ILRI Research Computing

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====== taxpasta ======
The main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table.

===== Information =====

  * Version: 0.7.0
  * Added: March, 2025
  * Link: https://github.com/taxprofiler/taxpasta

===== Usage =====

See versions that are available:
<code>$ module avail taxpasta</code>

Load one version into your environment and run it:
<code>$ module load taxpasta/0.7.0
$ taxpasta</code>


===== Installation ======
Notes from the sysadmin during installation.

<code>$ module load python/3.10
$ sudo mkdir -p /export/apps/taxpasta/0.7.0
$ sudo chown aorth /export/apps/taxpasta/0.7.0
$ python -m venv /export/apps/taxpasta/0.7.0
$ source /export/apps/taxpasta/0.7.0/bin/activate
$ python -m pip install -U pip setuptools wheel
$ python -m pip install -U taxpasta==0.7.0
$ sudo chown -R root:root /export/apps/taxpasta/0.7.0</code>