Update .gitlab-ci.yml

before_script:

  - echo "Creating cellranger test install"

  - mkdir -p ~/local/lib

  - if [[ -w ~/local/lib ]]; then echo "install directory writeable"; else echo "install directory not writeable"; fi

  - cd ~/local/lib

  - echo "Downloading cellranger"

  - wget -O cellranger-3.1.0.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-3.1.0.tar.gz?Expires=1564080778&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTMuMS4wLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU2NDA4MDc3OH19fV19&Signature=m6fJx3etqOoywnpHgADfRzpCSZ04YZEe0sA3ZyVl1EQMn5Zm60qLk7v4KVPRLy6a9Qi2zE5DKWr8EpFfAg3kWqZ5-vDYtZtlYAnl0~OhtijIyYs7Rm8Uqzal-lk8tmD4SQaZQVQY~RLEed7iWq7stYwc4QTXRUjtojGqwMvqf5t4dMQbn7tNs513shjC4lGfL7~xCWpc5vaxaSN9wGSRF8ex9Hy-GsMYG2Dm8ya7ajplR1SPqTcHd9sDfro1UzOK~IGkHh9GGO9EicXQ6ypExvKB-WrDLLLZ66rEJjeNoSS6qnTKeEzyKw-3UoEYfho~Ph4eKrFS-XSZhtEX-UDItg__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"

  - tar -xzvf cellranger-3.1.0.tar.gz

  - echo "Downloading reference for human genome"

  - wget http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz

  - tar -xzvf refdata-cellranger-GRCh38-3.0.0.tar.gz

  - echo "cellranger added to PATH"

  - export PATH=~/local/lib/cellranger-3.1.0:$PATH

#  - mkdir -p ~/local/lib/bin

#  - if [[ -w ~/local/lib/bin ]]; then echo "install directory writeable"; else echo "install directory not writeable"; fi

#  - cd ~/local/lib/bin

#  - echo "Downloading cellranger"

#  - wget -O cellranger-3.1.0.tar.gz "http://cf.10xgenomics.com/releases/cell-exp/cellranger-3.1.0.tar.gz?Expires=1564080778&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cDovL2NmLjEweGdlbm9taWNzLmNvbS9yZWxlYXNlcy9jZWxsLWV4cC9jZWxscmFuZ2VyLTMuMS4wLnRhci5neiIsIkNvbmRpdGlvbiI6eyJEYXRlTGVzc1RoYW4iOnsiQVdTOkVwb2NoVGltZSI6MTU2NDA4MDc3OH19fV19&Signature=m6fJx3etqOoywnpHgADfRzpCSZ04YZEe0sA3ZyVl1EQMn5Zm60qLk7v4KVPRLy6a9Qi2zE5DKWr8EpFfAg3kWqZ5-vDYtZtlYAnl0~OhtijIyYs7Rm8Uqzal-lk8tmD4SQaZQVQY~RLEed7iWq7stYwc4QTXRUjtojGqwMvqf5t4dMQbn7tNs513shjC4lGfL7~xCWpc5vaxaSN9wGSRF8ex9Hy-GsMYG2Dm8ya7ajplR1SPqTcHd9sDfro1UzOK~IGkHh9GGO9EicXQ6ypExvKB-WrDLLLZ66rEJjeNoSS6qnTKeEzyKw-3UoEYfho~Ph4eKrFS-XSZhtEX-UDItg__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA"

#  - tar -xzvf cellranger-3.1.0.tar.gz

#  - echo "Downloading reference for human genome"

#  - wget http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz

#  - tar -xzvf refdata-cellranger-GRCh38-3.0.0.tar.gz

#  - echo "cellranger added to PATH"

  - export PATH=~/local/lib/bin/cellranger-3.1.0:$PATH

  - cellranger --version

  - cellranger testrun --id "test"

  - cd -