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instruction_summary.txt
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instruction_summary.txt
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These instructions assume you are working from a up to date base Ubuntu image
1) Install python 2.7
sudo apt install python2.7
2) Download miniconda (https://docs.conda.io/en/latest/miniconda.html#linux-installers)
3) Install miniconda
bash Miniconda2-latest-Linux-x86_64.sh
4) Update conda
5) Add the bioconda channel
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
6) Install the core software
conda install bcftools
conda install bedtools
conda install igv
7) Install the software for QC module
conda install picard
8) Install the software for read alignment module
conda install bwa
9) Install the software for SV module
conda install breakdancer
conda install lumpy-sv
conda install minimap2
conda install sniffles
10) Install the software for RNA-seq module
conda install hisat2
conda install kallisto
conda install r-sleuth
11) Install the software for CHiP-seq module
conda install bowtie2
conda install macs2
conda install meme
conda install ucsc-fetchchromsizes
conda install ucsc-bedgraphtobigwig
12) Install the software for assembly module
conda install assembly-stats
conda install canu
conda install kmer-jellyfish
conda install seqtk
conda install velvet
conda install wtdbg2
13) Install the software for group projects
conda install freebayes
conda install gatk4
14) Install genomescope (only software outside of bioconda)
Download the R file, move it to the bin directory and make it executable
wget https://raw.githubusercontent.com/schatzlab/genomescope/d2aefddd32ce48aa1144d9fbd80ed6b37785cd8d/genomescope.R
mv genomescope.R $HOME/miniconda/bin
chmod 754 $HOME/miniconda/genomescope.R
15) Install samtools last to ensure latest version is installed
conda install samtools=1.10
16) Install git
conda install git
17) Install the course modules (command to be completed once the repos are ready)
git clone <repo>
18) Run a test script to check installs (tests/test_software.sh)
19) Run the module test scripts (tests/test_unix.sh etc.)
20)Issues to address:
Install the web browsers firefox and chrome
Install a pdfviewer
Add a shortcut to the take screenshot application
Issues with lumpy-sv (only software that still requires python 2.7)
Issues with picard, commandline is not consistent use of picard versus PicardCommandLine
Rendering a remote desktop, this is only needed only for
Viewing graphs in firefox/chrome
IGV
Other?