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| author | Michael Larabel <michael@phx-laptop.(none)> | 2008-06-01 16:42:32 -0400 |
|---|---|---|
| committer | Michael Larabel <michael@phx-laptop.(none)> | 2008-06-01 16:42:32 -0400 |
| commit | 3540db62b4ef915a29110cc43647002dca31d586 (patch) | |
| tree | 1db9032dcb04e88624fcb7d1042aa158c5c22baf /pts/test-resources/mafft | |
| parent | c436b07614a2f6c7449e706d2ee49be7644a4f9f (diff) | |
| download | phoronix-test-suite-upstream-3540db62b4ef915a29110cc43647002dca31d586.tar.gz phoronix-test-suite-upstream-3540db62b4ef915a29110cc43647002dca31d586.tar.xz phoronix-test-suite-upstream-3540db62b4ef915a29110cc43647002dca31d586.zip | |
Add mafft test profile: a computational biology tools for aligning
biological sequence data
Diffstat (limited to 'pts/test-resources/mafft')
| -rw-r--r-- | pts/test-resources/mafft/downloads.xml | 12 | ||||
| -rw-r--r-- | pts/test-resources/mafft/install.sh | 32 | ||||
| -rw-r--r-- | pts/test-resources/mafft/parse-results.php | 4 |
3 files changed, 48 insertions, 0 deletions
diff --git a/pts/test-resources/mafft/downloads.xml b/pts/test-resources/mafft/downloads.xml new file mode 100644 index 0000000..e348b1b --- /dev/null +++ b/pts/test-resources/mafft/downloads.xml @@ -0,0 +1,12 @@ +<PhoronixTestSuite> + <Downloads> + <Package> + <URL>http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.240-src.tgz</URL> + <MD5>e603c1dbef35913d46286d5b98b601a3</MD5> + </Package> + <Package> + <URL>http://fire-salamander.co.uk/pts-tests/pyruvate_decarboxylase.fasta.bz2</URL> + <MD5>22cd5efc1199a72fbb3f19960f56010d</MD5> + </Package> + </Downloads> +</PhoronixTestSuite> diff --git a/pts/test-resources/mafft/install.sh b/pts/test-resources/mafft/install.sh new file mode 100644 index 0000000..79ecb4a --- /dev/null +++ b/pts/test-resources/mafft/install.sh @@ -0,0 +1,32 @@ +#!/bin/sh + +THIS_DIR=$(pwd) + +mkdir $THIS_DIR/mafft_ + +tar -xvf mafft-6.240-src.tgz +cd mafft-6.240/src/ + +make clean +sed -i -e "s|PREFIX = /usr/local/lib/mafft|PREFIX = $THIS_DIR/mafft_|g" Makefile + +make -j $NUM_CPU_JOBS +make install +cd ../.. +cp -f mafft-6.240/scripts/mafft mafft_/ + +bunzip2 pyruvate_decarboxylase.fasta.bz2 -c > mafft_/pyruvate_decarboxylase.fasta + +cat>align<<EOT +#!/bin/sh +cd mafft_/ +./mafft --localpair --maxiterate 10000 pyruvate_decarboxylase.fasta 1>/dev/null 2>&1 +cd .. +EOT +chmod +x align + +cat>mafft<<EOT +#!/bin/sh +/usr/bin/time -f "Sequence Alignment Time: %e Seconds" ./align 2>&1 | grep Seconds +EOT +chmod +x mafft
\ No newline at end of file diff --git a/pts/test-resources/mafft/parse-results.php b/pts/test-resources/mafft/parse-results.php new file mode 100644 index 0000000..84f126b --- /dev/null +++ b/pts/test-resources/mafft/parse-results.php @@ -0,0 +1,4 @@ +<?php +$BENCHMARK_RESULTS = substr($argv[1], strrpos($argv[1], "Sequence Alignment Time:") + 25); +echo trim(substr($BENCHMARK_RESULTS, 0, strpos($BENCHMARK_RESULTS, "Seconds"))); +?> |