improve install script

Author: maxulysse

scripts/install.sh

@@ -1,14 +1,14 @@
 #!/bin/bash
 set -euo pipefail
 
-TOOL="all"
+CONTAINER_ENGINE="singularity"
 
 while [[ $# -gt 0 ]]
 do
   key="$1"
   case $key in
-    -t|--tool)
-    TOOL="$2"
+    -e|--engine)
+    CONTAINER_ENGINE="$2"
     shift # past argument
     shift # past value
     ;;
@@ -19,25 +19,27 @@ do
 done
 
 # Install Nextflow
-if [[ "$TOOL" = nextflow ]] || [[ "$TOOL" = all ]]
-then
-  cd $HOME
-  curl -fsSL get.nextflow.io | bash
-  chmod +x nextflow
-  sudo mv nextflow /usr/local/bin/
-fi
+mkdir /tmp/nextflow
+cd /tmp/nextflow
+wget -qO- get.nextflow.io | bash
+sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
 
 # Install Singularity
-if [[ "$TOOL" = singularity ]] || [[ "$TOOL" = all ]]
+if [[ "$CONTAINER_ENGINE" = singularity ]]
 then
-  sudo apt-get install squashfs-tools
-  cd $HOME
+  if [[ "$SGT_VER" = '' ]]
+  then
+    SGT_VER=$(curl --silent "https://api.github.com/repos/Singularityware/Singularity/releases/latest" | grep -Po '"tag_name": "\K.*?(?=")')
+  fi
+  sudo apt-get install libarchive-dev squashfs-tools
+  mkdir /tmp/singularity
+  cd /tmp/singularity
   wget https://github.com/singularityware/singularity/releases/download/$SGT_VER/singularity-$SGT_VER.tar.gz
   tar xvf singularity-$SGT_VER.tar.gz
   cd singularity-$SGT_VER
   ./configure --prefix=/usr/local
   make
   sudo make install
-  cd ..
-  rm -rf singularity-$SGT_VER*
+  cd ${TRAVIS_BUILD_DIR}
+  rm -rf /tmp/singularity
 fi