MAGpurify2

# Installation

# Installing MAGpurify2

MAGpurify2 can be installed using pip or conda. Alternatively, you can execute it via Docker.

# External dependencies

If you choose install MAGpurify2 via pip, make sure that you have also installed the third-party dependencies: Prodigal (opens new window) [1] and MMseqs2 (opens new window) [2]. The conda installation method will automatically download and install these software for you.

External dependencies are not required in fast mode

If you are executing MAGpurify2 with the --fast_mode parameter you don't need to install Progidal or MMseqs2. These software are only required to run the codon_usage and taxonomy modules.

# Docker

Foo.

# Test the installation

  • Download test data:
fileId="1-Gf-FsVIcARqrUb-LHS_FZlb-sCGAmfo"
fileName="magpurify2_test_data.tar.gz"
curl -sc /tmp/cookie "https://drive.google.com/uc?export=download&id=${fileId}" > /dev/null
code="$(awk '/_warning_/ {print $NF}' /tmp/cookie)"
curl -Lb /tmp/cookie "https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}" -o ${fileName}
tar zxfv magpurify2_test_data.tar.gz
  • Download database:
fileId="1ooWiR3LplBy5GsY5wZ7o6dwswiCWVvmi"
fileName="magpurify2DB.v1.0.tar.gz"
curl -sc /tmp/cookie "https://drive.google.com/uc?export=download&id=${fileId}" > /dev/null
code="$(awk '/_warning_/ {print $NF}' /tmp/cookie)"
curl -Lb /tmp/cookie "https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}" -o ${fileName}
tar zxfv magpurify2DB.v1.0.tar.gz

  1. Hyatt, Doug, et al. "Prodigal: prokaryotic gene recognition and translation initiation site identification." (opens new window) BMC Bioinformatics 11.1 (2010): 119. ↩︎

  2. Steinegger, Martin, and Johannes Söding. "MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets." (opens new window) Nature Biotechnology 35.11 (2017): 1026-1028. ↩︎

← Using MAGpurify2 →