Merge pull request #121 from DashaZhernakova/master

added multithreading in Beagle
fixed parameter file
Merge pull request #122 from georgebyelas/master

fixed parameter file
removed one parameter, which was not correct
the same for 5gpm
Merge pull request #123 from georgebyelas/master

removed R_HOME, which does not work from 2 workflows
changed realignment protocol from 1 to 4 cores
Merge pull request #124 from RoanKanninga/master

changed realignment protocol from 1 to 4 cores
updated the parameters file
put the tmpIntermediateDir back
Merge pull request #125 from RoanKanninga/master

updated the parameters file
symlink with a relative path for the first stage rocket
Merge pull request #126 from georgebyelas/master

symlink with a relative path for the first stage rocket
added the first rocket to computeje5
removed ftl file
Merge pull request #127 from RoanKanninga/master

added the first stage rocket to computeje5
Added minor changes