Timed HMMer Search 1.1.0

pts/hmmer-1.1.0 - 06 December 2010 - Initial import into OpenBenchmarking.org

downloads.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v3.0.0a3 (Iveland) [ http://www.phoronix-test-suite.com/ ]-->
<PhoronixTestSuite>
  <Downloads>
    <Package>
      <URL>ftp://ftp.eenet.ee/pub/FreeBSD/distfiles/hmmer-2.3.2.tar.gz, ftp://ftp.uni-frankfurt.de/pub/Mirrors2/gentoo.org/distfiles/hmmer-2.3.2.tar.gz, ftp://ftp.mgts.by/pub/FreeBSD/ports/distfiles/hmmer-2.3.2.tar.gz, ftp://ftp.dei.uc.pt/pub/linux/gentoo/distfiles/hmmer-2.3.2.tar.gz</URL>
      <MD5>5f073340c0cf761288f961a73821228a</MD5>
      <FileSize>1024933</FileSize>
    </Package>
    <Package>
      <URL>ftp://ftp.embl-heidelberg.de/ftp.ebi.ac.uk/pub/delete_databases/Pfam/Pfam_ls.gz</URL>
      <MD5>bcc3ea17f61eb22dc0d4375f79e0ced5</MD5>
      <FileSize>111043685</FileSize>
    </Package>
  </Downloads>
</PhoronixTestSuite>

install.sh

#!/bin/sh

mkdir -p $HOME/hmmer_

tar -zxvf hmmer-2.3.2.tar.gz
cd hmmer-2.3.2/
./configure --enable-threads --prefix=$HOME/hmmer_
make -j $NUM_CPU_JOBS
echo $? > ~/install-exit-status
make install
cd ..
cp -r hmmer-2.3.2/tutorial hmmer_
rm -rf hmmer-2.3.2/
gunzip Pfam_ls.gz -c > hmmer_/tutorial/Pfam_ls

cat>hmmpfam<<EOT
#!/bin/sh
cd hmmer_/tutorial
../bin/hmmpfam -E 0.1 Pfam_ls 7LES_DROME > /dev/null
cd ../..
EOT
chmod +x hmmpfam

cat>hmmer<<EOT
#!/bin/sh
./hmmpfam 2>&1
echo \$? > ~/test-exit-status
EOT
chmod +x hmmer

results-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v3.0.0a3 (Iveland) [ http://www.phoronix-test-suite.com/ ]-->
<PhoronixTestSuite>
  <SystemMonitor>
    <Sensor>sys.time</Sensor>
  </SystemMonitor>
</PhoronixTestSuite>

test-definition.xml

<?xml version="1.0"?>
<!--Phoronix Test Suite v3.0.0a3 (Iveland) [ http://www.phoronix-test-suite.com/ ]-->
<PhoronixTestSuite>
  <TestInformation>
    <Title>Timed HMMer Search</Title>
    <AppVersion>2.3.2</AppVersion>
    <Description>This test searches through the Pfam database of profile hidden markov models. The search finds the domain structure of Drosophila Sevenless protein.</Description>
    <ResultScale>Seconds</ResultScale>
    <Proportion>LIB</Proportion>
    <SubTitle>Pfam Database Search</SubTitle>
    <TimesToRun>3</TimesToRun>
  </TestInformation>
  <TestProfile>
    <Version>1.1.0</Version>
    <SupportedPlatforms>Linux, Solaris, BSD</SupportedPlatforms>
    <SoftwareType>Scientific</SoftwareType>
    <TestType>Processor</TestType>
    <License>Free</License>
    <Status>Verified</Status>
    <ExternalDependencies>build-utilities</ExternalDependencies>
    <EnvironmentSize>707</EnvironmentSize>
    <ProjectURL>http://hmmer.janelia.org/</ProjectURL>
    <InternalTags>SMP</InternalTags>
    <Maintainer>Andrew Schofield</Maintainer>
  </TestProfile>
</PhoronixTestSuite>