diff options
| -rw-r--r-- | sci-biology/elph/ChangeLog | 10 | ||||
| -rw-r--r-- | sci-biology/elph/Manifest | 17 | ||||
| -rw-r--r-- | sci-biology/elph/elph-0.1.4.ebuild | 4 | ||||
| -rw-r--r-- | sci-biology/elph/elph-0.1.5.ebuild | 36 | ||||
| -rw-r--r-- | sci-biology/elph/files/digest-elph-0.1.5 | 1 | ||||
| -rw-r--r-- | sci-biology/elph/files/elph-0.1.5-usage.patch | 133 |
6 files changed, 185 insertions, 16 deletions
diff --git a/sci-biology/elph/ChangeLog b/sci-biology/elph/ChangeLog index 98b9ce1b0bde..b3d325f73a25 100644 --- a/sci-biology/elph/ChangeLog +++ b/sci-biology/elph/ChangeLog @@ -1,6 +1,12 @@ # ChangeLog for sci-biology/elph -# Copyright 2000-2004 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/ChangeLog,v 1.2 2004/12/23 20:16:48 swegener Exp $ +# Copyright 2000-2005 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/ChangeLog,v 1.3 2005/01/28 00:47:21 ribosome Exp $ + +*elph-0.1.5 (27 Jan 2005) + + 27 Jan 2005; Olivier Fisette <ribosome@gentoo.org> + +files/elph-0.1.5-usage.patch, +elph-0.1.5.ebuild: + New version. *elph-0.1.4 (23 Dec 2004) diff --git a/sci-biology/elph/Manifest b/sci-biology/elph/Manifest index ee2212eddb85..54af551f803f 100644 --- a/sci-biology/elph/Manifest +++ b/sci-biology/elph/Manifest @@ -1,15 +1,8 @@ ------BEGIN PGP SIGNED MESSAGE----- -Hash: SHA1 - -MD5 0749629e5d0bf9ad5e76a8b930de7294 elph-0.1.4.ebuild 940 -MD5 b3f72a573aef9beb43716b0c86b3c112 ChangeLog 902 +MD5 1a97b990dfa706d43f84306022589d4f elph-0.1.5.ebuild 941 +MD5 5b3d82bbc7b343bb1438579bb8eb0854 elph-0.1.4.ebuild 940 +MD5 a856a5676c398f6d50105884a1c1d179 ChangeLog 1051 MD5 13040a191bb49af836a11a1727f7841c metadata.xml 610 MD5 75fe098a9b1df66ed55f16b4cfde3922 files/elph-0.1.4-usage.patch 3909 +MD5 fdc58c9dcd2752ace3fb6520676c8414 files/elph-0.1.5-usage.patch 3913 MD5 170bc1e9213d1c70d75ae92411a3567c files/digest-elph-0.1.4 61 ------BEGIN PGP SIGNATURE----- -Version: GnuPG v1.9.10 (GNU/Linux) - -iD8DBQFByye2I1lqEGTUzyQRAsUsAKCCppm0zIJdxzep/14Hp95DPn6v8ACgrKpm -3v9rfLJ6EWezcNDsXlMjOqM= -=lUT8 ------END PGP SIGNATURE----- +MD5 edfbe76f341ee7fc8c683b7fe0b023bd files/digest-elph-0.1.5 62 diff --git a/sci-biology/elph/elph-0.1.4.ebuild b/sci-biology/elph/elph-0.1.4.ebuild index f3c41366b157..c74b9187477e 100644 --- a/sci-biology/elph/elph-0.1.4.ebuild +++ b/sci-biology/elph/elph-0.1.4.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2004 Gentoo Foundation +# Copyright 1999-2005 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/elph-0.1.4.ebuild,v 1.1 2004/12/23 18:22:19 ribosome Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/elph-0.1.4.ebuild,v 1.2 2005/01/28 00:47:21 ribosome Exp $ inherit eutils toolchain-funcs diff --git a/sci-biology/elph/elph-0.1.5.ebuild b/sci-biology/elph/elph-0.1.5.ebuild new file mode 100644 index 000000000000..ea8c56129428 --- /dev/null +++ b/sci-biology/elph/elph-0.1.5.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2005 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/elph/elph-0.1.5.ebuild,v 1.1 2005/01/28 00:47:21 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/sci-biology/elph/files/digest-elph-0.1.5 b/sci-biology/elph/files/digest-elph-0.1.5 new file mode 100644 index 000000000000..a19bc4883e4a --- /dev/null +++ b/sci-biology/elph/files/digest-elph-0.1.5 @@ -0,0 +1 @@ +MD5 0c1d0bbef483e7ee46ffb6b26824682c ELPH-0.1.5.tar.gz 153150 diff --git a/sci-biology/elph/files/elph-0.1.5-usage.patch b/sci-biology/elph/files/elph-0.1.5-usage.patch new file mode 100644 index 000000000000..139b83c1c1c6 --- /dev/null +++ b/sci-biology/elph/files/elph-0.1.5-usage.patch @@ -0,0 +1,133 @@ +--- elph.cc.old 2005-01-11 14:17:47.000000000 -0500 ++++ elph.cc 2005-01-27 19:42:30.218350552 -0500 +@@ -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:abcglvdxt: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++) |