new instance set up instructions

[taylorreiter]

I set up my instance like this:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
# follow the command prompts, allowing conda to prepend to path
source ~/.bashrc
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels defaults

# These two steps are optional, but should be run while using the instances that 
# were made for DC Genomics to avoid software installation conflicts. 
# These two steps create and activate a conda environment.
conda create -n variants python==3.6
source activate variants

conda install -c bioconda bwa=0.7.17=ha92aebf_3 samtools=1.9=h8ee4bcc_1 bcftools=1.8=h4da6232_3 trimmomatic=0.38=0 fastqc=0.11.7=5

[taylorreiter]

Thanks @jessicamizzi for catching this!

[raynamharris]

Note: I had to run mkdir sub to get this to work because the sub/ didn't exist as a path for the files.

[taylorreiter]

thanks @raynamharris! changed the above text to reflect that that does not need to be done in the setup period.