macify install scripts

mjoppich · Jan 18, 2017 · 77f704a · 77f704a
1 parent c397e9f
commit 77f704a
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Showing 14 changed files with 69 additions and 43 deletions.
diff --git a/install_templates/install_ballgown.igui b/install_templates/install_ballgown.igui
@@ -120,7 +120,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 
 <template description="Ballgown: Isoform-level differential expression analysis in R." title="${PROGNICE}">
 <window title="${PROGNICE}">

diff --git a/install_templates/install_bowtie1.igui b/install_templates/install_bowtie1.igui
@@ -57,7 +57,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 
 <template description="bowtie 1.1.2 aligner" title="bowtie 1.1.2">
 <window title="bowtie 1.1.2 aligner">
@@ -148,7 +148,7 @@ cat << EOF | netcat $IP $PORT
 </window>
 
 <execution>
-<const id="bindir">${APPBINARYDIR}</const>
+<const id="bindir">${PROGDIR}/${PROG}/</const>
 
 <if id="bowtie2_build_inref_rel" comp="EQUALS" value1="WSLsel" value2="true">
 <relocate from="\${bowtie2_build_inref}" wsl="true"/>

diff --git a/install_templates/install_bowtie2.igui b/install_templates/install_bowtie2.igui
@@ -57,7 +57,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 
 <template description="bowtie2 2.0.4 aligner" title="bowtie2 2.0.4">
 <window title="bowtie2 2.0.4 aligner">
@@ -146,7 +146,7 @@ cat << EOF | netcat $IP $PORT
 </window>
 
 <execution>
-<const id="bindir">${APPBINARYDIR}</const>
+<const id="bindir">${PROGDIR}/${PROG}/</const>
 
 <relocate id="bowtie2_build_inref_rel" wsl="\${WSLsel}" from="\${bowtie2_build_inref}"/>
 <relocate id="bowtie2_build_idx_out_rel" wsl="\${WSLsel}" from="\${bowtie2_build_idx_out}"/>

diff --git a/install_templates/install_glimmer.igui b/install_templates/install_glimmer.igui
@@ -1,5 +1,7 @@
 #! Install glimmer302b
 
+echo "This tool will not compile in folders where the absolute path contains spaces!"
+
 echo "Dependencies: csh"
 if [ ! "$2" = "" ]; then
 	echo "Installing dependencies"
@@ -27,7 +29,7 @@ mkdir -p "$PROGDIR/$PROG"
 #download and unzip
 wget http://ccb.jhu.edu/software/glimmer/$PROG.tar.gz -O "$PROGDIR/$PROG.tar.gz"
 
-cd $PROGDIR
+cd "$PROGDIR"
 tar -xzf "$PROG.tar.gz" --strip 1 -C "$PROGDIR/$PROG"
 
 #install prog
@@ -63,7 +65,7 @@ echo "sending template"
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 <!--<?xml version="1.0" encoding="UTF-8")>-->
 <template description="Glimmer3 scripts ($PROG)" title="Glimmer3">
 

diff --git a/install_templates/install_hisat.igui b/install_templates/install_hisat.igui
@@ -1,4 +1,4 @@
-#! Install hisat2-2.0.4
+#! Install hisat2-2.0.5
 
 echo "Dependencies: unzip"
 if [ ! "$2" = "" ]; then
@@ -11,7 +11,7 @@ else
 fi
 
 ## set all variables
-PROG=hisat2-2.0.4
+PROG=hisat2-2.0.5
 
 PROGDIR=$1
 if [ -z "${PROGDIR}" ]; then
@@ -26,10 +26,9 @@ mkdir -p "$PROGDIR"
 
 #download and unzip
 if [ ! -f "$PROGDIR/$PROG.zip" ]; then
-	wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.4-source.zip -O "$PROGDIR/$PROG.zip"
+	wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-source.zip -O "$PROGDIR/$PROG.zip"
 fi
 
-
 if [ ! -d "$PROGDIR/$PROG" ]; then
 cd "$PROGDIR"
 
@@ -42,6 +41,10 @@ cd "$PROGDIR/$PROG"
 
 make
 
+#now fix spaces in path
+perl -pi -e 's/my \$align_prog_s= File::Spec->catpath\(\$vol\,\$script_path\,\$align_bin_s\);/my \$align_prog_s= "\\\"".File::Spec->catpath(\$vol,\$script_path,\$align_bin_s).\"\\\"\";/' hisat2
+perl -pi -e 's/my \$align_prog_l= File::Spec->catpath\(\$vol\,\$script_path\,\$align_bin_l\);/my \$align_prog_l= "\\\"".File::Spec->catpath(\$vol,\$script_path,\$align_bin_l).\"\\\"\";/' hisat2
+
 if [ $# -gt 2 ]; then
 
 	if [ "$3" = "1" ]; then
@@ -58,10 +61,10 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 
-<template description="hisat2 2.0.4 aligner" title="hisat2 2.0.4">
-<window title="hisat2 2.0.4 aligner">
+<template description="hisat2 2.0.5 aligner" title="hisat2 2.0.5">
+<window title="hisat2 2.0.5 aligner">
 <vgroup>
 
   <group title="Alignment Information">
@@ -260,7 +263,7 @@ end
 <value from="hisat_align_mate_orientations"/>
 
 </add>
-	
+
   <execute program="hisat2" param="\${cl}" location="\${bindir}" exec="hisat2" wsl="WSLsel">
     <output type="COUT" color="green" to="outputstream1" />
     <output type="CERR" color="red" to="outputstream2" />

diff --git a/install_templates/install_hmmer.igui b/install_templates/install_hmmer.igui
@@ -15,18 +15,26 @@ PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
 mkdir -p "$PROGDIR"
 
 #download and unzip
-wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz -O "$PROGDIR/$PROG.tar.gz"
+if [ ! -f "$PROGDIR/$PROG.tar.gz" ]; then
+	wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz -O "$PROGDIR/$PROG.tar.gz"
+fi
+
+if [ ! -d "$PROGDIR/$PROG" ]; then
+
 
-cd $PROGDIR
+cd "$PROGDIR"
 tar -xzf $PROG.tar.gz -C "$PROGDIR/"
 
+fi
+
 #install prog
 cd "$PROGDIR/$PROG"
 
-./configure -prefix="$PROGDIR/$PROG"
+./configure# -prefix="$PROGDIR/$PROG"
 make
-make check
-make install
+#make check
+# does not really work on mac os
+#make install
 
 if [ $# -gt 2 ]; then
 
@@ -44,7 +52,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 <template rootid="hmmerroot" description="HMMER ($PROG)" title="HMMER">
 
 <window width="500" height="800" title="HMMER">
@@ -90,7 +98,7 @@ cat << EOF | netcat $IP $PORT
 <relocate id="loc_search_db" wsl="\${WSLsel}" from="\${search_db}"/>
 <relocate id="loc_search_output" wsl="\${WSLsel}" from="\${search_output}"/>
 
-<const id="bindir">${PROGDIR}/${PROG}/bin/</const>
+<const id="bindir">${PROGDIRESC}/${PROG}/src/</const>
 
 <add id="cl_build" sep=" ">
 <add sep="">
@@ -120,7 +128,7 @@ cat << EOF | netcat $IP $PORT
 
 <env id="ip" get="IPv4"/>
 
-<execute location="" exec="sh" wsl="WSLsel" param="-c &quot; \${cl} 2>&amp;1 | netcat \${ip} 55025 &quot;">
+<execute location="" exec="sh" wsl="WSLsel" param="-c &quot; \${cl} 2>&amp;1 &quot;">
     <output type="COUT" color="green" to="outputstream1" />
     <output type="CERR" color="red" to="outputstream2" />
   </execute>

diff --git a/install_templates/install_jellyfish.igui b/install_templates/install_jellyfish.igui
@@ -18,16 +18,17 @@ if [ ! -f "$PROGDIR/$PROG.tar.gz" ]; then
 	wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/$PROG.tar.gz -O "$PROGDIR/$PROG.tar.gz"
 fi
 
-cd $PROGDIR
+cd "$PROGDIR"
 tar -xzf $PROG.tar.gz -C "$PROGDIR/"
 
 #install prog
-cd $PROGDIR/$PROG
+cd "$PROGDIR/$PROG"
 
 ./configure --prefix="$PROGDIR/$PROG"
 make
 #make check
-make install
+# the following intall fails on mac os, what else ...
+#make install
 
 if [ $# -gt 2 ]; then
 
@@ -45,7 +46,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 <template rootid="blubb" intatt="111" description="Jellyfish ($PROG)" title="Jellyfish">
 
 <window width="500" height="1900" title="Jellyfish">
@@ -190,7 +191,7 @@ cat << EOF | netcat $IP $PORT
 </add>
 
 
-<add id="cl">
+<add id="cl" sep="">
 <if comp="EQUALS" value1="sel_cite" value2="TRUE"><value from="cl_cite"/></if>
 <if comp="EQUALS" value1="sel_count" value2="TRUE"><value from="cl_count"/></if>
 <if comp="EQUALS" value1="sel_merge" value2="TRUE"><value from="cl_merge"/></if>
@@ -200,7 +201,7 @@ cat << EOF | netcat $IP $PORT
 </add>
 
 <env id="ip" get="IPv4"/>
-<const id="bindir">${PROGDIRESC}/${PROG}/bin/</const>
+<const id="bindir">${PROGDIR}/${PROG}/bin/</const>
 
 		<execute wsl="WSLsel" exec="jellyfish" location="\${bindir}" param="\${cl}">
 			<output type="CERR" color="red" to="outputstream2" />

diff --git a/install_templates/install_rmats.igui b/install_templates/install_rmats.igui
@@ -53,7 +53,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 
 <template description="rMATS replicate MATS" title="$PROGNICE">
  <window title="$PROGNICE">
@@ -181,9 +181,9 @@ cat << EOF | netcat $IP $PORT
 </add> 
 
 
-  <const id="bindir">${PROGDIRESC}/${PROG}/</const>
+  <const id="bindir">${PROGDIR}/${PROG}/</const>
 
-  <execute location="" exec="python" param="\${bindir}/RNASeq-MATS.py \${cl} wsl="WSLsel">
+  <execute location="" exec="python" param="&quot;\${bindir}/RNASeq-MATS.py&quot; \${cl}" wsl="WSLsel">
     <output type="COUT" color="green" to="outputstream1" />
     <output type="CERR" color="red" to="outputstream2" />
   </execute>

diff --git a/install_templates/install_rsem.igui b/install_templates/install_rsem.igui
@@ -23,7 +23,7 @@ if [ -z "${PROGDIR}" ]; then
 fi
 
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=$PROGDIRESC/$PROG/
+APPBINARYDIR="$PROGDIR/$PROG/"
 
 
 ## create progdir
@@ -59,8 +59,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
-
+nc $IP $PORT << EOF
 
 <template description="RSEM: estimating gene/isoform expression levels" title="$PROGNICE">
  <window title="$PROGNICE">

diff --git a/install_templates/install_samtools.igui b/install_templates/install_samtools.igui
@@ -19,7 +19,7 @@ if [ -z "${PROGDIR}" ]; then
 fi
 
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=${PROGDIRESC}/${PROG}/bin
+APPBINARYDIR=${PROGDIR}/${PROG}/bin
 
 
 ## create progdir
@@ -57,7 +57,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 
 <template description="Samtools" title="${PROGNICE}">
 <window title="Samtools 1.3.1">

diff --git a/install_templates/install_stringtie.igui b/install_templates/install_stringtie.igui
@@ -22,7 +22,7 @@ if [ -z "${PROGDIR}" ]; then
 fi
 
 PROGDIRESC=$(echo $PROGDIR | sed 's/ /\\ /g')
-APPBINARYDIR=${PROGDIRESC}/${PROG}/
+APPBINARYDIR=${PROGDIR}/${PROG}/
 
 ## create progdir
 mkdir -p "$PROGDIR"
@@ -59,7 +59,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
+nc $IP $PORT << EOF
 
 <template description="StringTie Transcript Assembler" title="${PROGNICE}">
 <window title="StringTie 1.3.0">

diff --git a/install_templates/install_trimmomatic.igui b/install_templates/install_trimmomatic.igui
@@ -53,8 +53,7 @@ if [ $# -eq 5 ]; then
 IP=$4
 PORT=$5
 
-cat << EOF | netcat $IP $PORT
-
+nc $IP $PORT << EOF
 <template description="Trimming short RNA-Seq Reads" title="$PROGNICE">
  <window title="$PROGNICE">
   <vgroup>
@@ -300,9 +299,9 @@ cat << EOF | netcat $IP $PORT
    <value from="steps"/>
   </add>
 
-  <const id="bindir">${PROGDIRESC}/${PROG}/</const>
+  <const id="bindir">${PROGDIR}/${PROG}/</const>
 
-  <execute location="" exec="java" param="-jar \${bindir}/trimmomatic-0.36.jar \${cl}" wsl="WSLsel">
+  <execute location="" exec="java" param="-jar &quot;\${bindir}/trimmomatic-0.36.jar&quot; \${cl}" wsl="WSLsel">
     <output type="COUT" color="green" to="outputstream1" />
     <output type="CERR" color="red" to="outputstream2" />
   </execute>

diff --git a/src/app/ProcessLauncher.h b/src/app/ProcessLauncher.h
@@ -337,6 +337,15 @@ public slots:
 
             if ((sString.at(i) == ' ') || (sString.size()-1 == i))
             {
+
+                if (i >= 1)
+                {
+                    if ((sString.at(i-1) == '\\') && (sString.at(i) == ' '))
+                    {
+                        continue;
+                    }
+                }
+
                 size_t iOffSet = (sString.at(i) == ' ') ? 0 : 1;
 
                 std::string sPart = sString.substr(iLastArgPartStart, i-iLastArgPartStart+iOffSet);

diff --git a/templates/WSL_install.gui b/templates/WSL_install.gui
@@ -67,7 +67,12 @@
 
 <add id="cl" sep=" ">
 <value from="prog_wsl"/>
+<add sep="">
+<const>&quot;</const>
 <value from="user_instpath"/>
+<const>&quot;</const>
+</add>
+
 <add sep="">
 <const>&quot;</const>
 <value from="sudopw"/>