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| author | Michael Larabel <michael@phx-laptop.(none)> | 2008-05-31 19:25:59 -0400 |
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| committer | Michael Larabel <michael@phx-laptop.(none)> | 2008-05-31 19:25:59 -0400 |
| commit | 01f85573a364347603f4b0da89ddd42b5bb827c2 (patch) | |
| tree | a8c12bf2aecc171484a266833fb99e9868f933c7 | |
| parent | bdc233bd93ebbab1ccf03c57d35c86f414c4a77a (diff) | |
| download | phoronix-test-suite-upstream-01f85573a364347603f4b0da89ddd42b5bb827c2.tar.gz phoronix-test-suite-upstream-01f85573a364347603f4b0da89ddd42b5bb827c2.tar.xz phoronix-test-suite-upstream-01f85573a364347603f4b0da89ddd42b5bb827c2.zip | |
Add hmmer test profile
| -rw-r--r-- | CHANGE-LOG | 1 | ||||
| -rw-r--r-- | pts/test-profiles/hmmer.xml | 23 | ||||
| -rw-r--r-- | pts/test-resources/hmmer/downloads.xml | 12 | ||||
| -rw-r--r-- | pts/test-resources/hmmer/install.sh | 29 | ||||
| -rw-r--r-- | pts/test-resources/hmmer/parse-results.php | 4 |
5 files changed, 69 insertions, 0 deletions
@@ -12,6 +12,7 @@ Phoronix Test Suite - Add many more download mirrors to all of the test profiles - Add cryptography suite - User agreement update +- Add hmmer test profile Phoronix Test Suite 0.9.0 May 28, 2008 diff --git a/pts/test-profiles/hmmer.xml b/pts/test-profiles/hmmer.xml new file mode 100644 index 0000000..3048926 --- /dev/null +++ b/pts/test-profiles/hmmer.xml @@ -0,0 +1,23 @@ +<PhoronixTestSuite> + <TestProfile> + <Version>0.3</Version> + <TestType>Processor</TestType> + <SoftwareType>Scientific</SoftwareType> + <License>FREE</License> + <Status>VERIFIED</Status> + <Maintainer>Andrew Schofield</Maintainer> + <DownloadSize>107</DownloadSize> + <EnvironmentSize>707</EnvironmentSize> + </TestProfile> + <TestInformation> + <Title>Timed HMMer Search</Title> + <Version>2.3.2</Version> + <SubTitle>Pfam Database Search</SubTitle> + <ResultScale>Seconds</ResultScale> + <ExternalDependencies>build-utilities</ExternalDependencies> + <TimesToRun>1</TimesToRun> + <Description>This test searches through the Pfam database of profile hidden markov models. The search finds the domain structure of Drosophila Sevenless protein.</Description> + <Proportion>LIB</Proportion> + </TestInformation> +</PhoronixTestSuite> + diff --git a/pts/test-resources/hmmer/downloads.xml b/pts/test-resources/hmmer/downloads.xml new file mode 100644 index 0000000..c369f27 --- /dev/null +++ b/pts/test-resources/hmmer/downloads.xml @@ -0,0 +1,12 @@ +<PhoronixTestSuite> + <Downloads> + <Package> + <URL>ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-2.3.2.tar.gz</URL> + <MD5>5f073340c0cf761288f961a73821228a</MD5> + </Package> + <Package> + <URL>ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam_ls.gz, ftp://topaze.jouy.inra.fr/pub/pfam/current/Pfam_ls.gz, ftp://selab.janelia.org/pub/Pfam/Pfam_ls.gz</URL> + <MD5>31647337a0e8309fce3914da7e8f4a1c</MD5> + </Package> + </Downloads> +</PhoronixTestSuite> diff --git a/pts/test-resources/hmmer/install.sh b/pts/test-resources/hmmer/install.sh new file mode 100644 index 0000000..1d1aa63 --- /dev/null +++ b/pts/test-resources/hmmer/install.sh @@ -0,0 +1,29 @@ +#!/bin/sh + +THIS_DIR=$(pwd) +mkdir -p $THIS_DIR/hmmer_ + +tar -xvf hmmer-2.3.2.tar.gz +cd hmmer-2.3.2/ +./configure --enable-threads --prefix=$THIS_DIR/hmmer_ +make -j $NUM_CPU_JOBS +make install +cd .. +cp -r hmmer-2.3.2/tutorial hmmer_ +rm -rf hmmer-2.3.2/ +gunzip Pfam_ls.gz -c > hmmer_/tutorial/Pfam_ls + +cat>hmmpfam<<EOT +#!/bin/sh +cd hmmer_/tutorial +../bin/hmmpfam -E 0.1 Pfam_ls 7LES_DROME > /dev/null +cd ../.. +EOT +chmod +x hmmpfam + +cat>hmmer<<EOT +#!/bin/sh +/usr/bin/time -f "Pfam search time: %e seconds" ./hmmpfam 2>&1 | grep seconds +EOT +chmod +x hmmer + diff --git a/pts/test-resources/hmmer/parse-results.php b/pts/test-resources/hmmer/parse-results.php new file mode 100644 index 0000000..84612ea --- /dev/null +++ b/pts/test-resources/hmmer/parse-results.php @@ -0,0 +1,4 @@ +<?php +$BENCHMARK_RESULTS = substr($argv[1], strrpos($argv[1], "Pfam search time:") + 18); +echo trim(substr($BENCHMARK_RESULTS, 0, strpos($BENCHMARK_RESULTS, "seconds"))); +?> |