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Update bayescan to v2.1 (#64422)
* Update bayescan to v2.1 * Update build.sh * Update meta.yaml * Update build.sh
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Lines changed: 97 additions & 49 deletions

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‎recipes/bayescan/0001-Use-CXX-and-no-static.patch‎

Lines changed: 31 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -1,43 +1,49 @@
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--- source/Makefile
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+++ source/Makefile
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diff --git a/source/Makefile b/source/Makefile
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index fde05fc..c5b38c9 100644
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--- a/source/Makefile
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+++ b/source/Makefile
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@@ -1,31 +1,31 @@
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# BayeScan makefile
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bayescan2: start.o beta.o dirichlet.o RJupdates.o MHupdates.o likelihood.o read_write.o anyoption.o
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- g++ -o bayescan2 -static start.o beta.o dirichlet.o RJupdates.o MHupdates.o likelihood.o read_write.o anyoption.o
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+ $(CXX) $(LDFLAGS) -o bayescan2 start.o beta.o dirichlet.o RJupdates.o MHupdates.o likelihood.o read_write.o anyoption.o
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-bayescan_2.1: start.o beta.o dirichlet.o RJupdates.o MHupdates.o likelihood.o read_write.o anyoption.o
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- g++ -fopenmp -static -lpthread -o bayescan_2.1 start.o beta.o dirichlet.o RJupdates.o MHupdates.o likelihood.o read_write.o anyoption.o
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+bayescan_2.1: start.o beta.o dirichlet.o RJupdates.o MHupdates.o likelihood.o read_write.o anyoption.o
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp -static -pthread -o bayescan_2.1 start.o beta.o dirichlet.o RJupdates.o MHupdates.o likelihood.o read_write.o anyoption.o
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start.o: start.cpp errors.cpp anyoption.h global_defs.h
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- g++ -c start.cpp errors.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c start.cpp errors.cpp
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- g++ -fopenmp -c start.cpp errors.cpp
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c start.cpp errors.cpp
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beta.o: beta.cpp global_defs.h
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- g++ -c beta.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c beta.cpp
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- g++ -fopenmp -c beta.cpp
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-
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c beta.cpp
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+
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dirichlet.o: dirichlet.cpp global_defs.h
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- g++ -c dirichlet.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c dirichlet.cpp
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- g++ -fopenmp -c dirichlet.cpp
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c dirichlet.cpp
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RJupdates.o: RJupdates.cpp global_defs.h
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- g++ -c RJupdates.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c RJupdates.cpp
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- g++ -fopenmp -c RJupdates.cpp
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c RJupdates.cpp
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MHupdates.o: MHupdates.cpp global_defs.h
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- g++ -c MHupdates.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c MHupdates.cpp
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- g++ -fopenmp -c MHupdates.cpp
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c MHupdates.cpp
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likelihood.o: likelihood.cpp global_defs.h
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- g++ -c likelihood.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c likelihood.cpp
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- g++ -fopenmp -c likelihood.cpp
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c likelihood.cpp
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read_write.o: read_write.cpp errors.cpp global_defs.h
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- g++ -c read_write.cpp errors.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c read_write.cpp errors.cpp
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- g++ -fopenmp -c read_write.cpp errors.cpp
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c read_write.cpp errors.cpp
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anyoption.o: anyoption.cpp anyoption.h
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- g++ -c anyoption.cpp
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+ $(CXX) $(CXXFLAGS) $(CPPFLAGS) -c anyoption.cpp
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-anyoption.o: anyoption.cpp anyoption.h
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- g++ -fopenmp -c anyoption.cpp
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+anyoption.o: anyoption.cpp anyoption.h
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+ $(CXX) $(CXXFLAGS) -std=c++14 -fopenmp $(CPPFLAGS) -c anyoption.cpp
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clean:
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rm *.o bayescan2
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-clean:
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+clean:
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rm *.o bayescan_2.1

‎recipes/bayescan/0002-Fix-strcpy-overflow.patch‎

Lines changed: 0 additions & 8 deletions
This file was deleted.

‎recipes/bayescan/build.sh‎

Lines changed: 31 additions & 3 deletions
Original file line numberDiff line numberDiff line change
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#!/bin/bash
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cd source
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make CXXFLAGS="${CXXFLAGS} -std=c++14"
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export CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include"
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export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
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export CXXFLAGS="${CXXFLAGS} -O3"
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case $(uname -m) in
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aarch64)
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export CXXFLAGS="${CXXFLAGS} -march=armv8-a"
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;;
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arm64)
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export CXXFLAGS="${CXXFLAGS} -march=armv8.4-a"
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;;
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x86_64)
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export CXXFLAGS="${CXXFLAGS} -march=x86-64-v3"
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;;
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esac
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mkdir -p "${PREFIX}/bin"
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cp bayescan2 "${PREFIX}/bin/"
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if [[ `uname -s` == "Darwin" ]]; then
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sed -i.bak 's|-static||' source/Makefile
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fi
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sed -i.bak 's|BayeScan 2.0|BayeScan 2.1|' source/start.cpp
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sed -i.bak 's|strcpy (long_opt_prefix, _prefix)|strncpy (long_opt_prefix, _prefix, MAX_LONG_PREFIX_LENGTH)|' source/anyoption.cpp
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sed -i.bak 's|strcpy( long_opt_prefix , "--" )|strncpy( long_opt_prefix , "--", MAX_LONG_PREFIX_LENGTH )|' source/anyoption.cpp
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rm -f source/*.bak
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cd source
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make CXX="${CXX}" CXXFLAGS="${CXXFLAGS}" -j"${CPU_COUNT}"
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install -v -m 0755 bayescan_2.1 "${PREFIX}/bin"

‎recipes/bayescan/meta.yaml‎

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Original file line numberDiff line numberDiff line change
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package:
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name: bayescan
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version: 2.0.1
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{% set name = "bayescan" %}
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{% set version = "2.1" %}
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build:
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number: 7
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skip: True # [osx]
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package:
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name: {{ name }}
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version: {{ version }}
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source:
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url: http://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.01.zip
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sha256: 7859e581e62471b1c33289a89e80ab14b244b97f2d61a2560083ca073a7ef1e9
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url: https://cmpg.unibe.ch/software/BayeScan/files/BayeScan{{ version }}.zip
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sha256: c6bbc52a5a6a30e895951faf2bd6291ca47fdccdc708e693fce02389548d5547
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patches:
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- 0001-Use-CXX-and-no-static.patch
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- 0002-Fix-strcpy-overflow.patch
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build:
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number: 0
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run_exports:
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- {{ pin_subpackage(name, max_pin="x") }}
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requirements:
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build:
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- make
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- {{ compiler('cxx') }}
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host:
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- libgomp # [linux]
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- llvm-openmp # [osx]
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run:
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- libgomp # [linux]
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- llvm-openmp # [osx]
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test:
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commands:
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- bayescan2 | grep -qF BayeScan
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- bayescan_2.1 | grep -qF BayeScan
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about:
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home: http://cmpg.unibe.ch/software/BayeScan/
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license: GPL
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summary: Phylogenetics - Randomized Axelerated Maximum Likelihood.
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home: "https://cmpg.unibe.ch/software/BayeScan"
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license: "GPL-3.0-or-later"
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license_family: GPL3
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license_file: source/COPYING
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summary: "Phylogenetics - Randomized Axelerated Maximum Likelihood."
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doc_url: "https://cmpg.unibe.ch/software/BayeScan/files/BayeScan{{ version }}_manual.pdf"
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dev_url: "https://cmpg.unibe.ch/software/BayeScan"
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extra:
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additional-platforms:
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- linux-aarch64
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- osx-arm64
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identifiers:
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- biotools:bayescan
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- usegalaxy-eu:BayeScan
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- doi:10.1534/genetics.108.092221
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skip-lints:
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- compiler_needs_stdlib_c

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