Timed MAFFT Alignment 1.6.2

pts/mafft-1.6.2 - 11 December 2020 - MAFFT fixes for BSD based on https://github.com/apurvanandan1997/pts-test-profiles-dev/tree/master/mafft-1.5.0

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.2.0m2-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>https://mafft.cbrc.jp/alignment/software/mafft-7.471-without-extensions-src.tgz</URL>
      <MD5>42e01606c2e55a3534bf7b04bc44aa72</MD5>
      <SHA256>60f8ec7bab80e00dbb24be65b8000312ffc98ff10eb72fc2219869d1dd382964</SHA256>
      <FileName>mafft-7.471-without-extensions-src.tgz</FileName>
      <FileSize>614447</FileSize>
      <PlatformSpecific>Linux, MacOSX, BSD</PlatformSpecific>
    </Package>
    <Package>
      <URL>https://mafft.cbrc.jp/alignment/software/mafft-7.471-win64-signed.zip</URL>
      <MD5>d5ef5a920f816d4e8c9d8992a4f99791</MD5>
      <SHA256>c7911c5a8514118228dc11b74aa4470e85eb4b2b001c5d749295298f6ebdd5b4</SHA256>
      <FileName>mafft-7.471-win64-signed.zip</FileName>
      <FileSize>26636027</FileSize>
      <PlatformSpecific>Windows</PlatformSpecific>
    </Package>
    <Package>
      <URL>https://mafft.cbrc.jp/alignment/software/ex1.txt</URL>
      <MD5>e24394b0dcc1cc6f89cc3d85ae6656e1</MD5>
      <SHA256>aecfc44e2321573f1e0cdc1c6922a85e2a0a986654dc1f59d07dec54c929a045</SHA256>
      <FileName>mafft-ex1-lsu-rna.txt</FileName>
      <FileSize>198841</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

rm -rf $HOME/mafft_
mkdir $HOME/mafft_
tar -xvf mafft-7.471-without-extensions-src.tgz
cd mafft-7.471-without-extensions/core/

if [ $OS_TYPE = "BSD" ]
then
	gmake clean
else
	make clean
fi

sed -i -e "s|PREFIX = /usr/local|PREFIX = $HOME/mafft_|g" Makefile

if [ $OS_TYPE = "BSD" ]
then
	gmake -j $NUM_CPU_CORES ENABLE_MULTITHREAD=-Denablemultithread
else
	make -j $NUM_CPU_CORES ENABLE_MULTITHREAD=-Denablemultithread
fi

echo $? > ~/install-exit-status
if [ $OS_TYPE = "BSD" ]
then
	gmake install
else
	make install
fi
cd ~/
cp -f mafft-7.471-without-extensions/scripts/mafft mafft_/
rm -rf mafft-7.471-without-extensions/

cp mafft-ex1-lsu-rna.txt mafft_

if [ -x /usr/pkg/bin/bash ]
then
	# bsd fix
	sed -i -e "s|/bin/bash|/usr/pkg/bin/bash|g" mafft_/mafft
fi

cat>mafft<<EOT
#!/bin/sh
cd mafft_/
./mafft --thread \$NUM_CPU_CORES --auto mafft-ex1-lsu-rna.txt > \$LOG_FILE
echo \$? > ~/test-exit-status
EOT
chmod +x mafft

install_windows.sh

#!/bin/sh

unzip -o mafft-7.471-win64-signed.zip
cp mafft-ex1-lsu-rna.txt mafft-win/usr/bin

cat>mafft<<EOT
#!/bin/sh
cd mafft-win/usr/bin
./mafft --thread \$NUM_CPU_CORES --auto mafft-ex1-lsu-rna.txt > \$LOG_FILE
EOT
chmod +x mafft

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.2.0m2-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v10.2.0m2-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>Timed MAFFT Alignment</Title>
    <AppVersion>7.471</AppVersion>
    <Description>This test performs an alignment of 100 pyruvate decarboxylase sequences.</Description>
    <ResultScale>Seconds</ResultScale>
    <Proportion>LIB</Proportion>
    <SubTitle>Multiple Sequence Alignment - LSU RNA</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.6.2</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>