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fix Windows, Canu, graphmap, zero length arguments
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,5 @@ | ||
| [server] | ||
| location=https://services.bio.ifi.lmu.de:1047/biogui/ | ||
| location=https://services.bio.ifi.lmu.de:1047/biogui/ | ||
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| [bash] | ||
| location=C:\\WINDOWS\\Sysnative\\wsl.exe |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,175 @@ | ||
| #! Install canu (github) | ||
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| echo "This tool will not compile in folders where the absolute path contains spaces!" | ||
| echo "Dependencies: None" | ||
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| if [ ! "$2" = "" ]; then | ||
| echo "Installing dependencies" | ||
| #echo $2 | sudo -S apt-get update | ||
| #echo $2 | sudo -S apt-get -y install csh | ||
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| else | ||
| echo "No sudo password, not installing dependencies" | ||
| fi | ||
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| ## set all variables | ||
| PROG=canu | ||
| PROGDIR=$1 | ||
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| if [ -z "${PROGDIR}" ]; then | ||
| PROGDIR=~/bioGUI/progs/ | ||
| fi | ||
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| PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g') | ||
| APPBINARYDIR=${PROGDIRESC}/${PROG}/Linux-amd64/bin/ | ||
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| if [ -d "$PROGDIR/$PROG" ]; then | ||
| echo "Removing Folder $PROGDIR/$PROG" | ||
| #rm -rf $PROGDIR/$PROG | ||
| fi | ||
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| ## create progdir | ||
| mkdir -p "$PROGDIR/$PROG" | ||
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| echo "Fetching $PROG - this may take a while." | ||
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| #download and unzip | ||
| #git clone https://github.com/marbl/canu.git $PROGDIR/$PROG | ||
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| cd "$PROGDIR/$PROG/src" | ||
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| make -j 2 | ||
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| if [ $# -gt 2 ]; then | ||
| if [ "$3" = "1" ]; then | ||
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| if ! grep -q "$APPBINARYDIR" ~/.bashrc; then | ||
| echo "export PATH=\"$APPBINARYDIR:\$PATH\" " >> ~/.bashrc; | ||
| fi | ||
| fi | ||
| fi | ||
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| if [ $# -eq 5 ]; then | ||
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| IP=$4 | ||
| PORT=$5 | ||
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| echo "Sending Template to $IP at $PORT" | ||
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| nc -q 0 $IP $PORT <<EOF | ||
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| <!--<?xml version="1.0" encoding="UTF-8")>--> | ||
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| <template description="canu ($PROG)" title="canu"> | ||
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| <window width="500" height="1000" title="canu"> | ||
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| <vgroup> | ||
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| <group title="Assembly Options"> | ||
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| <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> | ||
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| <label>Assembly Output</label> <filedialog id="canu_tmp_folder" output="true" foler="true">Select Assembly Folder</filedialog> | ||
| <label>Assembly Prefix</label><input id="canu_assembly_prefix"></input> | ||
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| <label>Expected Genome Size</label><input id="canu_genome_size" type="float"></input> | ||
| <label>Read Error Rate</label><input id="canu_error_rate" min="0.0" max="1.0" type="float"></input> | ||
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| <label>Additional Options</label><input id="canu_options"></input> | ||
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| <action program="canu" hint="click here to run program">Run canu</action> | ||
| </group> | ||
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| <group title="General Options"> | ||
| <label>Run in WSL on Windows?</label><checkbox id="WSLsel" value="true" selectonwindows="true">Run in WSL?</checkbox> | ||
| </group> | ||
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| <streambox id="output1"> | ||
| <stream id="outputstream1">OS1</stream> | ||
| <stream id="outputstream2">OS2</stream> | ||
| </streambox> | ||
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| </vgroup> | ||
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| </window> | ||
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| <execution> | ||
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| <const id="bindir">${APPBINARYDIR}/</const> | ||
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| <relocate id="canu_pacbio_rel" from="\${canu_pacbio}" wsl="\${WSLsel}"/> | ||
| <relocate id="canu_oxford_rel" from="\${canu_oxford}" wsl="\${WSLsel}"/> | ||
| <relocate id="canu_tmp_folder_rel" from="\${canu_tmp_folder}" wsl="\${WSLsel}"/> | ||
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| <add id="args"> | ||
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| <value from="\${canu_options}"/> | ||
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| <if comp="IS_SET" value1="\${canu_assembly_prefix}"> | ||
| <const>-p</const> | ||
| <value from="\${canu_assembly_prefix}"/> | ||
| </if> | ||
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| <if comp="IS_SET" value1="\${canu_tmp_folder_rel}"> | ||
| <const>-d</const> | ||
| <value from="\${canu_tmp_folder_rel}"/> | ||
| </if> | ||
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| <if comp="IS_SET" value1="\${canu_error_rate}"> | ||
| <const>errorRate=</const> | ||
| <value from="\${canu_error_rate}"/> | ||
| </if> | ||
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| <if comp="IS_SET" value1="\${canu_genome_size}"> | ||
| <const>genomeSize=</const> | ||
| <value from="\${canu_genome_size}"/> | ||
| <const>m</const> | ||
| </if> | ||
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| <if comp="IS_SET" value1="\${canu_pacbio_rel}"> | ||
| <const>-pacbio-raw</const> | ||
| <value from="\${canu_pacbio_rel}"/> | ||
| </if> | ||
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| <if comp="IS_SET" value1="\${canu_oxford}"> | ||
| <const>-oxford-raw</const> | ||
| <value from="\${canu_oxford}"/> | ||
| </if> | ||
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| </add> | ||
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| <execute program="canu" param="\${args}" location="\${bindir}" exec="canu" wsl="WSLsel"> | ||
| <output type="COUT" color="green" to="outputstream1" /> | ||
| <output type="CERR" color="red" to="outputstream2" /> | ||
| </execute> | ||
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| </execution> | ||
| </template> | ||
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| EOF | ||
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| fi |
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