mafft profile update

[uncle_fungus]

Updates mafft to 6.706

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