Timed MAFFT Alignment 1.5.0

pts/mafft-1.5.0 - 04 March 2018 - Update against MAFFT 7.392, add Windows support.

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.0.0m0-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://mafft.cbrc.jp/alignment/software/mafft-7.392-without-extensions-src.tgz</URL>
      <MD5>17450a262e3e3e381bc8ccdd0afaadb5</MD5>
      <SHA256>31949c940a03cd873f4b369def745a06fe991987042578aa3c2ac7a194d9d26c</SHA256>
      <FileSize>592236</FileSize>
      <PlatformSpecific>Linux, MacOSX, BSD</PlatformSpecific>
    </Package>
    <Package>
      <URL>https://mafft.cbrc.jp/alignment/software/mafft-7.392-win64-signed.zip</URL>
      <MD5>431a31933db7a3f9bea2e27521c2a22b</MD5>
      <SHA256>4bedaa39bc0be64d33462fe97c7ef018e5348b03b049a04b9de38b1b7edf1bf5</SHA256>
      <FileSize>24192113</FileSize>
      <PlatformSpecific>Windows</PlatformSpecific>
    </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-7.392-without-extensions-src.tgz
cd mafft-7.392-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-7.392-without-extensions/scripts/mafft mafft_/
rm -rf mafft-7.392-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 20000 pyruvate_decarboxylase.fasta > \$LOG_FILE
echo \$? > ~/test-exit-status
EOT
chmod +x mafft

install_windows.sh

#!/bin/sh

unzip -o mafft-7.392-win64-signed.zip
bunzip2 pyruvate_decarboxylase.fasta.bz2 -c > mafft-win/usr/bin

cat>mafft<<EOT
#!/bin/sh
cd mafft-win/usr/bin
./mafft --thread \$NUM_CPU_CORES --localpair --maxiterate 20000 pyruvate_decarboxylase.fasta > \$LOG_FILE
EOT
chmod +x mafft

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.0.0m0-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v8.0.0m0-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>Timed MAFFT Alignment</Title>
    <AppVersion>7.392</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>1.5.0</Version>
    <SupportedPlatforms>Linux, MacOSX, BSD, Windows</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>