs* args)
- {
--    
--  if (args->startNonOpt()) { //parse the non-options arguments 
-+
-+  if (args->startNonOpt()) { //parse the non-options arguments
-                           //(usually filenames)
-         infile=args->nextNonOpt();
-   }
- 
--  if (infile.is_empty() || args->getOpt('h')!=NULL) 
-+  if (infile.is_empty() || args->getOpt('h')!=NULL)
-     GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input
- 
-   testfile=args->nextNonOpt();
--  
-+
-   GString outfile=args->getOpt('o');
-   if (!outfile.is_empty()) {
-     outf=fopen(outfile, "w");
-@@ -156,7 +156,7 @@
-   matrixfile=args->getOpt('t');
- 
-   GString param;
--  
-+
-   pattern=args->getOpt('m');
-   if(pattern.is_empty()) {
-     param=args->getOpt("LEN");
-@@ -200,7 +200,7 @@
- 
-   seqType t;
-   if(args->getOpt('a')!=NULL) t=aac; else t=nucl;
--  
-+
-   return(t);
- 
- }
-@@ -210,7 +210,7 @@
-   Motif *M;
- 
-   double llcmax=-HUGE_VAL;
--  GString seed;	
-+  GString seed;
-   for(int i1=0;i1<4;i1++)
-     for(int i2=0;i2<4;i2++)
-       for(int i3=0;i3<4;i3++)
diff --git a/app-sci/elph/metadata.xml b/app-sci/elph/metadata.xml
deleted file mode 100644
index ffbf25e2aaae..000000000000
--- a/app-sci/elph/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer>
-		<email>ribosome@gentoo.org</email>
-		<name>Olivier Fisette</name>
-	</maintainer>
-	<herd>sci</herd>
-	<longdescription>
-		ELPH is a general-purpose Gibbs sampler for finding motifs in a set of
-		DNA or protein sequences. The program takes as input a set containing
-		anywhere from a few dozen to thousands of sequences, and searches
-		through them for the most common motif, assuming that each sequence
-		contains one copy of the motif.
-	</longdescription>
-</pkgmetadata>