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Timed MrBayes Analysis 1.4.0
pts/mrbayes-1.4.0
- 11 October 2019 -
Update against upstream, add Windows support.
downloads.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v9.0.1--> <PhoronixTestSuite> <Downloads> <Package> <URL>https://github.com/NBISweden/MrBayes/archive/v3.2.7a.tar.gz</URL> <MD5>504236626ce9a2de1066a8520672f0cc</MD5> <SHA256>3eed2e3b1d9e46f265b6067a502a89732b6f430585d258b886e008e846ecc5c6</SHA256> <FileName>MrBayes-3.2.7a.tar.gz</FileName> <FileSize>545968</FileSize> <PlatformSpecific>Linux, Solaris, BSD, MacOSX</PlatformSpecific> </Package> <Package> <URL>https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/MrBayes-3.2.7-WIN.zip</URL> <MD5>1c785876594fb64ca3d5d75d2877306a</MD5> <SHA256>d9dcf4190f11a9489875d0b9c7ff9caea720b6f17df0b5f8cd0fce428e60cebe</SHA256> <FileName>MrBayes-3.2.7-WIN.zip</FileName> <FileSize>6514059</FileSize> <PlatformSpecific>Windows</PlatformSpecific> </Package> </Downloads> </PhoronixTestSuite>
install.sh
#!/bin/sh tar -zxvf MrBayes-3.2.7a.tar.gz cd MrBayes-3.2.7a ./configure make -j $NUM_CPU_CORES echo $? > ~/install-exit-status cat>job.nex<<EOT begin mrbayes; set autoclose=yes nowarn=yes; execute examples/primates.nex; lset nst=2; mcmc nruns=1 ngen=1000000 samplefreq=10000; sump burnin=250; sumt burnin=250; end; EOT cd ~ cat>mrbayes<<EOT #!/bin/sh cd MrBayes-3.2.7a/ mpiexec --allow-run-as-root -np \$NUM_CPU_PHYSICAL_CORES ./src/mb job.nex 2>&1 echo \$? > ~/test-exit-status EOT chmod +x mrbayes
install_windows.sh
#!/bin/sh unzip -o MrBayes-3.2.7-WIN.zip cd MrBayes-3.2.7-WIN/ cat>job.nex<<EOT begin mrbayes; set autoclose=yes nowarn=yes; execute examples/primates.nex; lset nst=2; mcmc nruns=1 ngen=1000000 samplefreq=10000; sump burnin=250; sumt burnin=250; end; EOT cd ~ cat>mrbayes<<EOT #!/bin/sh cd MrBayes-3.2.7-WIN/ ./bin/mb.3.2.7-win64.exe job.nex 2>&1 echo \$? > ~/test-exit-status EOT chmod +x mrbayes
results-definition.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v9.0.1--> <PhoronixTestSuite> <SystemMonitor> <Sensor>sys.time</Sensor> </SystemMonitor> </PhoronixTestSuite>
test-definition.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v9.0.1--> <PhoronixTestSuite> <TestInformation> <Title>Timed MrBayes Analysis</Title> <AppVersion>3.2.7</AppVersion> <Description>This test performs a bayesian analysis of a set of primate genome sequences in order to estimate their phylogeny.</Description> <ResultScale>Seconds</ResultScale> <Proportion>LIB</Proportion> <SubTitle>Primate Phylogeny Analysis</SubTitle> <TimesToRun>3</TimesToRun> </TestInformation> <TestProfile> <Version>1.4.0</Version> <SupportedPlatforms>Linux, Solaris, BSD, MacOSX, Windows</SupportedPlatforms> <SoftwareType>Scientific</SoftwareType> <TestType>Processor</TestType> <License>Free</License> <Status>Verified</Status> <ExternalDependencies>build-utilities, openmpi-development</ExternalDependencies> <EnvironmentSize>22</EnvironmentSize> <ProjectURL>https://github.com/NBISweden/MrBayes</ProjectURL> <InternalTags>SMP, MPI</InternalTags> <Maintainer>Andrew Schofield</Maintainer> </TestProfile> </PhoronixTestSuite>