Qiime2 Tools

Repository of utilities for Qiime2. Experimental.

Qiime 2.0 is a complete rewrite of Qiime, and introduces the concept of artifacts to simplify the workflow, tracking metadata and provenance. This repository is used to store experimental scripts to inspect or manipulate such artifacts.

:package: qzoom.pl

Updated utility to extract data from Qiime 2 artifacts. See qzoom documentation.

It works independently from Qiime2, its meant to automate common tasks (e.g. extract .biom file and automatically converts it to .tsv if the biom tool is available).

Example usage

Extract a set of visualizations into a directory. A subdirectory with the name of the visualization file will be created for each "qzv" artifact:

qzoom.pl -x -o ./html *.qzv

View the main file contained in each artifact:

qzoom.pl  *.qz?

Default mode: "ls" like

Screenshot in info mode:

Extract mode

In extract mode we want to extract the content of the data directory for regular artifacts (qza), the whole HTML directory for visualizations (qzv).

Combining -x (extract) with -r (rename), will extract the single file of the data directory getting the name from the artifact.

Downloading this repository

From the command line type the following command from the directory you want to have the repository copied in:

git clone https://github.com/telatin/qiime2tools/

Keep note of the installation directory, I'll refer to as $INSTALLDIR.

Running a script from this repository

From the command line:

perl $INSTALLDIR/qiime2tools/script_name.pl