From: pvtroshin <pvtroshin@e3abac25-378b-4346-85de-24260fe3988d>
Date: Mon, 27 Jun 2011 14:55:27 +0000 (+0000)
Subject: Dundee compiled x86 binaries a few fixes for compile script
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=777a62395761a88d4f8510395e4552a7bf4ec288;p=jabaws.git

Dundee compiled x86 binaries a few fixes for compile script

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4338 e3abac25-378b-4346-85de-24260fe3988d
---

diff --git a/binaries/src/compilebin.sh b/binaries/src/compilebin.sh
index c530cca..10113cb 100644
--- a/binaries/src/compilebin.sh
+++ b/binaries/src/compilebin.sh
@@ -26,9 +26,8 @@ cd ..
 
 echo "Compiling Muscle..."
 cd muscle
-rm -f *.o
+rm -f *.o muscle
 make
-chmod +x muscle
 cd ..
 
 echo "Compiling Probcons..."
@@ -54,6 +53,7 @@ chmod +x disembl DisEMBL.py
 
 echo "Compiling DisEMBL dependancy Tisean... "
 cd Tisean_3.0.1
+chmod +x ./configure
 ./configure
 make
 cp source_c/sav_gol ../
@@ -62,12 +62,11 @@ echo "DONE"
 chmod +x sav_gol
 cd ..
 
-# TODO copy sav_gol other from disembl
-echo "Compiling GlobPlot..."
+echo "Setting up GlobPlot ..."
+cp disembl/sav_gol globplot/sav_gol
 cd globplot
-echo "DONE"
-# TODO deal with the links
 chmod +x GlobPlot.py
+echo "DONE"
 cd ..
 
 echo "Compiling IUPred..."
diff --git a/build.xml b/build.xml
index 3d55caa..27a2cf9 100644
--- a/build.xml
+++ b/build.xml
@@ -388,6 +388,7 @@
 				<include name="lib/*"/>
 			</zipfileset>
 			<zipfileset dir="${basedir}/ExecutionStatistic" prefix="ExecutionStatistic" />
+			<zipfileset dir="${basedir}/statpages" prefix="statpages" />
 			<zipfileset dir="${basedir}/jobsout" prefix="jobsout" excludes="**/*"/>
 			<zipfileset dir="conf" prefix="conf" >
 				<exclude name="**/temp/**"/>
@@ -398,8 +399,6 @@
 			<zipfileset dir="." includes="${full-jaba-client}" fullpath="WEB-INF/lib/jaba-client.jar"/>
 			<!-- Put a copy of log4j configuration file where it can be used  -->
 			<zipfileset dir="conf" includes="log4j.properties" prefix="WEB-INF/classes"/>
-			<!-- This is runtime dependency must be supplied by the container -->
-			<!-- zipfileset dir="${web.lib.path}" includes="servlet-api.jar" prefix="WEB-INF/lib" / -->
 		</zip>
 	</target>
 
diff --git a/website/archive/binaries/linux_x64_dundee/clustalw2 b/website/archive/binaries/linux_x64_dundee/clustalw2
new file mode 100644
index 0000000..47f1fb3
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/clustalw2 differ
diff --git a/website/archive/binaries/linux_x64_dundee/disembl b/website/archive/binaries/linux_x64_dundee/disembl
new file mode 100644
index 0000000..1234099
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/disembl differ
diff --git a/website/archive/binaries/linux_x64_dundee/fasta34.zip b/website/archive/binaries/linux_x64_dundee/fasta34.zip
new file mode 100644
index 0000000..cd14f09
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/fasta34.zip differ
diff --git a/website/archive/binaries/linux_x64_dundee/iupred b/website/archive/binaries/linux_x64_dundee/iupred
new file mode 100644
index 0000000..ca86ab3
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/iupred differ
diff --git a/website/archive/binaries/linux_x64_dundee/mafft.zip b/website/archive/binaries/linux_x64_dundee/mafft.zip
new file mode 100644
index 0000000..dcb8491
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/mafft.zip differ
diff --git a/website/archive/binaries/linux_x64_dundee/muscle b/website/archive/binaries/linux_x64_dundee/muscle
new file mode 100644
index 0000000..6ce2910
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/muscle differ
diff --git a/website/archive/binaries/linux_x64_dundee/probcons b/website/archive/binaries/linux_x64_dundee/probcons
new file mode 100644
index 0000000..8f7ce92
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/probcons differ
diff --git a/website/archive/binaries/linux_x64_dundee/sav_gol b/website/archive/binaries/linux_x64_dundee/sav_gol
new file mode 100644
index 0000000..fcaf35e
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/sav_gol differ
diff --git a/website/archive/binaries/linux_x64_dundee/t_coffee b/website/archive/binaries/linux_x64_dundee/t_coffee
new file mode 100644
index 0000000..581db9b
Binary files /dev/null and b/website/archive/binaries/linux_x64_dundee/t_coffee differ