fix templates

mjoppich · Mar 13, 2019 · 29df8c8 · 29df8c8
1 parent 53a548e
commit 29df8c8
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Showing 4 changed files with 497 additions and 17 deletions.
diff --git a/install_templates/install_canu.igui b/install_templates/install_canu.igui
@@ -45,7 +45,7 @@ fi
 
 if [ -d "$PROGDIR/$PROG" ]; then
     echo "Removing Folder $PROGDIR/$PROG"
-    #rm -rf $PROGDIR/$PROG
+    rm -rf $PROGDIR/$PROG
 fi
 
 ## create progdir

diff --git a/install_templates/install_featurecounts.igui b/install_templates/install_featurecounts.igui
@@ -0,0 +1,192 @@
+#! Install featureCounts (github)
+
+
+
+if [ ! "$2" = "" ]; then
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "Installing brew gcc"
+        brew install gcc
+
+        alias gcc='gcc-8'
+        alias g++='g++-8'
+
+    else
+
+        echo "No dependencies"
+
+    fi
+
+else
+   echo "No sudo password, not installing dependencies"
+fi
+
+
+## set all variables
+PROG=featureCounts
+PROGDIR=$1
+
+
+
+if [ -z "${PROGDIR}" ]; then
+   PROGDIR=~/bioGUI/progs/
+fi
+
+
+PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
+APPBINARYDIR=${PROGDIR}/${PROG}/bin/
+
+if [ -d "$PROGDIR/$PROG" ]; then
+    echo "Removing Folder $PROGDIR/$PROG"
+    rm -rf "$PROGDIR/$PROG"
+fi
+
+## create progdir
+mkdir -p "$PROGDIR/$PROG"
+
+#download and unzip
+#wget https://sourceforge.net/projects/subread/files/subread-1.6.3/subread-1.6.3-source.tar.gz/download -O subread.tar.gz
+
+tar xfz subread.tar.gz -C "$PROGDIR/$PROG/"
+
+cd "$PROGDIR"/$PROG/
+
+mv */* .
+
+cd "$PROGDIR/$PROG/src"
+
+if [ "$(uname)" == "Darwin" ]; then
+	make -f Makefile.MacOS
+else
+	make -f Makefile.Linux
+fi
+
+
+if [ $# -gt 2 ]; then
+   if [ "$3" = "1" ]; then
+
+      if ! grep -q "$PROGDIRESC/$PROG/bin/" ~/.bashrc; then
+         echo "export PATH=\"$PROGDIRESC/$PROG/bin/:\$PATH\" " >> ~/.bashrc;
+      fi
+   fi
+fi
+
+
+
+if [ $# -eq 5 ]; then
+
+IP=$4
+PORT=$5
+
+echo "Sending Template to $IP at $PORT"
+
+
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
+
+<template description="featureCounts (subread)" title="featureCounts">
+
+<window width="500" height="1000" title="featureCounts">
+
+  <vgroup>
+
+
+    <group title="Alignment Options">
+
+
+        <label>Input Annotation</label> <filedialog id="featureCounts_annotation" output="false">Select Input Annotation (GTF/GFF)</filedialog>
+        <label>Output File</label> <filedialog id="featureCounts_output" output="true">Select Output Count-File</filedialog>
+
+        <label>Input Files</label> <filedialog id="featureCounts_input" output="false" multiples="true" multiples_delim=";">Select Input Files (sam or bam)</filedialog>
+
+        <label>Program Mode (not all options used in all modes)</label>
+        <combobox id="featureCounts_annot_format" selected="GTF">
+            <comboitem value="GTF">GTF or compatible GFF</comboitem>
+            <comboitem value="SAF">SAF format</comboitem>
+        </combobox>
+
+
+        <label>Feature type</label><input id="featureCounts_feature_type">exon</input>
+
+
+        <label>Additional Options</label><input id="featureCounts_options"></input>
+
+
+        <action program="featureCounts" hint="click here to run program">Run featureCounts</action>  
+    </group>
+
+
+    <group title="General Options">
+       <label>Run in WSL on Windows?</label><checkbox id="WSLsel" value="true" selectonwindows="true">Run in WSL?</checkbox>
+       <label>Threads</label><input id="featureCounts_threads" type="int">1</input>
+    </group>
+
+    <streambox id="output1">
+      <stream id="outputstream1">OS1</stream>
+      <stream id="outputstream2">OS2</stream>
+    </streambox>
+
+
+  </vgroup>
+
+</window>
+
+
+
+<execution>
+
+    <const id="bindir">${APPBINARYDIR}/</const>
+
+
+    <relocate id="featureCounts_annotation_rel" from="\${featureCounts_annotation}" wsl="\${WSLsel}"/>
+    <relocate id="featureCounts_output_rel" from="\${featureCounts_output}" wsl="\${WSLsel}"/>
+    <relocate id="featureCounts_input_rel" from="\${featureCounts_input}" sep=" " insep=";" wsl="\${WSLsel}"/>
+
+    <add id="args" sep=" ">
+        <if comp="IS_SET" value1="\${featureCounts_feature_type}" sep=" ">
+            <const>-t</const>
+            <value from="\${featureCounts_feature_type}"/>
+        </if>        
+
+        <const>-F</const>
+        <value from="\${featureCounts_annot_format}"/>
+
+        <value from="\${featureCounts_options}"/>
+
+        <if comp="IS_SET" value1="\${featureCounts_annotation_rel}" sep=" ">
+            <const>-a</const>
+            <value from="\${featureCounts_annotation_rel}"/>
+        </if>
+
+        <if comp="IS_SET" value1="\${featureCounts_output_rel}" sep=" ">
+            <const>-o</const>
+            <value from="\${featureCounts_output_rel}"/>
+        </if>
+
+        <value from="\${featureCounts_input_rel}"/>     
+
+    </add>
+
+    <execute program="featureCounts" param="\${args}" location="\${bindir}" exec="featureCounts" wsl="WSLsel">
+        <output type="COUT" color="green" to="outputstream1" />
+        <output type="CERR" color="red" to="outputstream2" />
+    </execute>
+
+
+
+</execution>
+</template>
+
+
+EOF
+
+fi
diff --git a/install_templates/install_mm_asm_racon.igui b/install_templates/install_mm_asm_racon.igui
@@ -38,8 +38,6 @@ fi
 ## create progdir
 mkdir -p "$PROGDIR/$PROG"
 
-wget -O "$PROGDIR/$PROG/assemble.sh" https://gist.githubusercontent.com/mjoppich/18b7a07074b59bd34056df6fe7b08d05/raw/505494921348d6dc952148ac6c6d86568c49fe79/mmr_assemble.sh
-
 
 cd "$PROGDIR/$PROG"
 git clone https://github.com/lh3/minimap2 minimap2
@@ -105,6 +103,52 @@ if [ $# -gt 2 ]; then
 	fi
 fi
 
+APPBINARYDIR=${PROGDIRESC}/${PROG}/
+
+cat <<EOS > $APPBINARYDIR/assemble.sh
+#!/usr/bin/sh
+INREADS=\$1
+ASMFOLDER=\$2
+ASMPREFIX=\$3
+
+# path to used executables
+MINIMAP2BIN="\${4-minimap2}"
+MINIASMBIN="\${5-miniasm}"
+GRAPHMAPBIN="\${6-graphmap}"
+RACONBIN="\${7-racon}"
+
+THREADS="\${8-4}"
+
+#echo \$INREADS
+#echo \$ASMFOLDER
+#echo \$ASMPREFIX
+#echo \$MINIMAP2BIN
+#echo \$MINIASMBIN
+#echo \$GRAPHMAPBIN
+#echo \$RACONBIN
+
+# first we must overlap all reads with each other
+\$MINIMAP2BIN -x ava-ont -t\$THREADS \$INREADS $INREADS > \$ASMFOLDER/\$ASMPREFIX.paf
+
+# then miniasm can create alignment
+\$MINIASMBIN -f \$INREADS \$ASMFOLDER/\$ASMPREFIX.paf > \$ASMFOLDER/\$ASMPREFIX.gfa
+
+# extract unitigs from miniasm
+awk '\$1 ~/S/ {print ">"\$2"\n"\$3}' \$ASMFOLDER/\$ASMPREFIX.gfa > \$ASMFOLDER/\$ASMPREFIX.unitigs.fasta
+
+# align reads with unitigs
+\$MINIMAP2BIN \$ASMFOLDER/\$ASMPREFIX.unitigs.fasta \$INREADS > \$ASMFOLDER/\$ASMPREFIX.unitigs.paf
+
+# find contigs from unitigs
+\$RACONBIN \$INREADS \$ASMFOLDER/\$ASMPREFIX.unitigs.paf \$ASMFOLDER/\$ASMPREFIX.unitigs.fasta > \$ASMFOLDER/\$ASMPREFIX.contigs.fasta
+
+\$MINIMAP2BIN -x map-ont -a -t\$THREADS \$ASMFOLDER/\$ASMPREFIX.contigs.fasta \$INREADS > \$ASMFOLDER/\$ASMPREFIX.reads.mm2.sam
+\$GRAPHMAPBIN align -r \$ASMFOLDER/\$ASMPREFIX.contigs.fasta -d \$INREADS -o \$ASMFOLDER/\$ASMPREFIX.reads.gm.sam
+
+
+EOS
+
+
 
 
 if [ $# -eq 5 ]; then
@@ -125,9 +169,7 @@ fi
 
 $NCCMD <<EOF
 
-<!--<?xml version="1.0" encoding="UTF-8")>-->
-
-<template description="minimap/miniasm/racon assembly pipeline" title="graphmap">
+<template description="minimap/miniasm/racon assembly pipeline" title="MiMiRa">
 
 <window width="500" height="1000" title="MiMiRa">
 
@@ -137,8 +179,8 @@ $NCCMD <<EOF
     <group title="Assembly Options">
 
 
-        <label>Input Reads</label> <filedialog id="assembly_reads" output="false">Select Input Reference (fq)</filedialog>
-        <label>Input Folder</label> <filedialog id="assembly_dir" output="false" folder="true">Select Assembly Folder</filedialog>
+        <label>Input Reads (Fastq)</label> <filedialog id="assembly_reads" output="false">Select Input Reference (fq)</filedialog>
+        <label>Assembly/Output Folder</label> <filedialog id="assembly_dir" output="false" folder="true">Select Assembly Folder</filedialog>
 
         <label>Assembly Prefix</label><input id="assembly_prefix"></input>
 
@@ -164,30 +206,42 @@ $NCCMD <<EOF
 
 
 <execution>
-
     <const id="bindir">${APPBINARYDIR}/</const>
 
 
     <relocate id="assembly_reads_rel" from="\${assembly_reads}" wsl="\${WSLsel}"/>
     <relocate id="assembly_dir_rel" from="\${assembly_dir}" wsl="\${WSLsel}"/>
-
     <add id="args">
-
-        <value from="\${assembly_reads}"/>
-        <value from="\${assembly_dir}"/>
-        <value from="\${assembly_prefix}"/>
+	<const>${APPBINARYDIR}/assemble.sh</const>
+    <value from="\${assembly_reads_rel}"/>
+    <value from="\${assembly_dir_rel}"/>
+    <value from="\${assembly_prefix}"/>
+	<add sep="/">
+		<value from="\${bindir}"/>
+		<const>minimap2/minimap2</const>
+	</add>
+	<add sep="/">
+		<value from="\${bindir}"/>
+		<const>miniasm/miniasm</const>
+	</add>
+	<add sep="/">
+		<value from="\${bindir}"/>
+		<const>graphmap/bin/Linux-x64/graphmap</const>
+	</add>
+	<add sep="/">
+		<value from="\${bindir}"/>
+		<const>racon/build/bin/racon</const>
+	</add>
 
         <if comp="IS_SET" value1="\${assembly_threads}">
             <value from="\${assembly_threads}"/>
         </if>             
-
     </add>
 
-    <execute program="graphmap" param="\${args}" location="\${bindir}" exec="graphmap" wsl="WSLsel">
+    <execute program="assembly" param="bash \${args}" location="/usr/bin/" exec="env" wsl="WSLsel">
         <output type="COUT" color="green" to="outputstream1" />
         <output type="CERR" color="red" to="outputstream2" />
     </execute>
-
 
 
 </execution>