cwl and personal R libraries

[sibylgisela]

Description

When running cwl, cwl cannot find packages which are in the personal R libraries, i.e. those stored in the R_LIBS_USER variable in the R environment.

To recreate

Working on avg_DNAm branch.

If I run the following line (from .travis.yml, slightly modified)
cwltool cwl/preprocess.cwl --toConvert test_data/GSM1589192_K562.1_2.txt.chr19 --format farlik2013

I get the following error:
Error in library(getopt) : there is no package called 'getopt'

notes:

• the getopt package was installed in my home directory on Orca and was found when I ran Rscripts via command line
• I added the path to the getopt package to the PATH environment variable, but that did not help