add cellranger 3.0.2 install to testing environment

image: busybox:latest

before_script:

  - echo "Installing cellranger dependencies

  - sudo apt-get install install go rust rustup node python

  - export GOPATH="${HOME}/.go"

  - export GOROOT="$(brew --prefix golang)/libexec"

  - export PATH="$PATH:${GOPATH}/bin:${GOROOT}/bin"

  - test -d "${GOPATH}" || mkdir "${GOPATH}"

  - test -d "${GOPATH}/src/github.com" || mkdir -p "${GOPATH}/src/github.com"

  - export PATH=/usr/lib/go-1.11/bin:$PATH # Add golang to path

  - rustup install 1.28.0

  - rustup default 1.28.0

  - sudo apt-get install make clang-6.0 golang-1.11-go libz-dev libbz2-dev liblzma-dev

  - echo "Creating cellranger test install"

  - git clone https://github.com/10XGenomics/cellranger.git

  - cd cellranger

  - git checkout 3.0.2

  - make

  - cd ..

#  - mkdir -p ~/local/bin

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

#  - cd ~/local/bin

#  - 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=/home/tom/local/bin/cellranger-3.1.0:$PATH

  - export PATH=./cellranger:$PATH

  - cellranger --version

  - cellranger testrun --id "test"

  - cd -