diff options
| -rw-r--r-- | academic/PhyML/20131112.patch (renamed from academic/PhyML/20130219.patch) | 90 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.SlackBuild | 35 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.info | 4 | ||||
| -rw-r--r-- | academic/PhyML/README | 2 | ||||
| -rw-r--r-- | academic/PhyML/References | 4 |
5 files changed, 117 insertions, 18 deletions
diff --git a/academic/PhyML/20130219.patch b/academic/PhyML/20131112.patch index 59250c71db..e7eb2670b6 100644 --- a/academic/PhyML/20130219.patch +++ b/academic/PhyML/20131112.patch @@ -1,5 +1,4 @@ -Common subdirectories: ./phyml-20120412/src/.deps and ./phyml-20120412-new-bak/src/.deps -diff -uN ./phyml-20120412/src/help.c ./phyml-20120412-new-bak/src/help.c +unchanged: --- ./phyml-20120412/src/help.c 2011-09-22 14:51:57.000000000 +1200 +++ ./phyml-20120412-new-bak/src/help.c 2013-02-18 21:51:51.448662440 +1300 @@ -96,7 +96,7 @@ @@ -11,7 +10,7 @@ diff -uN ./phyml-20120412/src/help.c ./phyml-20120412-new-bak/src/help.c PhyML_Printf("%s\t\tChanges interleaved format (default) to sequential format.\n",FLAT); PhyML_Printf("\n"); -diff -uN ./phyml-20120412/src/lk.c ./phyml-20120412-new-bak/src/lk.c +unchanged: --- ./phyml-20120412/src/lk.c 2012-04-05 14:47:37.000000000 +1200 +++ ./phyml-20120412-new-bak/src/lk.c 2013-02-19 10:22:22.665284529 +1300 @@ -472,7 +472,7 @@ @@ -217,7 +216,7 @@ diff -uN ./phyml-20120412/src/lk.c ./phyml-20120412-new-bak/src/lk.c if(p_lk[site*NsNg+catg*Ns+i] < smallest_p_lk) smallest_p_lk = p_lk[site*NsNg+catg*Ns+i] ; } -diff -uN ./phyml-20120412/src/Makefile ./phyml-20120412-new-bak/src/Makefile +unchanged: --- ./phyml-20120412/src/Makefile 1970-01-01 12:00:00.000000000 +1200 +++ ./phyml-20120412-new-bak/src/Makefile 2013-02-18 21:54:46.957806553 +1300 @@ -0,0 +1,1082 @@ @@ -1303,7 +1302,7 @@ diff -uN ./phyml-20120412/src/Makefile ./phyml-20120412-new-bak/src/Makefile +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: -diff -uN ./phyml-20120412/src/mcmc.c ./phyml-20120412-new-bak/src/mcmc.c +unchanged: --- ./phyml-20120412/src/mcmc.c 2012-03-20 14:10:49.000000000 +1300 +++ ./phyml-20120412-new-bak/src/mcmc.c 2013-02-18 21:51:51.459662430 +1300 @@ -1977,7 +1977,7 @@ @@ -1315,7 +1314,7 @@ diff -uN ./phyml-20120412/src/mcmc.c ./phyml-20120412-new-bak/src/mcmc.c else { For(i,tree->mod->n_catg) PhyML_Fprintf(fp,"%G\t",tree->mod->gamma_r_proba->v[i]); -diff -uN ./phyml-20120412/src/optimiz.c ./phyml-20120412-new-bak/src/optimiz.c +unchanged: --- ./phyml-20120412/src/optimiz.c 2012-03-13 19:04:03.000000000 +1300 +++ ./phyml-20120412-new-bak/src/optimiz.c 2013-02-18 21:51:51.462662427 +1300 @@ -979,29 +979,18 @@ @@ -1355,13 +1354,13 @@ diff -uN ./phyml-20120412/src/optimiz.c ./phyml-20120412-new-bak/src/optimiz.c tree->mod->gamma_r_proba_unscaled->v[tree->mod->n_catg-1] = 100.; For(i,tree->mod->n_catg-1) -diff -uN ./phyml-20120412/src/tree ./phyml-20120412-new-bak/src/tree +unchanged: --- ./phyml-20120412/src/tree 1970-01-01 12:00:00.000000000 +1200 +++ ./phyml-20120412-new-bak/src/tree 2013-02-19 10:09:36.962892889 +1300 @@ -0,0 +1 @@ +((((((tax6:0.01,(tax5:0.01,tax1:0.026):0.008):0.003,(tax7:0.003,tax3:0.003):0.01271127):0.01,tax2:0.01):0.01,tax10:0.01):0.01,tax9:0.01):0.01,tax8:0.01,tax4:0.1); \ No newline at end of file -diff -uN ./phyml-20120412/src/utilities.c ./phyml-20120412-new-bak/src/utilities.c +unchanged: --- ./phyml-20120412/src/utilities.c 2012-04-11 11:48:30.000000000 +1200 +++ ./phyml-20120412-new-bak/src/utilities.c 2013-02-19 10:16:57.770281203 +1300 @@ -1668,6 +1668,7 @@ @@ -1505,7 +1504,7 @@ diff -uN ./phyml-20120412/src/utilities.c ./phyml-20120412-new-bak/src/utilities list = (t_node ***)mCalloc(node_list_size,sizeof(t_node **)); For(i,node_list_size) list[i] = (t_node **)mCalloc(2*tree->n_otu-1,sizeof(t_node *)); size = (int *)mCalloc(node_list_size,sizeof(int)); -diff -uN ./phyml-20120412/src/utilities.h ./phyml-20120412-new-bak/src/utilities.h +unchanged: --- ./phyml-20120412/src/utilities.h 2012-04-11 11:39:02.000000000 +1200 +++ ./phyml-20120412-new-bak/src/utilities.h 2013-02-18 21:51:51.452662435 +1300 @@ -272,6 +272,8 @@ @@ -1517,3 +1516,76 @@ diff -uN ./phyml-20120412/src/utilities.h ./phyml-20120412-new-bak/src/utilities /*!********************************************************/ +unchanged: +--- utilities.c 2013-10-31 08:57:09.622430940 +1300 ++++ utilities.new.c 2013-10-31 08:55:49.522433717 +1300 +@@ -4769,8 +4769,6 @@ + t_node *n_e, *n_f; + + n_otu = t_full->n_otu; +- t_empt->n_root = t_full->n_root; +- t_empt->e_root = t_full->e_root; + t_empt->c_lnL_sorted = t_full->c_lnL_sorted; + t_empt->log_site_lk_cat = t_full->log_site_lk_cat; + t_empt->cur_site_lk = t_full->cur_site_lk; +@@ -6993,6 +6991,7 @@ + boot_tree->mat = boot_mat; + } + ++ + boot_tree->mod = boot_mod; + boot_tree->io = tree->io; + boot_tree->data = boot_data; +@@ -7002,6 +7001,7 @@ + boot_tree->io->print_site_lnl = 0; + boot_tree->io->print_trace = 0; + ++ + if((boot_tree->mod->s_opt->random_input_tree) && (boot_tree->mod->s_opt->topo_search == SPR_MOVE)) Random_Tree(boot_tree); + Order_Tree_CSeq(boot_tree,boot_data); + Share_Lk_Struct(tree,boot_tree); +@@ -7010,6 +7010,7 @@ + Fill_Dir_Table(boot_tree); + Update_Dirs(boot_tree); + ++ + if(tree->mod->s_opt->greedy) Init_P_Lk_Tips_Double(boot_tree); + else Init_P_Lk_Tips_Int(boot_tree); + Init_Ui_Tips(boot_tree); +@@ -13307,11 +13308,15 @@ + Warn_And_Exit(""); + } + ++ has_outgrp = NO; ++ ++ /* 'Root' node is t_nodes[0] */ + if(strstr(tree->t_nodes[0]->name,"*")) + { + /* PhyML_Printf("\n. Found outgroup taxon: %s",tree->t_nodes[0]->name); */ + tree->t_nodes[0]->s_ingrp[0] = 0; + tree->t_nodes[0]->s_outgrp[0] = 1; ++ has_outgrp = YES; + } + else + { +@@ -13319,7 +13324,6 @@ + tree->t_nodes[0]->s_outgrp[0] = 0; + } + +- has_outgrp = NO; + Get_Best_Root_Position_Post(tree->t_nodes[0],tree->t_nodes[0]->v[0],&has_outgrp,tree); + Get_Best_Root_Position_Pre(tree->t_nodes[0],tree->t_nodes[0]->v[0],tree); + +only in patch2: +unchanged: +--- src/utilities.c 2012-04-11 11:48:30.000000000 +1200 ++++ src.new/utilities.c 2013-11-12 14:19:11.600689913 +1300 +@@ -13995,7 +13995,7 @@ int Check_Topo_Constraints(t_tree *big_t + For(i,2*big_tree_cpy->n_otu-3) big_tree_cpy->t_edges[i]->bip_score = 0; + For(i,2*small_tree->n_otu-3) small_tree->t_edges[i]->bip_score = 0; + +- diffs = Compare_Bip(small_tree,big_tree_cpy,YES); ++ diffs = Compare_Bip(small_tree,big_tree_cpy,NO); + + /* printf("\n"); */ + /* printf("\n. %s",Write_Tree(big_tree_cpy,NO)); */ diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild index 9946b20954..3578b7288c 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for PhyML -# Copyright 2011-2013 Petar Petrov, ppetrov@paju.oulu.fi +# Copyright 2011-2013 Petar Petrov, petar.petrov@student.oulu.fi # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ # Thanks to Niels Horn for some handy modifications and corrections. PRGNAM=PhyML -VERSION=${VERSION:-20130219} +VERSION=${VERSION:-20131112} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -69,16 +69,17 @@ tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz cd $SRCNAM-$SRCVER chown -R root:root . find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \ - -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \ - -exec chmod 644 {} \; + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Apply patch 20130219 +# Apply version patch cd src patch -i $CWD/$VERSION.patch cd .. +# This is PhyML ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ @@ -97,6 +98,26 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG +# And this is PhyTime +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --enable-phytime \ + --mandir=/usr/man \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux + +# Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" src/Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make +make install DESTDIR=$PKG + find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info index 52478c9962..e37d35be73 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,5 +1,5 @@ PRGNAM="PhyML" -VERSION="20130219" +VERSION="20131112" HOMEPAGE="http://code.google.com/p/phyml/" DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz" MD5SUM="d2207a3d6caf633c43239a01ce70f244" @@ -7,4 +7,4 @@ DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="" MAINTAINER="Petar Petrov" -EMAIL="ppetrov@paju.oulu.fi" +EMAIL="petar.petrov@student.oulu.fi" diff --git a/academic/PhyML/README b/academic/PhyML/README index b52080e622..60178833a8 100644 --- a/academic/PhyML/README +++ b/academic/PhyML/README @@ -9,6 +9,8 @@ It also implements two methods to evaluate branch supports in a sound statistical framework (the non-parametric bootstrap and the approximate likelihood ratio test). +The script also builds the additional program PhyTime. + For details and citation New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S., diff --git a/academic/PhyML/References b/academic/PhyML/References index 17fd35add2..41f1be6bb2 100644 --- a/academic/PhyML/References +++ b/academic/PhyML/References @@ -2,3 +2,7 @@ New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology, 59(3):307-21, 2010. + +Bayesian estimation of divergence times from large sequence alignments. +Mol Biol Evol. 2010 Aug;27(8):1768-81. doi: 10.1093/molbev/msq060. +Epub 2010 Mar 1. |