wsl mounter

README.md

@@ -49,6 +49,8 @@ Microsoft Windows 10 (build 17763, Oct. 2018 update) with Windows Subsystem for
 This page describes [how to setup WSL](http://biogui.readthedocs.io/en/latest/build_wsl.html).
 **Place bioGUI into a location which does not contain spaces in its name, e.g not `C:\Program Files\bioGUI` ! `C:\bioGUI` or `D:\bioGUI\` is fine though!**
 
+If you want to access external drives (USB stick, network drive), you first need to *mount* this drive into WSL.
+The WSL *Mount Drive* install module will install a script which can do this for you. Make sure to save the template and use the *Mount Drive (WSL)* template to make the drive available to WSL. You need to enter the drive-letter you want to mount (e.g. F), and your *sudo* password.
 
 ### Mac OS
 

doc/user_guide.rst

@@ -31,6 +31,8 @@ Follow the instructions to setup WSL: :ref:`build_wsl_intro`.
 
 **You can put bioGUI for instance into the locations** ``C:\bioGUI\`` **or** ``D:\bioGUI\`` **!**
 
+If you want to access external drives (USB stick, network drive), you first need to *mount* this drive into WSL.
+The WSL **Mount Drive** install module will install a script which can do this for you. Make sure to save the template and use the *Mount Drive (WSL)* template to make the drive available to WSL. You need to enter the drive-letter you want to mount (e.g. F), and your *sudo* password.
 
 Linux
 -----

install_templates/install_phanotate.igui

@@ -0,0 +1,158 @@
+#! Install PHANOTATE (github)
+
+if [ "$(uname)" == "Darwin" ]; then
+	source ~/.bash_profile
+else
+  echo ""
+fi
+
+echo "Dependencies: r-base"
+if [ ! "$2" = "" ]; then
+
+    if [ "$(uname)" == "Darwin" ]; then
+
+        echo "Installing R and setting PATH for R libraries"
+        brew install gcc@8
+
+    else
+        echo "No dependencies"
+    fi
+
+
+else
+	echo "No sudo password, not installing dependencies"
+fi
+
+## set all variables
+PROG=PHANOTATE
+PROGNICE=PHANOTATE
+PROGDIR=$1
+
+
+if [ -z "${PROGDIR}" ]; then
+	PROGDIR=~/bioGUI/progs/
+fi
+
+PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
+APPBINARYDIR="${PROGDIR}/${PROG}/"
+
+rm -rf "$PROGDIR/$PROG"
+
+## create progdir
+
+git clone --recursive git@github.com:deprekate/PHANOTATE.git $PROG
+
+cd "$PROGDIR/$PROG"
+
+if [ "$(uname)" == "Darwin" ]; then
+	make CC=gcc-8
+else
+	make
+fi
+
+
+if [ $# -gt 2 ]; then
+
+	if [ "$3" = "1" ]; then
+
+		if ! grep -q "$PROGDIRESC/$PROG" ~/.bashrc; then
+			echo "export PATH=\"$PROGDIRESC/$PROG:\$PATH\" " >> ~/.bashrc;
+		fi
+	fi
+
+fi
+
+PY3PATH=`which python3`
+
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/phanotate.py"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+fi
+
+if [ $# -eq 5 ]; then
+
+IP=$4
+PORT=$5
+
+NCCMD=""
+
+if [ "$(uname)" == "Darwin" ]; then
+	NCCMD="nc -c $IP $PORT"
+else
+	NCCMD="nc -q 0 $IP $PORT"
+fi
+
+
+$NCCMD <<EOF
+
+<template description="$PROGNICE" title="$PROGNICE">
+ <window title="$PROGNICE">
+  <vgroup>
+
+	<checkbox id="WSLsel" value="true" selectonwindows="true">Run in WSL?</checkbox>
+
+	<group title="Input Files Reference">
+
+	<filedialog id="phanotate_input" output="false" multiple="false">Input Fasta</filedialog>
+    <filedialog id="phanotate_output" output="true" multiple="false">Output ORFs</filedialog>
+
+    <label>Regular Expression for finding sample data</label>
+	<input id="msempire_sample_regex">*SRR*</input>
+
+		<action program="run_phanotate">Run $PROGNICE</action>
+
+	</group>
+
+
+   <streambox id="output1">
+    <stream id="outputstream1">COUT</stream>
+    <stream id="outputstream2">CERR</stream>
+   </streambox>
+
+  </vgroup>
+ </window>
+ <execution>
+
+    <relocate id="phanotate_infasta_rel" from="\${phanotate_input}" wsl="\${WSLsel}"/>
+
+
+  <const id="bindir">${APPBINARYDIR}/</const>
+
+  <execute program="run_phanotate" location="" exec="$PY3PATH" param="\${bindir}/phanotate.py \${phanotate_infasta_rel}" wsl="WSLsel">
+        <output type="FILE_STD" color="green" location="\${phanotate_output}" />
+    <output type="CERR" color="red" to="outputstream2" />
+  </execute>
+
+ </execution>
+</template>
+
+
+EOF
+
+fi

install_templates/install_wsl_mounter.igui

@@ -0,0 +1,171 @@
+#! Install Mount Drive (WSL only)
+
+if [ "$(uname)" == "Darwin" ]; then
+	echo "This will not run on Mac OS"
+    exit;
+else
+  echo ""
+fi
+
+if [ ! "$2" = "" ]; then
+
+    if [ "$(uname)" == "Darwin" ]; then
+        echo "This will not run on Mac OS"
+        exit;
+    else
+
+        echo "No Dependencies"
+
+    fi
+else
+   echo "No sudo password, not installing dependencies"
+fi
+
+## set all variables
+PROG=MNTDRV
+PROGDIR=$1
+
+if [ -z "${PROGDIR}" ]; then
+	PROGDIR=~/bioGUI/progs/
+fi
+
+
+PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
+APPBINARYDIR=${PROGDIRESC}/${PROG}/
+
+if [ -d "$PROGDIR/$PROG" ]; then
+    echo "Removing Folder $PROGDIR/$PROG"
+    rm -rf $PROGDIR/$PROG
+fi
+
+## create progdir
+mkdir -p "$PROGDIR/$PROG"
+
+APPBINARYDIR=${PROGDIRESC}/${PROG}/
+
+UMOUNTBIN=`which umount`
+MOUNTBIN=`which mount`
+
+cat <<EOS > $APPBINARYDIR/mntdrv.sh
+#!/usr/bin/env sh
+
+DRVLTR=\$1
+
+DRVLTR=\`echo "\$DRVLTR" | tr '[:upper:]' '[:lower:]'\`
+echo $2 | sudo -S mkdir -p /mnt/\$DRVLTR/
+
+echo $2 | sudo -S $UMOUNTBIN /mnt/\$DRVLTR/
+echo $2 | sudo -S $MOUNTBIN -t drvfs \$DRVLTR: /mnt/\$DRVLTR/ -o rw,noatime,uid=1000,gid=1000,case=off
+
+echo "Mounted windows drive \$DRVLTR:\\ to /mnt/\$DRVLTR"
+
+ls /mnt/\$DRVLTR/
+
+EOS
+
+APPBINARYESC="${PROGDIRESC}/${PROG}/"
+APPBINARY="${PROGDIRESC}/${PROG}/mntdrv.sh"
+if [ -z "$(ls -A ${APPBINARYESC})" ] || [ ! -f ${APPBINARY} ]; then
+   (>&2 echo ${APPBINARYESC})
+   (>&2 ls ${APPBINARYESC})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo ${PROGDIRESC})
+   (>&2 ls ${PROGDIRESC})
+
+    (>&2 echo " \n \n \n")
+
+   (>&2 echo ${APPBINARY})
+   (>&2 ls ${APPBINARY})
+
+   (>&2 echo " \n \n \n")
+
+   (>&2 echo "ERROR: The application directory is empty after installation.")
+   (>&2 echo "ERROR: If you experience problems please re-install the software and create an issue on https://github.com/mjoppich/bioGUI.")
+   (>&2 echo "ERROR: For creating the issue, please upload the log.txt file of your installation attempt.")
+
+    (>&2 echo " \n \n \n")
+
+else
+
+    echo "${PROG} has been installed into ${APPBINARYESC}"
+    echo "Binary location ${APPBINARY}"
+
+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="Mount Drive (WSL)" title="Mount Drive">
+
+<window width="500" height="1000" title="Mount Drive">
+
+  <vgroup>
+
+
+    <group title="Mount Options">
+
+
+        <label>Which Window Drive do you want to make accessible (mount)?</label><input id="mntr_drv"></input>
+        <label>WSL User/sudo Password</label><input id="mntr_pw"  type="password"></input>
+
+        <action program="assembly" hint="Click Here to mount the drive">Mount</action>  
+    </group>
+
+
+    <group title="General Options">
+       <label>Run in WSL on Windows?</label><checkbox id="WSLsel" value="true" selectonwindows="true">Run in WSL?</checkbox>
+    </group>
+
+    <streambox linebreaks="TRUE" id="output1">
+      <stream id="outputstream1">OS1</stream>
+      <stream id="outputstream2">OS2</stream>
+    </streambox>
+
+
+  </vgroup>
+
+</window>
+
+
+
+<execution>
+    <const id="bindir">${APPBINARYDIR}/</const>
+
+
+    <add id="args">
+	<const>${APPBINARYDIR}/mntdrv.sh</const>
+    <value from="\${mntr_drv}"/>
+    <value from="\${mntr_pw}"/>     
+    </add>
+
+    <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>
+</template>
+
+
+EOF
+
+fi