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Many of our users are performing computations in the Bioinformatics field. Python has a huge number of packages for this in the Bioinformatics channel. A “channel” is a repository for a collection of packages. So first you will need to install this channel.

See: https://bioconda.github.io You should read all of this as it covers what Bioconda is and how to cite Bioconda in your publications. Also see: https://hpc.research.uts.edu.au/faq/acknowledgement/.

Remember our help for Miniconda is here: https://hpc.research.uts.edu.au/software_general/python/python_miniconda/ You might need to refer to that for some of the steps below.

Install the Bioinformatics Channel

The instructions below are just following: https://bioconda.github.io/user/install.html#set-up-channels

Activate your Miniconda environment. Then add the channnels in this order.

(base) $ conda config --add channels defaults
(base) $ conda config --add channels bioconda
(base) $ conda config --add channels conda-forge

Searching for the Package you Need

(base)$ conda search cd-hit Loading channels: done

Name Version Build Channel

cd-hit 4.6.4 0 bioconda
cd-hit 4.6.4 1 bioconda
cd-hit 4.6.6 0 bioconda
cd-hit 4.6.8 0 bioconda
cd-hit 4.6.8 hfc679d8_2 bioconda
cd-hit 4.8.1 h2e03b76_4 bioconda
cd-hit 4.8.1 h2e03b76_5 bioconda
cd-hit 4.8.1 h5b5514e_6 bioconda
cd-hit 4.8.1 h8b12597_3 bioconda
cd-hit 4.8.1 hdbcaa40_0 bioconda
cd-hit 4.8.1 hdbcaa40_1 bioconda
cd-hit 4.8.1 hdbcaa40_2 bioconda
(base)$

(base) hpcnode01 playbooks/$ conda env list

conda environments:

base * /shared/homes/mlake/miniconda3 cwl-runner /shared/homes/mlake/miniconda3/envs/cwl-runner_py3 nextflow /shared/homes/mlake/miniconda3/envs/nextflow pytorch /shared/homes/mlake/miniconda3/envs/pytorch

conda install –name bio-env cd-hit=4.6.8

(base) hpcnode01 playbooks/$ conda install -n cwl-runner_py3 cd-hit=4.6.8 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: done

## Package Plan ##

environment location: /shared/homes/mlake/miniconda3/envs/cwl-runner_py3

added / updated specs: - cd-hit=4.6.8

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
ca-certificates-2022.5.18.1|       ha878542_0         144 KB  conda-forge
cd-hit-4.6.8               |       hfc679d8_2         232 KB  bioconda
certifi-2022.5.18.1        |   py37h89c1867_0         150 KB  conda-forge
------------------------------------------------------------
                                       Total:         526 KB

The following NEW packages will be INSTALLED:

cd-hit bioconda/linux-64::cd-hit-4.6.8-hfc679d8_2

The following packages will be UPDATED:

ca-certificates 2020.11.8-ha878542_0 –> 2022.5.18.1-ha878542_0 certifi 2020.11.8-py37h89c1867_0 –> 2022.5.18.1-py37h89c1867_0 openssl 1.1.1h-h516909a_0 –> 1.1.1k-h7f98852_0

https://stackoverflow.com/questions/48128029/installing-specific-build-of-an-anaconda-package

https://docs.conda.io/projects/conda-build/en/latest/resources/variants.html#differentiating-packages-built-with-different-variants