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  • mafft profile update

    Updates mafft to 6.706

    Code:
    diff --git a/pts/test-profiles/mafft.xml b/pts/test-profiles/mafft.xml
    index 6789dc8..d0d0d8c 100644
    --- a/pts/test-profiles/mafft.xml
    +++ b/pts/test-profiles/mafft.xml
    @@ -2,7 +2,7 @@
     <?xml-stylesheet type="text/xsl" href="xsl/pts-test-profile-viewer.xsl" ?>
     <PhoronixTestSuite>
         <TestProfile>
    -        <Version>1.1.0</Version>
    +        <Version>1.1.1</Version>
             <TestType>Processor</TestType>
             <SoftwareType>Scientific</SoftwareType>
             <License>FREE</License>
    @@ -15,7 +15,7 @@
         </TestProfile>
         <TestInformation>
             <Title>Timed MAFFT Alignment</Title>
    -        <Version>6.240</Version>
    +        <Version>6.706</Version>
             <SubTitle>Multiple Sequence Alignment</SubTitle>
             <ResultScale>Seconds</ResultScale>
             <TimesToRun>3</TimesToRun>
    diff --git a/pts/test-resources/mafft/downloads.xml b/pts/test-resources/mafft/downloads.xml
    index 7d1b812..75f3338 100644
    --- a/pts/test-resources/mafft/downloads.xml
    +++ b/pts/test-resources/mafft/downloads.xml
    @@ -1,9 +1,9 @@
     <PhoronixTestSuite>
         <Downloads>
             <Package>
    -            <URL>http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.240-src.tgz, http://gd.tuwien.ac.at/opsys/linux/gentoo/distfiles/mafft-6.240-src.tgz, ftp://ftp.swin.edu.au/gentoo/distfiles/mafft-6.240-src.tgz, ftp://ftp.uni-kassel.de/Mirrors/ftp.fhh.opensource-mirror.de/gentoo/distfiles/mafft-6.240-src.tgz</URL>
    -            <MD5>e603c1dbef35913d46286d5b98b601a3</MD5>
    -            <FileSize>657197</FileSize>
    +            <URL>http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.706-without-extensions-src.tgz</URL>
    +            <MD5>209064fe817c84e1228272244d78ca21</MD5>
    +            <FileSize>452729</FileSize>
             </Package>
             <Package>
                 <URL>http://fire-salamander.co.uk/pts-tests/pyruvate_decarboxylase.fasta.bz2</URL>
    diff --git a/pts/test-resources/mafft/install.sh b/pts/test-resources/mafft/install.sh
    index 0012a20..d88bdbe 100755
    --- a/pts/test-resources/mafft/install.sh
    +++ b/pts/test-resources/mafft/install.sh
    @@ -1,26 +1,24 @@
     #!/bin/sh
    
    -mkdir -p $HOME/mafft_/install
    -tar -xvf mafft-6.240-src.tgz
    -cd mafft-6.240/src/
    +mkdir $HOME/mafft_
    +tar -xvf mafft-6.706-without-extensions-src.tgz
    +cd mafft-6.706-without-extensions/core/
    
     make clean
    
    -sed -i -e "s|PREFIX = /usr/local/lib/mafft|PREFIX = $HOME/mafft_/install|g" Makefile
    +sed -i -e "s|PREFIX = /usr/local|PREFIX = $HOME/mafft_|g" Makefile
    
     make -j $NUM_CPU_JOBS
     echo $? > ~/install-exit-status
     make install
     cd ~/
    -cp -f mafft-6.240/scripts/mafft mafft_/install/
    -rm -rf mafft-6.240/
    -rm -rf bin/
    +cp -f mafft-6.706-without-extensions/scripts/mafft mafft_/
    
    -bunzip2 pyruvate_decarboxylase.fasta.bz2 -c > mafft_/install/pyruvate_decarboxylase.fasta
    +bunzip2 pyruvate_decarboxylase.fasta.bz2 -c > mafft_/pyruvate_decarboxylase.fasta
    
     cat>align<<EOT
     #!/bin/sh
    -cd mafft_/install/
    +cd mafft_/
     ./mafft --localpair --maxiterate 10000 pyruvate_decarboxylase.fasta 1>/dev/null 2>&1
     cd ..
     EOT
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