Follow these instructions to setup a new computer with commonly used tools and software for scientific data analysis (with emphasis on bioinformatics)
Use https://ninite.com/ to install the following open source software:
- FileZilla - FTP file transfer
- Firefox - web browser, add cliget addon for easy curl/wget download links
- PuTTY - remote shell access
- Java 8
- .NET - framework needed for Paint.net
- Inkscape - vector based graphic editing software
- Notepad++ - powerful text editor (with syntax highlighting)
- Peazip/7-zip - archive management
- VLC - media player
Reboot and then install also:
10. Paint.net - image editing
Update (26/09/2017)
Starting from Firefox (v54+), latest versions of Zotero (v5.0) must be installed as a standalone program (rather than a Firefox add-in).
- Add Zotero for Firefox, along with relevant references, citation styles and better-biblatex plugin (to be installed from file in Zotero, not Firefox)
- Add Putty colour and fonts template into registry from putty_theme.reg
- Download and install R and Rstudio, along with RTools, following these instructions (
install as admin)
Optional: Download my suggested .Rprofile intoDocuments\Rfolder and util.R intoDocuments\R\sourcefolder - Download and install Bioedit - sequence alignment and manipulation
- Download and install Fiji - scientific image processing (microscopy, gel, etc.)
- Download and install Git for windows - version control
- Download PDF-Xchange Editor (academic licence can be purchased with a 50% discount)
Follow the very simple instructions from the GitHub repo
curl -L https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash
echo 'export PATH="~/.pyenv/bin:$PATH"' >> ~/.bash_profile # or ~/.profile on RedHat systems
echo 'eval "$(pyenv init -)"' >> ~/.bash_profile # or ~/.profile on RedHat systems
echo 'eval "$(pyenv virtualenv-init -)"' >> ~/.bash_profile # or ~/.profile on RedHat systems
source ~/.bash_profile # start a new shell (use ~/.profile on RedHat systems)
pyenv install miniconda-latest
pyenv global miniconda-latest
conda install fonts-continuum libgcc libuuid pandoc qt scipy ncurses readline git # libgd
# conda install -c conda-forge tmux
conda install -c bioconda blast crb-blast salmon snap-aligner busco biopython trim-galore bedtools parafly \
blat bbmap bowtie bowtie2 hisat2 segemehl star bwa cd-hit cutadapt trimmomatic exonerate express samtools \
picard transdecoder trinity trinotate transrate-tools parallel khmer libdb stacks gawk rsem bioawk perl-bioperl \
qualimap perl-vcftools-vcf kallisto fastqc multiqc # perl-threaded perl-bioperl perl-vcftools-vcf
conda install -c biobuilds oases tassel
conda install -c ipyrad ipyrad
conda install -c r r-base r-rstudioapi rstudio
Follow the very simple instructions from my Gist
Follow the very simple instructions from the GitHub repo
git clone git://github.com/viking/Renv.git ~/.Renv
echo 'export PATH="~/.Renv/bin:$PATH"' >> ~/.bash_profile # or ~/.profile on RedHat systems
echo 'eval "$(Renv init -)"' >> ~/.bash_profile # or ~/.profile on RedHat systems
mkdir -p ~/.Renv/plugins && cd !$
git clone git://github.com/viking/R-build.git
# Install a new R
# Install linux dependencies
sudo apt-get install libreadline6 libreadline6-dev gfortran libpcre3-dev libcurl4-gnutls-dev libxml2-dev libssh2-1-dev
Renv install -l # list available versions
Renv install 3.4.0
Renv global 3.4.0
Download .Rprofile and util.R from my Gist into ~/R/ folder (~/R/Documents on Windows)
mkdir -p ~/R/source
curl -L -o ~/.Rprofile https://gist.githubusercontent.com/IdoBar/222ab8c0d10481f793dc54f4dc857d0e/raw/5fd2ceebeb5292253b5ef01fef83b761e1b3dc91/.Rprofile
curl -L -o ~/R/source/util.R https://gist.githubusercontent.com/IdoBar/7f63547158ecdbacf31b54a58af0d1cc/raw/1586455e0538141a027e2938d20beb109d11c3c0/util.R
Added gawk to conda install and update Zotero and Firefox status