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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>