Software
========

.. |rstudio_url| replace:: https://koch.uod.otago.ac.nz

.. |hostname| replace:: koch.uod.otago.ac.nz

.. |database_path| replace:: /scratch/DATABASES

.. contents::
   :depth: 1
   :local:

Anaconda
++++++++
See :ref:`conda`

.. include:: /common/spack/packages/beast2.rst

.. include:: /common/spack/packages/bedtools2.rst

.. include:: /common/spack/packages/bioperl.rst

.. include:: /common/spack/packages/blast-plus.rst

.. include:: /cluster/software/bohra.rst

.. include:: /common/spack/packages/bowtie2.rst

.. include:: /common/containers/apps/circlator.rst

.. include:: /common/spack/packages/clustalw.rst

.. include:: /common/spack/packages/conda.rst

.. include:: /common/spack/packages/diamond.rst

.. include:: /common/spack/packages/entrezdirect.rst

.. include:: /common/spack/packages/fasttree.rst

.. include:: /common/spack/packages/fastqc.rst

.. include:: /common/spack/packages/flye.rst

.. include:: /cluster/software/gubbins.rst

.. include:: /common/spack/packages/guppy.rst

.. include:: /common/spack/packages/hmmer.rst

.. include:: /common/spack/packages/humann3.rst

.. include:: /common/spack/packages/jupyter.rst

.. include:: /common/spack/packages/kraken2.rst

.. include:: /common/spack/packages/medaka.rst

.. include:: /common/spack/packages/metaphlan.rst

.. include:: /common/spack/packages/muscle.rst



Miniconda
+++++++++
See :ref:`conda`

.. include:: /common/spack/packages/minimap2.rst

.. include:: /common/containers/apps/nanopolish.rst

.. include:: /common/containers/apps/nullarbor.rst

.. include:: /common/spack/packages/phylophlan.rst

.. include:: /common/spack/packages/prokka.rst

.. include:: /common/spack/packages/python.rst

.. include:: /common/containers/apps/qiime.rst

.. include:: /common/spack/packages/r.rst

.. include:: /common/spack/packages/raxml.rst

.. include:: /common/spack/packages/rfplasmid.rst

.. include:: /common/containers/apps/rstudio.rst

.. include:: /common/spack/packages/samtools.rst

.. include:: /common/spack/packages/spades.rst

.. include:: /common/spack/packages/sratools.rst

.. include:: /common/containers/apps/tbprofiler.rst

.. include:: /common/containers/apps/trinity.rst

.. include:: /common/containers/apps/trycycler.rst

.. include:: /common/containers/apps/unicycler.rst


USEARCH
+++++++++
See :ref:`vsearch`

.. include:: /common/spack/packages/vsearch.rst