package_manager.md

Managing Programs

• Traditional software installation
  • config, make, make install
  • find dependencies
• Operating System specific precompiled binaries
• Anaconda package Manager
  • System calls
  • Python
  • Environments
• Python's Pip
• GitHub (versioning, collaboration, transparency)
• HPC Modules
• Containers

Install Anaconda

On Mac install xcode developer tools:

xcode-select --install

Download and install Miniconda Python 64-bit Installer
https://docs.anaconda.com/free/miniconda/#quick-command-line-install

Use installation defaults

Manage conda environment

See available modules

conda env list

conda update -n base -c defaults conda

conda create -n vsnp3 -c bioconda -c conda-forge vsnp3

If conda install is slow, restarting computer may help.

conda update --all

Test tool

vsnp3_download_fasta_gbk_gff_by_acc.py -fbg -a NC_045512

Download sratoolkit

Download from conda

conda install bioconda::sra-tools

Download compiled binaries

https://github.com/ncbi/sra-tools/wiki/01.-Downloading-SRA-Toolkit

tar -xzf sratoolkit*.tar.gz

add bin to PATH

PATH=$PATH:${HOME}/Downloads/sratoolkit.3.0.7-mac64/bin

fasterq-dump -S SRR3135071

mv SRR3135071_1.fastq SRR3135071_R1.fastq
mv SRR3135071_2.fastq SRR3135071_R2.fastq

pigz *fastq

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