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sci-biology/elph: Remove old
Package-Manager: Portage-2.3.4, Repoman-2.3.2 Closes: https://github.com/gentoo/gentoo/pull/4165
This commit is contained in:
David Seifert
@@ -1,2 +1 @@
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DIST ELPH-0.1.5.tar.gz 153150 SHA256 6ffa160f85cb2569bdf869cb0514dc624afcef4f2d8a36efbd1228d1a16cf361 SHA512 6a413d1141d8bbe88de8db64657beaf557331c11aa91add7316d301bfd71d8febf8a27aca6e56ed16e94c3d02f4932d7bc367819fceca387925d6ef6591b7a3f WHIRLPOOL d87835f180d33377dad7a23dc3fe5b78777baea1baeda588c897c6250b3eec9f68f66ee9951164764f6826b606f3081e060a10db2667b13e5580c5df355c1ad0
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DIST ELPH-1.0.1.tar.gz 113476 SHA256 6d944401d2457d75815a34dbb5780f05df569eb1edfd00909b33c4c4c4ff40b9 SHA512 a76cdcdaa1dc406fb0f1204b6a40ffc9f4c0840611b960a3d4299d447446e5bbf941abe7f70cee38f69a64862e186133fd60c1aac18b4b58d86f2ed5c4dd7d72 WHIRLPOOL 598dc3f95c93e5e36bcd20de3c985c22d650462ab27df31af54ca5b5b50c0a60fcc47637a41c449bdf7e572cee097289916aca4f0de79b804854d233ff3e20ff
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@@ -1,36 +0,0 @@
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# Copyright 1999-2008 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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inherit eutils toolchain-funcs
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DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
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LICENSE="Artistic"
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HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"
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SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"
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SLOT="0"
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IUSE=""
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KEYWORDS="x86"
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S="${WORKDIR}/ELPH/sources"
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src_unpack() {
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unpack ${A}
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cd "${S}"
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epatch "${FILESDIR}"/${P}-usage.patch
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sed -i -e "s/CC := g++/CC := $(tc-getCXX)/" \
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-e "s/-fno-exceptions -fno-rtti -D_REENTRANT -g/${CXXFLAGS}/" \
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-e "s/LINKER := g++/LINKER := $(tc-getCXX)/" \
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Makefile || die "Failed to patch Makefile."
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}
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src_compile() {
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make || die "Compilation failed."
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}
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src_install() {
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dobin elph || die "Failed to install program."
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cd "${WORKDIR}"/ELPH
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dodoc VERSION || die "Documentation installation failed."
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newdoc Readme.ELPH README || die "Readme installation failed."
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}
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@@ -1,27 +0,0 @@
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# Copyright 1999-2010 Gentoo Foundation
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# Distributed under the terms of the GNU General Public License v2
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inherit eutils toolchain-funcs
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DESCRIPTION="Estimated Locations of Pattern Hits - Motif finder program"
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LICENSE="Artistic"
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HOMEPAGE="http://cbcb.umd.edu/software/ELPH/"
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SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/elph/ELPH-${PV}.tar.gz"
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SLOT="0"
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IUSE=""
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
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S=${WORKDIR}/ELPH/sources
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src_compile() {
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emake CC="$(tc-getCXX)" LINKER="$(tc-getCXX)" \
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CFLAGS="${CXXFLAGS} -D_REENTRANT" LDFLAGS="${LDFLAGS}" || die
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}
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src_install() {
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dobin elph || die "Failed to install program."
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cd "${WORKDIR}"/ELPH
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dodoc VERSION || die "Documentation installation failed."
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newdoc Readme.ELPH README || die "Readme installation failed."
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}
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@@ -1,133 +0,0 @@
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--- elph.cc.old 2005-01-11 14:17:47.000000000 -0500
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+++ elph.cc 2005-01-27 19:42:30.218350552 -0500
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@@ -26,11 +26,11 @@
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period variable\n\
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-x : print maximum positions within sequences\n\
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-g : find significance of motif\n\
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- -t <matrix> : test if there is significant difference between the two
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- input files for a given motif matrix; <matrix> is the file
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+ -t <matrix> : test if there is significant difference between the two\n\
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+ input files for a given motif matrix; <matrix> is the file\n\
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containing the motif matrix\n\
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- -l : compute Least Likely Consensus (LLC) for given motif
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- -c : in conjunction with -m option: motif is not necessarily in
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+ -l : compute Least Likely Consensus (LLC) for given motif\n\
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+ -c : in conjunction with -m option: motif is not necessarily in\n\
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the closest edit distance from input motif\n\
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LEN=n : n = length of motif\n\
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ITERNO=n : n = no of iterations to compute the global maximum;\n\
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@@ -41,7 +41,7 @@
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default = 1000\n\
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"
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-// global variables:
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+// global variables:
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int ITER_NO=10;
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int MAX_LOOP=500;
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int printmax=0;
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@@ -66,7 +66,7 @@
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seqType t;
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GArgs args(argc, argv, "ho:abcglvdxt:p:s:m:n:LEN=ITERNO=MAXLOOP=SGFNO=");
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-
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+
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// == Process arguments.
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int e;
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@@ -83,7 +83,7 @@
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if(!testfile.is_empty()) { // if testfile is defined then only compute significance between the two files
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- M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
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+ M = new Motif(infile,outf,t,matrixfile,pattern,motiflen,ITER_NO,MAX_LOOP,inlocmax,mdet);
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M->twofilesignif(gdet,testfile,SignifNo,print,pattern);
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}
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@@ -93,11 +93,11 @@
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// given motif
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M = new Motif(infile,outf,t,pattern);
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- if(defLLC) {
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+ if(defLLC) {
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double llc=M->computeLLC(pattern,print);
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fprintf(outf,"LLC = %f\n",llc);
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}
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-
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+
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}
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else {
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@@ -108,7 +108,7 @@
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}
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double globAlignProb;
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-
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+
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globAlignProb=M->findMotif(ITER_NO,MAX_LOOP,inlocmax,1,mdet);
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@@ -116,13 +116,13 @@
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/*info=M->InfoPar(globAlignProb);
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fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,info);
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M->printMotif();*/
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-
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+
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// optimizing
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fprintf(stderr,"Optimizing...\n");
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globAlignProb=M->optimize(globAlignProb,info,closest);
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fprintf(outf,"\n\n**********************\n\nMotif after optimizing\n");
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fprintf(outf,"MAP for motif: %.3f InfoPar=%.3f\n\n",globAlignProb,M->InfoPar(globAlignProb));
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-
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+
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if(runsignif) {
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M->runforsignif(SignifNo,print,gdet,pattern);
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}
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@@ -134,17 +134,17 @@
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seqType Process_Options(GArgs* args)
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{
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-
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- if (args->startNonOpt()) { //parse the non-options arguments
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+
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+ if (args->startNonOpt()) { //parse the non-options arguments
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//(usually filenames)
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infile=args->nextNonOpt();
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}
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- if (infile.is_empty() || args->getOpt('h')!=NULL)
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+ if (infile.is_empty() || args->getOpt('h')!=NULL)
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GError("%s",usage); // the empty test is optional you can ignore it if you accept stdin input
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testfile=args->nextNonOpt();
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-
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+
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GString outfile=args->getOpt('o');
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if (!outfile.is_empty()) {
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outf=fopen(outfile, "w");
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@@ -156,7 +156,7 @@
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matrixfile=args->getOpt('t');
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GString param;
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-
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+
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pattern=args->getOpt('m');
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if(pattern.is_empty()) {
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param=args->getOpt("LEN");
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@@ -200,7 +200,7 @@
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seqType t;
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if(args->getOpt('a')!=NULL) t=aac; else t=nucl;
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-
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+
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return(t);
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}
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@@ -210,7 +210,7 @@
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Motif *M;
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double llcmax=-HUGE_VAL;
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- GString seed;
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+ GString seed;
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for(int i1=0;i1<4;i1++)
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for(int i2=0;i2<4;i2++)
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for(int i3=0;i3<4;i3++)
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