Timed MAFFT Alignment 1.4.2

pts/mafft-1.4.2 - 06 February 2018 - Minor cleanup to the install.sh

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v7.8.0m3-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>http://mafft.cbrc.jp/alignment/software/mafft-6.864-without-extensions-src.tgz, http://phoronix-test-suite.com/benchmark-files/mafft-6.864-without-extensions-src.tgz</URL>
      <MD5>0c889658c2b1eb41da02e36630ae6b27</MD5>
      <SHA256>660fdca1a61acf2910381d5b6084e2d249167d9c89937dad6c588b35d2b7d7d6</SHA256>
      <FileSize>384472</FileSize>
    </Package>
    <Package>
      <URL>http://phoronix-test-suite.com/benchmark-files/pyruvate_decarboxylase.fasta.bz2</URL>
      <MD5>22cd5efc1199a72fbb3f19960f56010d</MD5>
      <SHA256>0e08a3749b7196310b065a783f3cddc0a1f42876004d3f75ebe367d2ffe751bf</SHA256>
      <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>mafft<<EOT
#!/bin/sh
cd mafft_/
./mafft --thread \$NUM_CPU_CORES --localpair --maxiterate 10000 pyruvate_decarboxylase.fasta > \$LOG_FILE
echo \$? > ~/test-exit-status
EOT
chmod +x mafft

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v7.8.0m3-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v7.8.0m3-->
<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>1.4.2</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>