check STAR index version

# Pipeline to run UMI-seq analysis from fastq to read count tables.

# Authors: Swati Parekh, Christoph Ziegenhain, Beate Vieth & Ines Hellmann

# Contact: sparekh@age.mpg.de or christoph.ziegenhain@ki.se

vers=2.7.2a

vers=2.7.2b

currentv=`curl -s https://raw.githubusercontent.com/sdparekh/zUMIs/master/zUMIs-master.sh | grep '^vers=' | cut -f2 -d "="`

if [ "$currentv" != "$vers" ]; then echo -e "------------- \n\n Good news! A newer version of zUMIs is available at https://github.com/sdparekh/zUMIs \n\n-------------"; fi

staridxver=`grep "versionGenome" $staridxdir/genomeParameters.txt | awk '{print $2}' | sed 's/\s+//g'`

if [[ "$starver" != "$staridxver" ]]; then

  echo "WARNING: The STAR version used for mapping is $starver and the STAR index is created using the version $staridxver. This might lead to error while mapping. If you encounter error at the mapping stage, please make sure to create the STAR index using STAR $staridxver."

  echo "WARNING: The STAR version used for mapping is $starver and the STAR index was created using the version $staridxver. This may lead to an error while mapping. If you encounter any errors at the mapping stage, please make sure to create the STAR index using STAR $starver."

  #exit 1

fi

#close conda enviroment if necessary

if [ $conda = true ]; then

if [[ $conda = true ]]; then

  source $zumisenv/bin/deactivate

fi