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| author | Michael Larabel <michael@phx-laptop.(none)> | 2008-05-31 19:25:59 -0400 |
|---|---|---|
| committer | Michael Larabel <michael@phx-laptop.(none)> | 2008-05-31 19:25:59 -0400 |
| commit | 01f85573a364347603f4b0da89ddd42b5bb827c2 (patch) | |
| tree | a8c12bf2aecc171484a266833fb99e9868f933c7 /pts/test-resources/hmmer | |
| 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
Diffstat (limited to 'pts/test-resources/hmmer')
| -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 |
3 files changed, 45 insertions, 0 deletions
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"))); +?> |