fix errors on linux

mjoppich · May 15, 2019 · 62e50ba · 62e50ba
1 parent f6caf35
commit 62e50ba
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Showing 5 changed files with 17 additions and 8 deletions.
diff --git a/install_templates/install_bowtie1.igui b/install_templates/install_bowtie1.igui
@@ -41,7 +41,7 @@ APPBINARYDIR=${PROGDIR}/${PROG}/
 mkdir -p "$PROGDIR"
 
 #download and unzip
-wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.2/bowtie-1.2.2-src.zip/download -O "$PROGDIR/$PROG.zip"
+wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/bowtie-1.1.2-src.zip/download -O "$PROGDIR/$PROG.zip"
 
 
 

diff --git a/install_templates/install_bowtie2.igui b/install_templates/install_bowtie2.igui
@@ -41,6 +41,8 @@ fi
 ## create progdir
 mkdir -p "$PROGDIR"
 
+rm -rf ${PROGDIR}/${PROG}/
+
 #download and unzip
 wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.3/bowtie2-2.3.4.3-source.zip/download -O "$PROGDIR/$PROG.zip"
 

diff --git a/install_templates/install_pureseqtm.igui b/install_templates/install_pureseqtm.igui
@@ -20,7 +20,7 @@ if [ ! "$2" = "" ]; then
 
         echo $2 | sudo -S dpkg --add-architecture i386
         echo $2 | sudo -S apt-get update
-        echo $2 | sudo -S apt-get install libc6:i386 libncurses5:i386 libstdc++6:i386 gcc-multilib
+        echo $2 | sudo -S apt-get -y install libc6:i386 libncurses5:i386 libstdc++6:i386 gcc-multilib
 
     fi
 
@@ -166,7 +166,7 @@ $NCCMD <<EOF
     <if comp="IS_SET" value1="pureseqtm_plot" sep=" "><const>-P 1</const></if>
   </add>
 
-  <execute program="run_pureseqtm" location="" exec="sh" param="\${bindir}/PureseqTM.sh \${cl} wsl="WSLsel">
+  <execute program="run_pureseqtm" location="" exec="sh" param="\${bindir}/PureseqTM.sh" \${cl} wsl="WSLsel">
     <output type="FILE_STD" color="green" location="\${pureseqtm_output}" />
     <output type="CERR" color="red" to="outputstream2" />
   </execute>

diff --git a/install_templates/install_rnahybrid.igui b/install_templates/install_rnahybrid.igui
@@ -58,9 +58,13 @@ tar xfz rnahybrid.tar.gz -C "$PROGDIR/$PROG/"
 cd "$PROGDIR/$PROG/"
 mv */* .
 
-CC=gcc-8 CXX=g++-8 ./configure
-make
-
+if [ "$(uname)" == "Darwin" ]; then
+    CC=gcc-8 CXX=g++-8 ./configure
+    make
+else
+  ./configure
+  make
+fi
 
 if [ $# -gt 2 ]; then
    if [ "$3" = "1" ]; then

diff --git a/install_templates/install_spades.igui b/install_templates/install_spades.igui
@@ -57,8 +57,11 @@ mv */* .
 
 cd "$PROGDIR/$PROG/"
 
-CC=gcc-8 CXX=g++-8 PREFIX="$PROGDIR/$PROG/" ./spades_compile.sh
-
+if [ "$(uname)" == "Darwin" ]; then
+    CC=gcc-8 CXX=g++-8 PREFIX="$PROGDIR/$PROG/" ./spades_compile.sh
+else
+    PREFIX="$PROGDIR/$PROG/" ./spades_compile.sh
+fi
 
 if [ $# -gt 2 ]; then
    if [ "$3" = "1" ]; then