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Timed MAFFT Alignment 1.4.0
pts/mafft-1.4.0
- 21 February 2012 -
Support multi-threaded MAFFT build.
downloads.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v3.8.0m2 (Bygland)--> <PhoronixTestSuite> <Downloads> <Package> <URL>http://mafft.cbrc.jp/alignment/software/mafft-6.864-without-extensions-src.tgz</URL> <MD5>0c889658c2b1eb41da02e36630ae6b27</MD5> <FileName>mafft-6.864-without-extensions-src.tgz</FileName> <FileSize>384472</FileSize> </Package> <Package> <URL>http://fire-salamander.co.uk/pts-tests/pyruvate_decarboxylase.fasta.bz2</URL> <MD5>22cd5efc1199a72fbb3f19960f56010d</MD5> <FileName>pyruvate_decarboxylase.fasta.bz2</FileName> <FileSize>13847</FileSize> </Package> </Downloads> </PhoronixTestSuite>
install.sh
#!/bin/sh rm -rf $HOME/mafft_ mkdir $HOME/mafft_ tar -xvf mafft-6.864-without-extensions-src.tgz cd mafft-6.864-without-extensions/core/ make clean sed -i -e "s|PREFIX = /usr/local|PREFIX = $HOME/mafft_|g" Makefile make -j $NUM_CPU_JOBS ENABLE_MULTITHREAD=-Denablemultithread echo $? > ~/install-exit-status make install cd ~/ cp -f mafft-6.864-without-extensions/scripts/mafft mafft_/ rm -rf mafft-6.864-without-extensions/ bunzip2 pyruvate_decarboxylase.fasta.bz2 -c > mafft_/pyruvate_decarboxylase.fasta cat>align<<EOT #!/bin/sh cd mafft_/ ./mafft --thread \$NUM_CPU_CORES --localpair --maxiterate 10000 pyruvate_decarboxylase.fasta 1>/dev/null 2>&1 cd .. EOT chmod +x align cat>mafft<<EOT #!/bin/sh ./align 2>&1 echo \$? > ~/test-exit-status EOT chmod +x mafft
results-definition.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v3.8.0m2 (Bygland)--> <PhoronixTestSuite> <SystemMonitor> <Sensor>sys.time</Sensor> </SystemMonitor> </PhoronixTestSuite>
test-definition.xml
<?xml version="1.0"?> <!--Phoronix Test Suite v3.8.0m2 (Bygland)--> <PhoronixTestSuite> <TestInformation> <Title>Timed MAFFT Alignment</Title> <AppVersion>6.864</AppVersion> <Description>This test performs an alignment of 100 pyruvate decarboxylase sequences.</Description> <ResultScale>Seconds</ResultScale> <Proportion>LIB</Proportion> <SubTitle>Multiple Sequence Alignment</SubTitle> <TimesToRun>3</TimesToRun> </TestInformation> <TestProfile> <Version>1.4.0</Version> <SupportedPlatforms>Linux, MacOSX, BSD</SupportedPlatforms> <SoftwareType>Scientific</SoftwareType> <TestType>Processor</TestType> <License>Free</License> <Status>Verified</Status> <ExternalDependencies>build-utilities</ExternalDependencies> <EnvironmentSize>18</EnvironmentSize> <ProjectURL>http://align.bmr.kyushu-u.ac.jp/mafft/software/</ProjectURL> <Maintainer>Andrew Schofield</Maintainer> </TestProfile> </PhoronixTestSuite>