[med-svn] [Git][med-team/bppsuite][master] 3 commits: New upstream version 2.4.1
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Aug 22 08:24:24 BST 2018
Julien Y. Dutheil pushed to branch master at Debian Med / bppsuite
Commits:
5524c887 by Julien Y. Dutheil at 2018-08-22T07:18:03Z
New upstream version 2.4.1
- - - - -
eb8c5bde by Julien Y. Dutheil at 2018-08-22T07:18:04Z
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir 2b388ba14be5ef280973e4479a489bca129bfcd9
- - - - -
e34c1cda by Julien Y. Dutheil at 2018-08-22T07:23:21Z
Version 2.4.1.
Compatibility update with gcc 8.
- - - - -
5 changed files:
- CMakeLists.txt
- README.md
- bppsuite.spec
- debian/changelog
- doc/bppsuite.texi
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -23,7 +23,7 @@ IF(NOT NO_DEP_CHECK)
ENDIF(NOT NO_DEP_CHECK)
IF(NO_DEP_CHECK)
- MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
+ MESSAGE(STATUS "Dependencies checking disabled. Only distribution can be built.")
ELSE(NO_DEP_CHECK)
@@ -34,7 +34,7 @@ IF(NOT BUILD_STATIC)
FORCE)
ENDIF()
IF(BUILD_STATIC)
- MESSAGE("-- Static linkage requested.")
+ MESSAGE(STATUS "Static linkage requested.")
SET(CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
ENDIF()
@@ -88,10 +88,10 @@ ENDIF(NO_DEP_CHECK)
# Packager
SET(CPACK_PACKAGE_NAME "bppsuite")
SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
SET(CPACK_PACKAGE_VERSION_MAJOR "2")
SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Program Suite")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
=====================================
README.md
=====================================
--- a/README.md
+++ b/README.md
@@ -78,5 +78,8 @@ Many examples are available in the subdirectory of <tt>Examples</tt>.
### Documentation
-Documentation can be found at https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.
+
+Documentation can be found in one page at: http://bioweb.me/bppsuite-doc
+
+Or on github: https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.
\ No newline at end of file
=====================================
bppsuite.spec
=====================================
--- a/bppsuite.spec
+++ b/bppsuite.spec
@@ -3,7 +3,7 @@
URL: https://github.com/BioPP
Name: bppsuite
-Version: 2.4.0
+Version: 2.4.1
Release: 1%{?dist}
License: CECILL-2.0
Vendor: The Bio++ Project
@@ -88,6 +88,7 @@ rm -rf $RPM_BUILD_ROOT
%{_prefix}/share/man/man1/*.1*
%changelog
+* Wed Aug 15 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.1-1
* Mon Mar 12 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.0-1
* Tue Jun 06 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.1-1
* Wed May 10 2017 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.3.0-1
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+bppsuite (2.4.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+
+ -- Julien Dutheil <julien.dutheil at univ-montp2.fr> Wed, 22 Aug 2018 09:18:13 +0200
+
bppsuite (2.4.0-1) unstable; urgency=medium
[ Julien Dutheil ]
=====================================
doc/bppsuite.texi
=====================================
--- a/doc/bppsuite.texi
+++ b/doc/bppsuite.texi
@@ -1667,8 +1667,34 @@ Concerning the optimization procedure, this choice may entail the non-
identifiability of several parameters (here the probabilities in model
3), so the user should be careful about this.
+
+When the submodel is aliased behind a model name, the paths should be
+defined as combinations of the model that is mixed. For example,
+YNGP_M2 is made of 3 YN98 models, depending of three @var{omega}
+values: <1, =1, >1. If we want a site to switch between <1 and >1
+omega values between two sets of branches:
+
+ at cartouche
+ at example
+nonhomogeneous = general
+nonhomogeneous.number_of_models = 2
+
+model1=YNGP_M2(frequencies=F1X4)
+model2=YNGP_M2(frequencies=F1X4)
+
+model1.nodes_id=0:1
+model2.nodes_id=2:3
+
+site.number_of_paths=3
+site.path1=model1[YN98.omega_1] & model2[YN98.omega_3]
+site.path2=model1[YN98.omega_2] & model2[YN98.omega_2]
+site.path3=model1[YN98.omega_3] & model2[YN98.omega_1]
+
+ at end example
+ at end cartouche
+
Another example in the case of mixtures of mixed models, where the
-submodels are defined by their names;
+submodels are defined by their names:
@cartouche
@example
@@ -1730,6 +1756,17 @@ For nucleotides only, set the G content equal to the C content.
Full parametrization. Contains N free parameters, where N is equal to the size of the alphabet - 1. For codon models, N is the size of the alphabet - 1 - the number of stop codons, whose frequencies are set to 0.
For nucleotide sequences, theta is the GC content, theta1 is the proportion of A over A+T, and theta2 is the proportion of G over G+C.
+ at item Empirical(file=@{path@} [,col=@{int@}])
+Read frequencies from a file. Each frequencies is set as plain column
+in the file. If several columns are in the file, the number of the
+column can be given with @{col@} argument (default: 1).
+
+ at item Empirical+F(name=@{chars@}, file=@{path@}, [theta=@{real]0,1[@}, theta1=@{real]0,1[@}, theta2=@{real]0,1[@}, ..., "equilibrium frequencies"])
+Build a protein substitution model from a file in PAML format, and use
+free equilibrium frequencies. 'name' will be used as a parameter
+namespace, including for frequencies.
+
+
@item Word(frequency=@{frequency set description@})
or
View it on GitLab: https://salsa.debian.org/med-team/bppsuite/compare/69a6c847dddc4355841d5c1ad66a286718fe56d6...e34c1cdafebe9bac44420431bbd8e3dfb54fc450
--
View it on GitLab: https://salsa.debian.org/med-team/bppsuite/compare/69a6c847dddc4355841d5c1ad66a286718fe56d6...e34c1cdafebe9bac44420431bbd8e3dfb54fc450
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