diff options
Diffstat (limited to 'academic/PhyML')
| -rw-r--r-- | academic/PhyML/20131112.patch | 1591 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.SlackBuild | 61 | ||||
| -rw-r--r-- | academic/PhyML/PhyML.info | 10 | ||||
| -rw-r--r-- | academic/PhyML/README | 10 | ||||
| -rw-r--r-- | academic/PhyML/slack-desc | 2 |
5 files changed, 62 insertions, 1612 deletions
diff --git a/academic/PhyML/20131112.patch b/academic/PhyML/20131112.patch deleted file mode 100644 index e7eb2670b6..0000000000 --- a/academic/PhyML/20131112.patch +++ /dev/null @@ -1,1591 +0,0 @@ -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 @@ - PhyML_Printf("\n"); - - -- PhyML_Printf("%s\n\t-q (or --sequential)\n",BOLD); -+ PhyML_Printf("%s\n\t-q (or --sequential)%s\n",BOLD,FLAT); - PhyML_Printf("%s\t\tChanges interleaved format (default) to sequential format.\n",FLAT); - PhyML_Printf("\n"); - -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 @@ - phydbl site_lk_cat, site_lk; - int sum_scale_left, sum_scale_rght; - int fact_sum_scale; -- phydbl max_sum_scale; -+ phydbl max_sum_scale,min_sum_scale; - phydbl sum; - int ambiguity_check,state; - int catg,ns,k,l,site; -@@ -481,11 +481,12 @@ - phydbl multiplier; - int exponent, piecewise_exponent; - phydbl tmp; -- phydbl logbig; -+ phydbl logbig,logsmall; - phydbl inv_site_lk; - - -- logbig = LOG((phydbl)BIG); -+ logbig = LOG((phydbl)BIG); -+ logsmall = LOG((phydbl)SMALL); - - dim1 = tree->mod->n_catg * tree->mod->ns; - dim2 = tree->mod->ns; -@@ -555,7 +556,7 @@ - b->Pij_rr[catg*dim3+k*dim2+l] * - b->p_lk_left[site*dim1+catg*dim2+l]; - } -- -+ - site_lk_cat += - sum * - tree->mod->pi->v[k] * -@@ -578,7 +579,7 @@ - b->Pij_rr[catg*dim3+k*dim2+l] * - b->p_lk_left[site*dim1+catg*dim2+l]; - } -- -+ - site_lk_cat += - sum * - tree->mod->pi->v[k] * -@@ -588,8 +589,9 @@ - } - tree->site_lk_cat[catg] = site_lk_cat; - } -- -+ - max_sum_scale = (phydbl)BIG; -+ min_sum_scale = (phydbl)SMALL; - For(catg,tree->mod->n_catg) - { - sum_scale_left_cat[catg] = -@@ -606,18 +608,30 @@ - - if(sum < .0) - { -- PhyML_Printf("\n. sum = %G",sum); -- PhyML_Printf("\n. Err in file %s at line %d\n\n",__FILE__,__LINE__); -+ PhyML_Printf("\n== sum = %G",sum); -+ PhyML_Printf("\n== Err in file %s at line %d\n\n",__FILE__,__LINE__); - Warn_And_Exit("\n"); - } - - tmp = sum + (logbig - LOG(tree->site_lk_cat[catg]))/(phydbl)LOG2; - if(tmp < max_sum_scale) max_sum_scale = tmp; /* min of the maxs */ -+ -+ tmp = sum + (logsmall - LOG(tree->site_lk_cat[catg]))/(phydbl)LOG2; -+ if(tmp > min_sum_scale) min_sum_scale = tmp; /* max of the mins */ - } - --/* fact_sum_scale = (int)((max_sum_scale + min_sum_scale) / 2); */ -+ if(min_sum_scale > max_sum_scale) -+ { -+ /* PhyML_Printf("\n== Numerical precision issue alert."); */ -+ /* PhyML_Printf("\n== min_sum_scale = %G max_sum_scale = %G",min_sum_scale,max_sum_scale); */ -+ /* PhyML_Printf("\n== Err in file %s at line %d\n\n",__FILE__,__LINE__); */ -+ /* Warn_And_Exit("\n"); */ -+ min_sum_scale = max_sum_scale; -+ } -+ -+ fact_sum_scale = (int)((max_sum_scale + min_sum_scale) / 2); - -- fact_sum_scale = (int)(max_sum_scale / 2); -+ /* fact_sum_scale = (int)(max_sum_scale / 2); */ - - /* Apply scaling factors */ - For(catg,tree->mod->n_catg) -@@ -651,12 +665,13 @@ - - if(isinf(site_lk_cat)) - { -- PhyML_Printf("\n+ site=%4d cat=%4d site_lk_cat=%G sum_scale=%d max=%G fact=%d expo=%d dbl=%G", -+ PhyML_Printf("\n+ site=%4d cat=%4d site_lk_cat=%G sum_scale=%d max=%G min=%G fact=%d expo=%d dbl=%G", - tree->curr_site, - catg, - tree->site_lk_cat[catg], - sum_scale_left_cat[catg]+sum_scale_rght_cat[catg], - max_sum_scale, -+ min_sum_scale, - fact_sum_scale, - -(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale, - (double)tree->site_lk_cat[catg] * pow(2.,-(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale)); -@@ -678,13 +693,11 @@ - fact_sum_scale, - -(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale, - (double)tree->site_lk_cat[catg] * pow(2.,-(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale)); -- -+ - Exit("\n"); - } -- - site_lk_cat = .0; - } -- - tree->site_lk_cat[catg] = site_lk_cat; - } - -@@ -694,6 +707,24 @@ - site_lk += tree->site_lk_cat[catg] * tree->mod->gamma_r_proba->v[catg]; - } - -+ if(isinf(site_lk)) -+ { -+ PhyML_Printf("\n= Site = %d",site); -+ PhyML_Printf("\n= invar = %d",tree->data->invar[site]); -+ PhyML_Printf("\n= scale_left = %d scale_rght = %d",sum_scale_left,sum_scale_rght); -+ PhyML_Printf("\n= lk = %G log(lk) = %f < %G",site_lk,log_site_lk,-BIG); -+ PhyML_Printf("\n= fact_sum_scale = %d",fact_sum_scale); -+ For(catg,tree->mod->n_catg) PhyML_Printf("\n. rr=%f p=%f lk=%G expo=%d", -+ tree->mod->gamma_rr->v[catg], -+ tree->mod->gamma_r_proba->v[catg], -+ tree->site_lk_cat[catg], -+ -(sum_scale_left_cat[catg]+sum_scale_rght_cat[catg])+fact_sum_scale); -+ PhyML_Printf("\n= pinv = %G",tree->mod->pinvar->v); -+ PhyML_Printf("\n= bl mult = %G",tree->mod->br_len_multiplier->v); -+ PhyML_Printf("\n. Err in file %s at line %d",__FILE__,__LINE__); -+ Warn_And_Exit("\n"); -+ } -+ - - inv_site_lk = 0.; - -@@ -741,19 +772,22 @@ - - log_site_lk = LOG(site_lk) - (phydbl)LOG2 * fact_sum_scale; - -- - For(catg,tree->mod->n_catg) tree->log_site_lk_cat[catg][site] = LOG(tree->site_lk_cat[catg]) - (phydbl)LOG2 * fact_sum_scale; - - if(isinf(log_site_lk) || isnan(log_site_lk)) - { -- PhyML_Printf("\n. Site = %d",site); -- PhyML_Printf("\n. invar = %d",tree->data->invar[site]); -- PhyML_Printf("\n. scale_left = %d scale_rght = %d",sum_scale_left,sum_scale_rght); -- PhyML_Printf("\n. inv_site_lk = %f",inv_site_lk); -- PhyML_Printf("\n. Lk = %G LOG(Lk) = %f < %G",site_lk,log_site_lk,-BIG); -- For(catg,tree->mod->n_catg) PhyML_Printf("\n. rr=%f p=%f",tree->mod->gamma_rr->v[catg],tree->mod->gamma_r_proba->v[catg]); -- PhyML_Printf("\n. pinv = %G",tree->mod->pinvar->v); -- PhyML_Printf("\n. bl mult = %G",tree->mod->br_len_multiplier->v); -+ PhyML_Printf("\n= Site = %d",site); -+ PhyML_Printf("\n= invar = %d",tree->data->invar[site]); -+ PhyML_Printf("\n= scale_left = %d scale_rght = %d",sum_scale_left,sum_scale_rght); -+ PhyML_Printf("\n= inv_site_lk = %f",inv_site_lk); -+ PhyML_Printf("\n= lk = %G log(lk) = %f < %G",site_lk,log_site_lk,-BIG); -+ For(catg,tree->mod->n_catg) PhyML_Printf("\n. rr=%f p=%f lk=%G", -+ tree->mod->gamma_rr->v[catg], -+ tree->mod->gamma_r_proba->v[catg], -+ tree->site_lk_cat[catg]); -+ PhyML_Printf("\n= pinv = %G",tree->mod->pinvar->v); -+ PhyML_Printf("\n= bl mult = %G",tree->mod->br_len_multiplier->v); -+ PhyML_Printf("\n= fact_sum_scale = %d",fact_sum_scale); - - /* int i; */ - /* For(i,2*tree->n_otu-3) */ -@@ -802,6 +836,7 @@ - Alias_One_Subpatt((d==b->left)?(b->rght):(b->left),d,tree); - - if(d->tax) return; -+ - - if(tree->mod->use_m4mod == NO) - { -@@ -813,6 +848,10 @@ - { - Update_P_Lk_AA(tree,b,d); - } -+ else -+ { -+ Update_P_Lk_Generic(tree,b,d); -+ } - } - else - { -@@ -1044,7 +1083,7 @@ - - p_lk[site*NsNg+catg*Ns+i] = p1_lk1 * p2_lk2; - -- /* PhyML_Printf("\n+ %G",p_lk[site*NsNg+catg*Ns+i]); */ -+ /* PhyML_Printf("\n+ %G",p_lk[site*NsNg+catg*Ns+i]); */ - - if(p_lk[site*NsNg+catg*Ns+i] < smallest_p_lk) smallest_p_lk = p_lk[site*NsNg+catg*Ns+i] ; - } -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 @@ -+# Makefile.in generated by automake 1.11.1 from Makefile.am. -+# src/Makefile. Generated from Makefile.in by configure. -+ -+# Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, -+# 2003, 2004, 2005, 2006, 2007, 2008, 2009 Free Software Foundation, -+# Inc. -+# This Makefile.in is free software; the Free Software Foundation -+# gives unlimited permission to copy and/or distribute it, -+# with or without modifications, as long as this notice is preserved. -+ -+# This program is distributed in the hope that it will be useful, -+# but WITHOUT ANY WARRANTY, to the extent permitted by law; without -+# even the implied warranty of MERCHANTABILITY or FITNESS FOR A -+# PARTICULAR PURPOSE. -+ -+ -+ -+ -+pkgdatadir = $(datadir)/phyml -+pkgincludedir = $(includedir)/phyml -+pkglibdir = $(libdir)/phyml -+pkglibexecdir = $(libexecdir)/phyml -+am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd -+install_sh_DATA = $(install_sh) -c -m 644 -+install_sh_PROGRAM = $(install_sh) -c -+install_sh_SCRIPT = $(install_sh) -c -+INSTALL_HEADER = $(INSTALL_DATA) -+transform = $(program_transform_name) -+NORMAL_INSTALL = : -+PRE_INSTALL = : -+POST_INSTALL = : -+NORMAL_UNINSTALL = : -+PRE_UNINSTALL = : -+POST_UNINSTALL = : -+build_triplet = x86_64-unknown-linux-gnu -+host_triplet = x86_64-unknown-linux-gnu -+bin_PROGRAMS = phyml$(EXEEXT) -+#bin_PROGRAMS = test$(EXEEXT) -+#bin_PROGRAMS = phyml-mpi$(EXEEXT) -+#bin_PROGRAMS = rf$(EXEEXT) -+#bin_PROGRAMS = m4$(EXEEXT) -+#bin_PROGRAMS = tiporder$(EXEEXT) -+#bin_PROGRAMS = part$(EXEEXT) -+#bin_PROGRAMS = \ -+# phycont$(EXEEXT) -+#bin_PROGRAMS = phytime$(EXEEXT) -+subdir = src -+DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in -+ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 -+am__aclocal_m4_deps = $(top_srcdir)/configure.ac -+am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ -+ $(ACLOCAL_M4) -+mkinstalldirs = $(install_sh) -d -+CONFIG_HEADER = $(top_builddir)/config.h -+CONFIG_CLEAN_FILES = -+CONFIG_CLEAN_VPATH_FILES = -+am__installdirs = "$(DESTDIR)$(bindir)" -+PROGRAMS = $(bin_PROGRAMS) -+am__m4_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ -+ mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \ -+ draw.c draw.h stats.c stats.h tiporder.c tiporder.h m4.c m4.h -+#am_m4_OBJECTS = main.$(OBJEXT) \ -+# utilities.$(OBJEXT) \ -+# optimiz.$(OBJEXT) \ -+# lk.$(OBJEXT) \ -+# bionj.$(OBJEXT) \ -+# models.$(OBJEXT) \ -+# free.$(OBJEXT) \ -+# help.$(OBJEXT) \ -+# simu.$(OBJEXT) \ -+# eigen.$(OBJEXT) \ -+# pars.$(OBJEXT) \ -+# alrt.$(OBJEXT) \ -+# interface.$(OBJEXT) \ -+# cl.$(OBJEXT) \ -+# mg.$(OBJEXT) \ -+# times.$(OBJEXT) \ -+# mcmc.$(OBJEXT) \ -+# rates.$(OBJEXT) \ -+# spr.$(OBJEXT) \ -+# draw.$(OBJEXT) \ -+# stats.$(OBJEXT) \ -+# tiporder.$(OBJEXT) \ -+# m4.$(OBJEXT) -+m4_OBJECTS = $(am_m4_OBJECTS) -+m4_DEPENDENCIES = -+am__part_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ -+ mg.h spr.c spr.h m4.c m4.h draw.c draw.h stats.c stats.h \ -+ tiporder.c tiporder.h -+#am_part_OBJECTS = main.$(OBJEXT) \ -+# utilities.$(OBJEXT) \ -+# optimiz.$(OBJEXT) \ -+# lk.$(OBJEXT) \ -+# bionj.$(OBJEXT) \ -+# models.$(OBJEXT) \ -+# free.$(OBJEXT) \ -+# help.$(OBJEXT) \ -+# simu.$(OBJEXT) \ -+# eigen.$(OBJEXT) \ -+# pars.$(OBJEXT) \ -+# alrt.$(OBJEXT) \ -+# interface.$(OBJEXT) \ -+# cl.$(OBJEXT) \ -+# mg.$(OBJEXT) \ -+# spr.$(OBJEXT) \ -+# m4.$(OBJEXT) \ -+# draw.$(OBJEXT) \ -+# stats.$(OBJEXT) \ -+# tiporder.$(OBJEXT) -+part_OBJECTS = $(am_part_OBJECTS) -+part_DEPENDENCIES = -+am__phycont_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ -+ spr.h times.c times.h m4.c m4.h draw.c draw.h rates.c rates.h \ -+ mcmc.c mcmc.h stats.c stats.h mg.c mg.h tiporder.c tiporder.h -+#am_phycont_OBJECTS = \ -+# main.$(OBJEXT) \ -+# utilities.$(OBJEXT) \ -+# optimiz.$(OBJEXT) \ -+# lk.$(OBJEXT) \ -+# bionj.$(OBJEXT) \ -+# models.$(OBJEXT) \ -+# free.$(OBJEXT) \ -+# help.$(OBJEXT) \ -+# simu.$(OBJEXT) \ -+# eigen.$(OBJEXT) \ -+# pars.$(OBJEXT) \ -+# alrt.$(OBJEXT) \ -+# interface.$(OBJEXT) \ -+# cl.$(OBJEXT) \ -+# spr.$(OBJEXT) \ -+# times.$(OBJEXT) \ -+# m4.$(OBJEXT) \ -+# draw.$(OBJEXT) \ -+# rates.$(OBJEXT) \ -+# mcmc.$(OBJEXT) \ -+# stats.$(OBJEXT) \ -+# mg.$(OBJEXT) \ -+# tiporder.$(OBJEXT) -+phycont_OBJECTS = $(am_phycont_OBJECTS) -+phycont_DEPENDENCIES = -+am__phyml_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ -+ spr.h draw.c draw.h stats.c stats.h rates.c rates.h mcmc.c \ -+ mcmc.h times.c times.h tiporder.c tiporder.h mg.c mg.h m4.c \ -+ m4.h -+am_phyml_OBJECTS = main.$(OBJEXT) \ -+ utilities.$(OBJEXT) \ -+ optimiz.$(OBJEXT) \ -+ lk.$(OBJEXT) \ -+ bionj.$(OBJEXT) \ -+ models.$(OBJEXT) \ -+ free.$(OBJEXT) \ -+ help.$(OBJEXT) \ -+ simu.$(OBJEXT) \ -+ eigen.$(OBJEXT) \ -+ pars.$(OBJEXT) \ -+ alrt.$(OBJEXT) \ -+ interface.$(OBJEXT) \ -+ cl.$(OBJEXT) \ -+ spr.$(OBJEXT) \ -+ draw.$(OBJEXT) \ -+ stats.$(OBJEXT) \ -+ rates.$(OBJEXT) \ -+ mcmc.$(OBJEXT) \ -+ times.$(OBJEXT) \ -+ tiporder.$(OBJEXT) \ -+ mg.$(OBJEXT) \ -+ m4.$(OBJEXT) -+phyml_OBJECTS = $(am_phyml_OBJECTS) -+phyml_DEPENDENCIES = -+am__phyml_mpi_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ -+ spr.h draw.c draw.h mpi_boot.c mpi_boot.h stats.c stats.h \ -+ rates.c rates.h mcmc.c mcmc.h times.c times.h tiporder.c \ -+ tiporder.h mg.c mg.h m4.c m4.h xml.c xml.h -+#am_phyml_mpi_OBJECTS = main.$(OBJEXT) \ -+# utilities.$(OBJEXT) \ -+# optimiz.$(OBJEXT) \ -+# lk.$(OBJEXT) \ -+# bionj.$(OBJEXT) \ -+# models.$(OBJEXT) \ -+# free.$(OBJEXT) \ -+# help.$(OBJEXT) \ -+# simu.$(OBJEXT) \ -+# eigen.$(OBJEXT) \ -+# pars.$(OBJEXT) \ -+# alrt.$(OBJEXT) \ -+# interface.$(OBJEXT) \ -+# cl.$(OBJEXT) \ -+# spr.$(OBJEXT) \ -+# draw.$(OBJEXT) \ -+# mpi_boot.$(OBJEXT) \ -+# stats.$(OBJEXT) \ -+# rates.$(OBJEXT) \ -+# mcmc.$(OBJEXT) \ -+# times.$(OBJEXT) \ -+# tiporder.$(OBJEXT) \ -+# mg.$(OBJEXT) \ -+# m4.$(OBJEXT) \ -+# xml.$(OBJEXT) -+phyml_mpi_OBJECTS = $(am_phyml_mpi_OBJECTS) -+phyml_mpi_DEPENDENCIES = -+am__phytime_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ -+ spr.h times.c times.h m4.c m4.h draw.c draw.h rates.c rates.h \ -+ mcmc.c mcmc.h stats.c stats.h mg.c mg.h tiporder.c tiporder.h -+#am_phytime_OBJECTS = main.$(OBJEXT) \ -+# utilities.$(OBJEXT) optimiz.$(OBJEXT) \ -+# lk.$(OBJEXT) bionj.$(OBJEXT) \ -+# models.$(OBJEXT) free.$(OBJEXT) \ -+# help.$(OBJEXT) simu.$(OBJEXT) \ -+# eigen.$(OBJEXT) pars.$(OBJEXT) \ -+# alrt.$(OBJEXT) interface.$(OBJEXT) \ -+# cl.$(OBJEXT) spr.$(OBJEXT) times.$(OBJEXT) \ -+# m4.$(OBJEXT) draw.$(OBJEXT) rates.$(OBJEXT) \ -+# mcmc.$(OBJEXT) stats.$(OBJEXT) mg.$(OBJEXT) \ -+# tiporder.$(OBJEXT) -+phytime_OBJECTS = $(am_phytime_OBJECTS) -+phytime_DEPENDENCIES = -+am__rf_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ -+ mg.h times.c times.h mcmc.c mcmc.h rates.c rates.h spr.c spr.h \ -+ draw.c draw.h stats.c stats.h tiporder.c tiporder.h m4.c m4.h -+#am_rf_OBJECTS = main.$(OBJEXT) \ -+# utilities.$(OBJEXT) \ -+# optimiz.$(OBJEXT) \ -+# lk.$(OBJEXT) \ -+# bionj.$(OBJEXT) \ -+# models.$(OBJEXT) \ -+# free.$(OBJEXT) \ -+# help.$(OBJEXT) \ -+# simu.$(OBJEXT) \ -+# eigen.$(OBJEXT) \ -+# pars.$(OBJEXT) \ -+# alrt.$(OBJEXT) \ -+# interface.$(OBJEXT) \ -+# cl.$(OBJEXT) \ -+# mg.$(OBJEXT) \ -+# times.$(OBJEXT) \ -+# mcmc.$(OBJEXT) \ -+# rates.$(OBJEXT) \ -+# spr.$(OBJEXT) \ -+# draw.$(OBJEXT) \ -+# stats.$(OBJEXT) \ -+# tiporder.$(OBJEXT) \ -+# m4.$(OBJEXT) -+rf_OBJECTS = $(am_rf_OBJECTS) -+rf_DEPENDENCIES = -+am__test_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h spr.c \ -+ spr.h draw.c draw.h stats.c stats.h rates.c rates.h mcmc.c \ -+ mcmc.h times.c times.h tiporder.c tiporder.h mg.c mg.h m4.c \ -+ m4.h xml.c xml.h -+#am_test_OBJECTS = main.$(OBJEXT) \ -+# utilities.$(OBJEXT) \ -+# optimiz.$(OBJEXT) \ -+# lk.$(OBJEXT) \ -+# bionj.$(OBJEXT) \ -+# models.$(OBJEXT) \ -+# free.$(OBJEXT) \ -+# help.$(OBJEXT) \ -+# simu.$(OBJEXT) \ -+# eigen.$(OBJEXT) \ -+# pars.$(OBJEXT) \ -+# alrt.$(OBJEXT) \ -+# interface.$(OBJEXT) \ -+# cl.$(OBJEXT) \ -+# spr.$(OBJEXT) \ -+# draw.$(OBJEXT) \ -+# stats.$(OBJEXT) \ -+# rates.$(OBJEXT) \ -+# mcmc.$(OBJEXT) \ -+# times.$(OBJEXT) \ -+# tiporder.$(OBJEXT) \ -+# mg.$(OBJEXT) \ -+# m4.$(OBJEXT) \ -+# xml.$(OBJEXT) -+test_OBJECTS = $(am_test_OBJECTS) -+test_DEPENDENCIES = -+am__tiporder_SOURCES_DIST = main.c utilities.c utilities.h optimiz.c \ -+ optimiz.h lk.c lk.h bionj.c bionj.h models.c models.h free.c \ -+ free.h help.c help.h simu.c simu.h eigen.c eigen.h pars.c \ -+ pars.h alrt.c alrt.h interface.c interface.h cl.c cl.h mg.c \ -+ 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clean-binPROGRAMS \ -+ clean-generic ctags distclean distclean-compile \ -+ distclean-generic distclean-tags distdir dvi dvi-am html \ -+ html-am info info-am install install-am install-binPROGRAMS \ -+ install-data install-data-am install-dvi install-dvi-am \ -+ install-exec install-exec-am install-html install-html-am \ -+ install-info install-info-am install-man install-pdf \ -+ install-pdf-am install-ps install-ps-am install-strip \ -+ installcheck installcheck-am installdirs maintainer-clean \ -+ maintainer-clean-generic mostlyclean mostlyclean-compile \ -+ mostlyclean-generic pdf pdf-am ps ps-am tags uninstall \ -+ uninstall-am uninstall-binPROGRAMS -+ -+ -+# all-am: intro $(bin_PROGRAMS)$(EXEEXT) -+all-am: intro $(bin_PROGRAMS) -+ @echo "" -+ @echo "Done." -+ -+intro: -+ @echo "" -+ @echo "" -+ @echo ":: Building [$(bin_PROGRAMS)]. Version $(VERSION) ::" -+ @echo "" -+ @echo "" -+ -+# 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: -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 @@ - if(tree->mod->n_catg > 1) - { - if(tree->mod->free_mixt_rates == NO) -- PhyML_Fprintf(fp,"%G\t",tree->mod->alpha); -+ PhyML_Fprintf(fp,"%G\t",tree->mod->alpha->v); - else - { - For(i,tree->mod->n_catg) PhyML_Fprintf(fp,"%G\t",tree->mod->gamma_r_proba->v[i]); -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 @@ - - if((tree->mod->s_opt->opt_free_mixt_rates) && (tree->mod->free_mixt_rates == YES)) - { -- /* int failed; */ -+ int failed; - int i; - -- /* failed = 0; */ -- /* tree->mod->update_eigen = 1; */ -- /* BFGS(tree,tree->mod->gamma_r_proba_unscaled,tree->mod->n_catg,1.e-5,1.e-5, */ -- /* &Return_Abs_Lk, */ -- /* &Num_Derivative_Several_Param, */ -- /* &Lnsrch_Free_Mixt_Rates,&failed); */ -- - if(verbose) Print_Lk(tree,"[Rate class freqs. ]"); - -+ failed = 0; -+ tree->mod->update_eigen = 1; -+ BFGS(tree,tree->mod->gamma_r_proba_unscaled,tree->mod->n_catg,1.e-5,1.e-5, -+ &Return_Abs_Lk, -+ &Num_Derivative_Several_Param, -+ &Lnsrch_Free_Mixt_Rates,&failed); - -- /* For(i,tree->mod->n_catg-1) */ -- /* { */ -- /* Generic_Brent_Lk(&(tree->mod->gamma_r_proba_unscaled->v[i]), */ -- /* 0., */ -- /* 100, */ -- /* tree->mod->s_opt->min_diff_lk_global, */ -- /* tree->mod->s_opt->brent_it_max, */ -- /* tree->mod->s_opt->quickdirty, */ -- /* Wrap_Lk,NULL,tree,NULL); */ -- /* } */ - - tree->mod->gamma_r_proba_unscaled->v[tree->mod->n_catg-1] = 100.; - For(i,tree->mod->n_catg-1) -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 -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 @@ - - Detect_Align_File_Format(io); - -+ - switch(io->data_file_format) - { - case PHYLIP: -@@ -1861,7 +1862,7 @@ - { - if(!Get_Token(fp,token)) break; - --/* PhyML_Printf("\n+ Token: '%s' next_token=%d cur_token=%d",token,nxt_token_t,cur_token_t); */ -+ PhyML_Printf("\n+ Token: '%s' next_token=%d cur_token=%d",token,nxt_token_t,cur_token_t); - - if(token[0] == ';') - { -@@ -1940,7 +1941,7 @@ - } - while(c != '"'); - *token = c; -- c = fgetc(fp); -+ /* c = fgetc(fp); */ - if(c == EOF) return 0; - *(token+1) = '\0'; - return 1; -@@ -1950,6 +1951,8 @@ - { - Skip_Comment(fp); - c = fgetc(fp); -+ *token = c; -+ token++; - if(c == EOF) return 0; - return 1; - } -@@ -1967,7 +1970,7 @@ - else if(c == '-') { *token = c; token++; } - else - { -- while(isgraph(c) && c != ';' && c != '-' && c != ',') -+ while(isgraph(c) && c != ';' && c != '-' && c != ',' && c != '=') - { - *(token++) = c; - c = fgetc(fp); -@@ -2308,8 +2311,6 @@ - - } - -- -- - ////////////////////////////////////////////////////////////// - ////////////////////////////////////////////////////////////// - -@@ -7756,7 +7757,7 @@ - - #ifndef PHYTIME - mod->l_min = 1.E-8; -- mod->l_max = 100.0; -+ mod->l_max = 10.0; - #else - mod->l_min = 1.E-8; - mod->l_max = 2.0; -@@ -8049,11 +8050,23 @@ - t_node **bip1, **bip2; - int bip_size1, bip_size2, bip_size; - int different,identical; -+ int n_edges; - - /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!*/ - /* WARNING: call Match_Tip_Numbers and Get_Bip before using this function. */ - /* !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!*/ - -+ if(on_existing_edges_only == YES) -+ { -+ n_edges = 0; -+ For(i,2*tree1->n_otu-3) -+ if(tree1->t_edges[i]->does_exist && tree2->t_edges[i]->does_exist) n_edges++; -+ n_edges -= tree1->n_otu; -+ } -+ else -+ { -+ n_edges = tree1->n_otu-3; -+ } - - identical = 0; - different = 0; -@@ -8070,7 +8083,7 @@ - bip_size2 = MIN(b2->left->bip_size[b2->l_r],b2->rght->bip_size[b2->r_l]); - - if(bip_size2 > 1 && ((on_existing_edges_only == YES && b2->does_exist) || (on_existing_edges_only == NO))) -- { -+ { - if(bip_size1 == bip_size2) - { - bip_size = bip_size1; -@@ -8139,17 +8152,21 @@ - b1->bip_score++; - b2->bip_score++; - identical++; -- break; -+ goto out; -+ } -+ else -+ { -+ different++; // Bipartitions have identical sizes but distinct elements - } -- else different++; // Bipartitions has identical size but distinct elements - } - else different++; // Biparition have different sizes - } - } - } -+ out: ; - } -- -- return different; -+ return n_edges - identical; -+ /* return different; */ - } - - ////////////////////////////////////////////////////////////// -@@ -12242,6 +12259,9 @@ - - aLRT(tree); - -+ Br_Len_Involving_Invar(tree); -+ Rescale_Br_Len_Multiplier_Tree(tree); -+ - Free(s_tree); - s_tree = Write_Tree(tree,NO); - -@@ -12481,6 +12501,9 @@ - Warn_And_Exit(""); - } - -+ -+ if(node_list_size == 1) return node_list[0]; -+ - 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)); -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 @@ - /* #define P_LK_LIM_SUP 2.037035976e+90 /\* R: format(2^(+300),digits=10) *\/ */ - #define P_LK_LIM_INF 3.054936e-151 /* 2^-500 */ - #define P_LK_LIM_SUP 3.273391e+150 /* 2^500 */ -+/* #define P_LK_LIM_INF 1.499697e-241 /\* 2^-800 *\/ */ -+/* #define P_LK_LIM_SUP 6.668014e+240 /\* 2^800 *\/ */ - - - /*!********************************************************/ -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 6c8ccdd3a4..d4b3d67cae 100644 --- a/academic/PhyML/PhyML.SlackBuild +++ b/academic/PhyML/PhyML.SlackBuild @@ -25,16 +25,16 @@ # Thanks to Niels Horn for some handy modifications and corrections. PRGNAM=PhyML -VERSION=${VERSION:-20131112} +VERSION=${VERSION:-3.2.20160530} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} SRCNAM=$(echo $PRGNAM | tr A-Z a-z) -SRCVER=20120412 +SRCVER=3.2.20160530 if [ -z "$ARCH" ]; then case "$( uname -m )" in - i?86) ARCH=i486 ;; + i?86) ARCH=i586 ;; arm*) ARCH=arm ;; *) ARCH=$( uname -m ) ;; esac @@ -45,8 +45,8 @@ TMP=${TMP:-/tmp/SBo} PKG=$TMP/package-$PRGNAM OUTPUT=${OUTPUT:-/tmp} -if [ "$ARCH" = "i486" ]; then - SLKCFLAGS="-O2 -march=i486 -mtune=i686" +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" LIBDIRSUFFIX="" elif [ "$ARCH" = "i686" ]; then SLKCFLAGS="-O2 -march=i686 -mtune=i686" @@ -65,7 +65,13 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM-$SRCVER -tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz + +if [ -e $CWD/v${SRCVER}.tar.gz ]; then + tar xvf $CWD/v${SRCVER}.tar.gz +else + tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz +fi + cd $SRCNAM-$SRCVER chown -R root:root . find -L . \ @@ -74,18 +80,38 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Apply version patch -cd src - patch -i $CWD/$VERSION.patch -cd .. +# This is PhyML, the main component of the package. If this is all you want, you +# can comment out the sections that build PhyML MPI and Phyrex below. +./autogen.sh +./configure \ + --prefix=/usr \ + --libdir=/usr/lib${LIBDIRSUFFIX} \ + --sysconfdir=/etc \ + --localstatedir=/var \ + --mandir=/usr/man \ + --enable-phyml \ + --docdir=/usr/doc/$PRGNAM-$VERSION \ + --build=$ARCH-slackware-linux -# This is PhyML +# Use our CFLAGS +sed -i "/^CFLAGS/s/=/+=/" src/Makefile +sed -i "/^CFLAGS/s/=/+=/" Makefile + +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make +make install DESTDIR=$PKG + +# This is PhyML MPI. If you do not want it, comment the lines below. Then you do +# not need to install openmpi. +./autogen.sh ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ --mandir=/usr/man \ + --enable-mpi \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux @@ -98,14 +124,15 @@ CXXFLAGS="$SLKCFLAGS" \ make make install DESTDIR=$PKG -# And this is PhyTime +# This is Phyrex +./autogen.sh ./configure \ --prefix=/usr \ --libdir=/usr/lib${LIBDIRSUFFIX} \ --sysconfdir=/etc \ --localstatedir=/var \ - --enable-phytime \ --mandir=/usr/man \ + --enable-phyrex \ --docdir=/usr/doc/$PRGNAM-$VERSION \ --build=$ARCH-slackware-linux @@ -121,9 +148,15 @@ make install DESTDIR=$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 +# Include some examples +mkdir -p $PKG/usr/share/$PRGNAM +cp -a \ + examples/{lg4x,phyrex_input_files,nexus_example.nxs,nucleic,proteic} \ + $PKG/usr/share/$PRGNAM + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a \ - doc/$SRCNAM-manual-20120306.pdf AUTHORS ChangeLog COPYING INSTALL README \ + doc/$SRCNAM-manual.pdf AUTHORS ChangeLog COPYING LICENSE README \ $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info index dd1f897135..739d1befc0 100644 --- a/academic/PhyML/PhyML.info +++ b/academic/PhyML/PhyML.info @@ -1,10 +1,10 @@ PRGNAM="PhyML" -VERSION="20131112" -HOMEPAGE="http://code.google.com/p/phyml/" -DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz" -MD5SUM="d2207a3d6caf633c43239a01ce70f244" +VERSION="3.2.20160530" +HOMEPAGE="https://github.com/stephaneguindon/phyml/" +DOWNLOAD="https://github.com/stephaneguindon/phyml/archive/v3.2.20160530.tar.gz" +MD5SUM="7a4689e2de3ac9efd7586980b07331f0" DOWNLOAD_x86_64="" MD5SUM_x86_64="" -REQUIRES="" +REQUIRES="openmpi" MAINTAINER="Petar Petrov" EMAIL="slackalaxy@gmail.com" diff --git a/academic/PhyML/README b/academic/PhyML/README index 60178833a8..fd66cda123 100644 --- a/academic/PhyML/README +++ b/academic/PhyML/README @@ -9,7 +9,15 @@ 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. +NOTE 1: This also builds Phyrex and the MPI (using multiple processors) +version of PhyML. The executable of the latter is called phyml-mpi and +requires openmpi. If you do not want them to be built in the package, +check the SlackBuild script. + +NOTE 2: PhyTime used to be part of the PhyML package. However, PhyTime +from the latest releases of PhyML does not build anymore. meanwhile, +PhyTime is available separately, which installs the latest version that +builds. For details and citation New Algorithms and Methods to Estimate Maximum-Likelihood diff --git a/academic/PhyML/slack-desc b/academic/PhyML/slack-desc index 76f3459318..ae498120bb 100644 --- a/academic/PhyML/slack-desc +++ b/academic/PhyML/slack-desc @@ -14,6 +14,6 @@ PhyML: wide range of options that were designed to facilitate standard PhyML: phylogenetic analyses. PhyML: PhyML: Home: http://code.google.com/p/phyml/ -PhyML: References: /usr/doc/PhyML-20131112/References +PhyML: References: /usr/doc/PhyML-3.2.20160530/References PhyML: PhyML: |