Skip to content
Commits on Source (9)
Hide whitespace changes
Inline Side-by-side
CMakeLists.txt
View file @ 75a49e03
......@@ -108,7 +108,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
if(${GCC_VERSION} VERSION_LESS 6.0)
set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -std=gnu++14")
else(${GCC_VERSION} VERSION_LESS 6.0)
set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -std=c++14")
set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3")
endif(${GCC_VERSION} VERSION_LESS 6.0)
if(NOAVX)
......@@ -190,14 +190,22 @@ endif(NOT ${OPENMP_FOUND})
#-------------------------------------------------------------------------------
set(INSTALL_PREFIX /usr/local CACHE PATH "Installation prefix")
set(CMAKE_INSTALL_PREFIX ${INSTALL_PREFIX} CACHE INTERNAL "Installation prefix" FORCE)
set(DEFAULT_LIBRARIES dl pthread)
if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
set(DEFAULT_LIBRARIES pthread)
else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
set(DEFAULT_LIBRARIES dl pthread)
endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
#-------------------------------------------------------------------------------
# LIBCurl support
#-------------------------------------------------------------------------------
find_package(CURL)
if(${CURL_FOUND} AND NOT APPLE)
set(DEFAULT_LIBRARIES dl pthread crypto curl ssl)
if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
set(DEFAULT_LIBRARIES pthread crypto curl ssl)
else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
set(DEFAULT_LIBRARIES dl pthread crypto curl ssl)
endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
add_definitions (-D__HYPHYCURL__)
endif(${CURL_FOUND} AND NOT APPLE)
......
debian/changelog
View file @ 75a49e03
hyphy (2.3.10+dfsg-1) UNRELEASED; urgency=medium
hyphy (2.3.13+dfsg-1) unstable; urgency=medium
* Team upload.
[ Steffen Moeller ]
* debian/upstream/metadata: Added ref to OMICtools
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.1.3
* debhelper 11
* Add Build-Depends: opencl-dev
* debian/rules:
- Do not parse d/changelog
- regard $(DEB_BUILD_OPTIONS) for override_dh_auto_test
[ Liubov Chuprikova ]
* Drop hyphygui as it was removed from upstream
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
-- Andreas Tille <tille@debian.org> Sun, 11 Feb 2018 10:45:54 +0100
-- Liubov Chuprikova <chuprikovalv@gmail.com> Tue, 10 Jul 2018 08:39:13 +0200
hyphy (2.2.7+dfsg-1) unstable; urgency=medium
......
debian/patches/debug_r_build.patch deleted 100644 → 0
View file @ d5c54d36
Author: Andreas Tille <tille@debian.org>
Last-Updated: Mon, 29 Jun 2015 11:13:57 +0200
Description: Just for debugging, not activated
--- a/src/lib/build.sh
+++ b/src/lib/build.sh
@@ -72,6 +72,7 @@ fi
# END MODIFY
+set -x
echo "Checking for curl";
echo "#include <curl/curl.h>\nint main(void) {return 0;}" > curl_check.cpp
@@ -86,7 +87,7 @@ else
fi
rm -rf curl_check*
-
+set +x
makedir () {
if [ -f $1 ]
debian/patches/drop_profiling_option.patch
View file @ 75a49e03
......@@ -5,7 +5,7 @@ Bug-Debian: http://bugs.debian.org/793345
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -408,8 +408,8 @@ add_custom_target(DEBUG DEPENDS HYPHYDEB
@@ -416,8 +416,8 @@ add_custom_target(DEBUG DEPENDS HYPHYDEB
set_target_properties(
HYPHYDEBUG
PROPERTIES
......@@ -16,7 +16,7 @@ Bug-Debian: http://bugs.debian.org/793345
)
@@ -433,8 +433,8 @@ set_property(
@@ -441,8 +441,8 @@ set_property(
set_target_properties(
HYPHYGTEST
PROPERTIES
......
debian/patches/msse_option_only_if_available.patch
View file @ 75a49e03
......@@ -5,7 +5,7 @@ Last-Update: Thu, 23 Jul 2015 13:12:54 +0200
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -430,12 +430,23 @@ set_property(
@@ -438,12 +438,23 @@ set_property(
TARGET HYPHYGTEST
APPEND PROPERTY COMPILE_DEFINITIONS __UNITTEST__
)
......
debian/patches/spelling.patch
View file @ 75a49e03
......@@ -4,7 +4,7 @@ Description: Fix two spelling issues
--- a/src/core/batchlan.cpp
+++ b/src/core/batchlan.cpp
@@ -7368,7 +7368,7 @@ bool _ElementaryCommand::ConstructMPI
@@ -7383,7 +7383,7 @@ bool _ElementaryCommand::ConstructMPI
//____________________________________________________________________________________
bool _ElementaryCommand::ConstructCategoryMatrix (_String&source, _ExecutionList&target)
......
debian/patches/use_debian_sqlite.patch
View file @ 75a49e03
......@@ -19,7 +19,7 @@ Description: Use Debian packaged sqlite3
#-------------------------------------------------------------------------------
@@ -202,6 +201,36 @@ if(${CURL_FOUND} AND NOT APPLE)
@@ -210,6 +209,36 @@ if(${CURL_FOUND} AND NOT APPLE)
endif(${CURL_FOUND} AND NOT APPLE)
#-------------------------------------------------------------------------------
......@@ -56,7 +56,7 @@ Description: Use Debian packaged sqlite3
# gtest dependency
#-------------------------------------------------------------------------------
add_subdirectory(contrib/gtest-1.7.0)
@@ -235,11 +264,6 @@ set_property(
@@ -243,11 +272,6 @@ set_property(
)
set_property(
......@@ -68,7 +68,7 @@ Description: Use Debian packaged sqlite3
SOURCE src/core/calcnode2.cpp
APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"
)
@@ -261,7 +285,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
@@ -269,7 +293,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
include_directories(
src/core/include
src/lib/Link src/new/include
......
debian/rules
View file @ 75a49e03
......@@ -2,11 +2,11 @@
# DH_VERBOSE := 1
# export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
pkg=$(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
export PYBUILD_NAME=$(pkg)
include /usr/share/dpkg/default.mk
export PYBUILD_NAME=$(DEB_SOURCE)
PYVERS = $(shell pyversions -r)
PY3VERS = $(shell py3versions -r)
......@@ -24,7 +24,9 @@ override_dh_auto_build:
dh_auto_build -- MP MPI GTEST # LIB
override_dh_auto_test:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
find obj-* -name HYPHYGTEST -exec \{\} \;
endif
override_dh_install:
# smallcaps for executables
......
res/TemplateBatchFiles/BUSTED-SRV.bf
View file @ 75a49e03
RequireVersion ("2.1320141020");
RequireVersion ("2.13.20141020");
console.log("ERROR: THIS BATCHFILE WILL NOT RUN PROPERLY WITH UPDATED TERMS BASE. QUITTING.");
exit();
......
res/TemplateBatchFiles/BranchSiteREL.bf
View file @ 75a49e03
RequireVersion ("2.1320141101");
RequireVersion ("2.13.20141101");
_BSREL_timers = {5,1};
taskTimerStart (4);
......
res/TemplateBatchFiles/DatedTipsMolecularClock.bf
View file @ 75a49e03
RequireVersion ("2.0020110101");
RequireVersion ("2.00.20110101");
VERBOSITY_LEVEL = -1;
......
res/TemplateBatchFiles/Gateaux.bf
View file @ 75a49e03
RequireVersion ("2.0020110101");
RequireVersion ("2.00.20110101");
ExecuteAFile (HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"TemplateModels"+DIRECTORY_SEPARATOR+"chooseGeneticCode.def");
ExecuteAFile (HYPHY_LIB_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"2RatesAnalyses"+DIRECTORY_SEPARATOR+"MG94xREVxBivariate.mdl");
......
res/TemplateBatchFiles/GateauxMR.bf
View file @ 75a49e03
RequireVersion ("0.9920060817");
RequireVersion ("0.99.20060817");
s_rateMin = 0.01;
......
res/TemplateBatchFiles/LEISR.bf
View file @ 75a49e03
......@@ -32,7 +32,7 @@ leisr.analysis_description = {
terms.io.info: "LEISR (Likelihood Estimation of Individual Site Rates) infer relative amino-acid or nucleotide rates from a fixed nucleotide or amino-acid alignment and tree, with possibility for partitions. Relative site-specific substitution rates are
inferred by first optimizing alignment-wide branch lengths, and then inferring a site-specific uniform tree scaler.",
terms.io.version: "0.4",
terms.io.reference: "Spielman, S.J. and Kosakovsky Pond, S.L. Relative evolutionary rate inference in HyPhy with LEISR. bioRxiv. https://doi.org/10.1101/206011. (2017); Pupko, T., Bell, R. E., Mayrose, I., Glaser, F. & Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18, S71–S77 (2002).",
terms.io.reference: "Spielman, S.J. and Kosakovsky Pond, S.L. (2018). Relative evolutionary rate inference in HyPhy with PeerJ 6:e4339. DOI 10.7717/peerj.4339 ; Pupko, T., Bell, R. E., Mayrose, I., Glaser, F. & Ben-Tal, N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18, S71–S77 (2002).",
terms.io.authors: "Sergei L Kosakovsky Pond and Stephanie J Spielman",
terms.io.contact: "{spond,stephanie.spielman}@temple.edu"
};
......@@ -144,6 +144,14 @@ leisr.alignment_wide_MLES = estimators.FitSingleModel_Ext (
leisr.baseline_model_desc,
None,
{terms.run_options.retain_lf_object: TRUE});
/* reconstruct ancestral states - */
// SW20180516 - NOT YET SUPPORTED
//leisr.ancestral_data = ancestral.build (leisr.alignment_wide_MLES[terms.likelihood_function], 0, FALSE);
//console.log (leisr.ancestral_data);
//return 0;
ConstructCategoryMatrix (leisr.site_level_log_likelihoods, ^(leisr.alignment_wide_MLES[terms.likelihood_function]), SITE_LOG_LIKELIHOODS);
DeleteObject (^(leisr.alignment_wide_MLES[terms.likelihood_function]));
......@@ -473,4 +481,4 @@ lfunction leisr.store_results (node, result, arguments) {
lfunction leisr.getIC(logl, params, samples) {
return -2 * logl + 2 * samples / (samples - params - 1) * params;
}
\ No newline at end of file
}
res/TemplateBatchFiles/MEDS.bf
View file @ 75a49e03
RequireVersion ("2.0020101201");
RequireVersion ("2.00.20101201");
/*----------Branch-Site Directional Selection Analysis---------*/
/*Usage: Takes an alignment and a tree (with foreground branches tagged with "{FG}"), a nucleotide model
......
res/TemplateBatchFiles/MEME_mf.bf
View file @ 75a49e03
RequireVersion ("2.0020110101");
RequireVersion ("2.00.20110101");
timer = Time(1);
......
res/TemplateBatchFiles/NucModelCompare.bf
View file @ 75a49e03
RequireVersion ("0.9920061127");
RequireVersion ("0.99.20061127");
/*
This file takes a nucleotide data set and a tree (either from the data file or from a separate file) and computes maximum likelihood estimates for every possible 4x4 reversible model on that data and tree.
......
res/TemplateBatchFiles/Plato.bf
View file @ 75a49e03
......@@ -5,7 +5,7 @@
October 2006
*/
RequireVersion ("0.9920060901");
RequireVersion ("0.99.20060901");
VERBOSITY_LEVEL = -1; /* HELPS REDUCE GUI REFRESH OVERHEAD */
ACCEPT_BRANCH_LENGTHS = 1;
......
res/TemplateBatchFiles/QuickSelectionDetectionMF.bf
View file @ 75a49e03
RequireVersion ("2.12");
RequireVersion ("2.1.2");
ExecuteAFile ("qndhelper1_mf.ibf");
LoadFunctionLibrary ("GrabBag.bf");
......
res/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
View file @ 75a49e03
RequireVersion ("2.1320141101");
RequireVersion ("2.13.20141101");
_BSREL_timers = {5,1};
taskTimerStart (4);
......