Bioconda Python packages

Many bioinformatics Python packages are now maintained and available for the popular Anaconda Python distribution. Python packages for the Anaconda distribution are distributed through a variety of different bundles, called channels. The bioconda channel is specifically set up for the maintenance and distribution of popular bioinformatics packages.

Available Versions

The current installation of Bioconda
incorporates the most popular packages. To find the available versions and learn how to load them, run:

module spider bioconda

The output of the command shows the available Bioconda
module versions.

For detailed information about a particular Bioconda
module, including how to load the module, run the module spider command with the module’s full version label. For example:

module spider bioconda/py3.10

Module	Version	Module Load Command
bioconda	py3.10	module load bioconda/py3.10

To view an up-to-date list of the Python packages provided by a particular bioconda module, load the bioconda module and run the conda list command. For example:

module load bioconda
conda list | grep bioconda

The environment contains a large number of packages, most of them to support the software of interest in bioinformatics. The grep command filters the Python package list to only show the Bioconda channel packages. The output may look like this:

# packages in environment at /apps/software/standard/core/bioconda/py3.10:
bcftools                  1.17                 h3cc50cf_1    bioconda
cyvcf2                    0.30.22         py310hcf1fb4a_0    bioconda
deeptools                 3.5.2              pyhdfd78af_1    bioconda
deeptoolsintervals        0.1.9           py310h8472f5a_5    bioconda
entrez-direct             16.2                 he881be0_1    bioconda
hisat2                    2.2.1                hdbdd923_6    bioconda
hmmer                     3.3.2                hdbdd923_4    bioconda
homer                     4.11            pl5262h9f5acd7_8    bioconda
htseq                     2.0.3           py310h5aa3a86_1    bioconda
htslib                    1.17                 h81da01d_2    bioconda
k8                        0.2.5                hdcf5f25_4    bioconda
kallisto                  0.50.0               hc877fd6_0    bioconda
minimap2                  2.26                 he4a0461_1    bioconda
multiqc                   1.15               pyhdfd78af_0    bioconda
munkres                   1.0.7                      py_1    bioconda
ngmlr                     0.2.7                hdcf5f25_6    bioconda
nseg                      1.0.1                h031d066_4    bioconda
perl-...
py2bit                    0.3.0           py310h4b81fae_8    bioconda
pybigwig                  0.3.22          py310h79000e5_1    bioconda
pysam                     0.21.0          py310h41dec4a_1    bioconda
pyspoa                    0.0.10          py310h0dbaff4_0    bioconda
python-edlib              1.3.9           py310h0dbaff4_4    bioconda
recon                     1.08                 h031d066_6    bioconda
repeatmasker              4.1.5           pl5321hdfd78af_0    bioconda
repeatmodeler             1.0.8                         0    bioconda
repeatscout               1.0.6                hec16e2b_3    bioconda
rmblast                   2.14.0               h4565617_2    bioconda
salmon                    1.10.2               hecfa306_0    bioconda
samtools                  1.17                 hd87286a_1    bioconda
stringtie                 2.2.1                h6b7c446_4    bioconda
subread                   2.0.6                he4a0461_0    bioconda
svim                      2.0.0              pyhdfd78af_0    bioconda
trf                       4.09.1               h031d066_4    bioconda
twobitreader              3.1.7              pyh864c0ab_1    bioconda