add new templates, fix bip

mjoppich · Jul 25, 2018 · 440b750 · 440b750
1 parent 5561a79
commit 440b750
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Showing 3 changed files with 32 additions and 31 deletions.
diff --git a/build-in-place.sh b/build-in-place.sh
@@ -5,17 +5,17 @@ apt-get -y install libglu1-mesa-dev
 
 #apt-get -y install qtbase5-dev libqt5xmlpatterns5-dev
 
-wget http://download.qt.io/official_releases/qt/5.7/5.7.0/qt-opensource-linux-x64-5.7.0.run
+wget http://download.qt.io/official_releases/qt/5.11/5.11.1/qt-opensource-linux-x64-5.11.1.run
 
-chmod u+x qt-opensource-linux-x64-5.7.0.run
-./qt-opensource-linux-x64-5.7.0.run --verbose -platform minimal --script ./silent_qt_install.qs
+chmod u+x qt-opensource-linux-x64-5.11.1.run
+./qt-opensource-linux-x64-5.11.1.run --verbose -platform minimal --script ./silent_qt_install.qs
 
-export PATH=/usr/local/qt/5.7/gcc_64/bin/:$PATH
+export PATH=/usr/local/qt/5.11.1/gcc_64/bin/:$PATH
 
 mkdir build
 
 cd build
 
 cmake ..
 
-make
+make
diff --git a/install_templates/install_canu.igui b/install_templates/install_canu.igui
@@ -5,8 +5,8 @@ echo "Dependencies: None"
 
 if [ ! "$2" = "" ]; then
 	echo "Installing dependencies"
-  #echo $2 | sudo -S apt-get update
-  #echo $2 | sudo -S apt-get -y install csh
+  echo $2 | sudo -S apt-get update
+  echo $2 | sudo -S apt-get -y install gnuplot
 
 else
 	echo "No sudo password, not installing dependencies"
@@ -39,7 +39,7 @@ mkdir -p "$PROGDIR/$PROG"
 echo "Fetching $PROG - this may take a while."
 
 #download and unzip
-#git clone https://github.com/marbl/canu.git $PROGDIR/$PROG
+git clone https://github.com/marbl/canu.git $PROGDIR/$PROG
 
 cd "$PROGDIR/$PROG/src"
 
@@ -81,10 +81,10 @@ nc -q 0 $IP $PORT <<EOF
 
 
 
-        <label>Input Reads (PacBio)</label> <filedialog id="canu_pacbio" output="false">Select Input Reads (PacBio)</filedialog>
-        <label>Input Reads (Oxford)</label> <filedialog id="canu_oxford" output="false">Select Input Reads (Oxford)</filedialog>
+        <label>Input Reads (PacBio)</label> <filedialog id="canu_pacbio" output="false" multiples="true" multiples_delim=" ">Select Input Reads (PacBio)</filedialog>
+        <label>Input Reads (Oxford)</label> <filedialog id="canu_oxford" output="false" multiples="true" multiples_delim=" ">Select Input Reads (Oxford)</filedialog>
 
-        <label>Assembly Output</label> <filedialog id="canu_tmp_folder" output="true" foler="true">Select Assembly Folder</filedialog>
+        <label>Assembly Output</label> <filedialog id="canu_tmp_folder" output="true" folder="true">Select Assembly Folder</filedialog>
         <label>Assembly Prefix</label><input id="canu_assembly_prefix"></input>
 
         <label>Expected Genome Size</label><input id="canu_genome_size" type="float"></input>
@@ -118,43 +118,44 @@ nc -q 0 $IP $PORT <<EOF
     <const id="bindir">${APPBINARYDIR}/</const>
 
 
-    <relocate id="canu_pacbio_rel" from="\${canu_pacbio}" wsl="\${WSLsel}"/>
-    <relocate id="canu_oxford_rel" from="\${canu_oxford}" wsl="\${WSLsel}"/>
+    <relocate id="canu_pacbio_rel" from="\${canu_pacbio}" sep=" " wsl="\${WSLsel}"/>
+    <relocate id="canu_oxford_rel" from="\${canu_oxford}" sep=" " wsl="\${WSLsel}"/>
     <relocate id="canu_tmp_folder_rel" from="\${canu_tmp_folder}" wsl="\${WSLsel}"/>
 
     <add id="args" sep=" ">
-
-            <value from="\${canu_options}"/>
+
+        <if comp="IS_SET" value1="\${canu_tmp_folder_rel}" sep=" ">
+            <const>-d</const>
+            <value from="\${canu_tmp_folder_rel}"/>
+        </if>   
 
         <if comp="IS_SET" value1="\${canu_assembly_prefix}" sep=" ">
             <const>-p</const>
             <value from="\${canu_assembly_prefix}"/>
-        </if>      
-
-        <if comp="IS_SET" value1="\${canu_tmp_folder_rel}" sep=" ">
-            <const>-d</const>
-            <value from="\${canu_tmp_folder_rel}"/>
-        </if>      
+        </if>         
 
-        <if comp="IS_SET" value1="\${canu_error_rate}" sep=" ">
+        <if comp="IS_SET" value1="\${canu_error_rate}">
             <const>errorRate=</const>
             <value from="\${canu_error_rate}"/>
         </if>
 
-        <if comp="IS_SET" value1="\${canu_genome_size}" sep=" ">
+        <if comp="IS_SET" value1="\${canu_genome_size}">
             <const>genomeSize=</const>
             <value from="\${canu_genome_size}"/>
             <const>m</const>
-        </if>                
+        </if>              
+
+        <const>useGrid=false</const>
+        <value from="\${canu_options}"/>  
 
         <if comp="IS_SET" value1="\${canu_pacbio_rel}" sep=" ">
             <const>-pacbio-raw</const>
             <value from="\${canu_pacbio_rel}"/>
         </if>
 
         <if comp="IS_SET" value1="\${canu_oxford}" sep=" ">
-            <const>-oxford-raw</const>
-            <value from="\${canu_oxford}"/>
+            <const>-nanopore-raw</const>
+            <value from="\${canu_oxford_rel}"/>
         </if>         
 
     </add>

diff --git a/install_templates/install_graphmap.igui b/install_templates/install_graphmap.igui
@@ -135,27 +135,27 @@ nc -q 0 $IP $PORT <<EOF
     <relocate id="graphmap_align_gtf_rel" from="\${graphmap_align_gtf}" wsl="\${WSLsel}"/>
     <relocate id="graphmap_align_output_rel" from="\${graphmap_align_output}" wsl="\${WSLsel}"/>
 
-    <add id="args" sep=" ">
+    <add id="args">
         <value from="\${graphmap_mode}"/>
-        <if comp="IS_SET" value1="\${graphmap_align_reference_rel}" sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_reference_rel}">
             <const>-r</const>
             <value from="\${graphmap_align_reference_rel}"/>
         </if>
 
-        <if comp="IS_SET" value1="\${graphmap_align_gtf}" sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_gtf}">
             <const>--gtf</const>
             <value from="\${graphmap_align_gtf_rel}"/>
         </if>
 
-        <if comp="IS_SET" value1="\${graphmap_align_reads_rel}" sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_reads_rel}">
             <const>-d</const>
             <value from="\${graphmap_align_reads_rel}"/>
         </if>        
 
 
         <value from="\${graphmap_options}"/>
 
-        <if comp="IS_SET" value1="\${graphmap_align_output_rel}" sep=" ">
+        <if comp="IS_SET" value1="\${graphmap_align_output_rel}">
             <const>-o</const>
             <value from="\${graphmap_align_output_rel}"/>
         </if>