Conda - modules

Description

Conda is an open-source package management system and environment management system that runs on Windows, macOS and Linux (available in Metacentrum). Conda quickly installs, runs and updates packages and their dependencies. Conda easily creates, saves, loads and switches between environments on the computer. In Metacentrum Conda is used for managing of python tools.

License

Conda is released under the 3-clause BSD license.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of conda-modules and load default version of conda-modules as

module avail conda-modules/ # list available modules
module load conda-modules   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail conda-modules

and choose explicit version you want to use.

#load initial Conda module
module add conda-modules-py37
#check the list of installed environments
conda env list
#acrivate selected environment (busco for example)
conda activate busco
#use application
busco --help
#quit and leave environment
conda deactivate

Note: Of course, all Metacentrum users are eligible to install tools via Conda in their home directory. The following manual can be very useful.

list of available environments in Conda modules:

• AmberTools22
• Argus
• aTRAM
• abyss_v2.3.5_py3.6

See ABySS wiki page how to use parallelization

• adapterremoval
• agat
• alevin-fry-0.8.1
• amoebamdpoltype
• ana38
• antismash
• argus
• augustus
• BAM2fastx
• bamscale
• blobtools
• bonito
• bonito-0.4
• braker2
• busco
• busco_v5.4.3_py3.8
• cactus-2.4.4
• cellprofiler
• dada2
• deepsignal
• deepsignal-plant-0.1.6
• dekupl
• dftbplus
• diamond
• eggNOG-mapper_v2.1.9_py3.9
• eggnog-mapper-1.0.3
• endhic
• epic2
• faqcs
• fast-bonito_v0.2.2_py3.7

User must specify absolute paths to the python script basecaller.py and to the model file batchsize200_chunksize6000.pb

python /software/conda-modules/5.3.1/envs/fast-bonito_v0.2.2_py3.7/fast-bonito/basecaller.py \
--model_directory /software/conda-modules/5.3.1/envs/fast-bonito_v0.2.2_py3.7/fast-bonito/models/batchsize200_chunksize6000.pb 

• fastp
• fenics
• ffpenv

Environment for FFParam tool
FFParam requires GUI
Usage is following:
$ module add conda-modules-py37
$ conda activate ffpenv
$ export LD_LIBRARY_PATH=/software/conda-modules/5.3.1/envs/ffpenv/lib/python3.7/site-packages/PySide2-5.15.2-py3.7-linux-x86_64.egg/PySide2/Qt/lib:/software/conda-modules/5.3.1/lib:/software/conda-modules/5.3.1/envs/ffpenv/lib/
$ ggparam-gui

• flair2
• fldpnn
• flexbar
• gdal
• geant4
• gemmi
• generax
• getorganelle-1.7.7.0
• gistic2
• gpaw
• hamster
• hapflk
• haslr
• haslr-0.8a1
• hgtector
• hicassembler
• htseq_v2.0.1_py3.9
• hybpiper_v2.0.2_py3.9
• hyphy
• infernal
• invadomed-2.9.6
• ipyrad_v0.9.85_py3.10
• iqtree
• ivadomed-2.9.6
• links

Available also as a module (can be easier to use as the Conda version lacks LINKS-make)

• lobstr
• locarna
• lsdalton
• LTR_retriever
• LTR_retriever-2.9.0

conda activate LTR_retriever-2.9.0 
module add ltr_retriever-2.9.0  
LTR_retriever -h 

• macs2
• mafft
• mapdamage
• medaka
• medaka_v1.6.0_py3.8
• megalodon

Prepared with Guppy 5.0.15 (CPU and GPU versions) placed in /software/conda-modules/5.3.1/envs/megalodon/bin/ont-guppy-cpu and /software/conda-modules/5.3.1/envs/megalodon/bin/ont-guppy-gpu
You should accept ONT licence.
GPU version requires CUDA capability 6.0 and higher (PBS parameter gpu_cap=cuda60)

• merqury
• metabat_v2.15_py3.9
• metaphlan
• metawrap-env

Environment for Metawrap version 1.3 with dependencies

• microbeannotator
• mitos
• mrbait
• msprime-env
• multiqc_v1.12_py3.7
• nanocaller_v3.0.0_py3.8
• nanoplot
• nanosv-1.2.4
• nanovar
• nextflow
• ngmlr
• octopus
• ont-tombo-1.5.1
• openMM
• orgasm
• panaroo_v1.2.10_py3.8
• pathweaver
• peakhood
• phrapl-0.62
• phylofisher
• phyloflash-3.4.2
• phyloligo
• phyluce
• picrust
• picrust2
• picrust2_2.4.1
• prokka
• psass-3.1.0
• psipred_v4.01_py2.7
• pureclip
• py2713
• py37
• py38
• pyclone
• pyseg
• pyseg_system
• pyseq
• pytorch_1.13.0_vision_audio_cpu
• pytorch_1.13.0_vision_audio_gpu
• qiime2-2020.2
• qiime2_v2022.2_py3.8
• quast_v5.2.0_py3.9
• quickmerge
• raven
• rdkit
• rmats-4.1.2
• smilei
• sniffles_v2.0.6_py3.9
• SNP-sites
• soapaligner
• spruceup
• sra-tools-3.0.3
• superfold
• tedensity_v0.9.1_py3.8

Call the main python script process_genome.py with an absolute path: python /software/conda-modules/5.3.1/envs/tedensity_v0.9.1_py3.8/TE_Density/process_genome.py

• tepid
• tigmint
• tombo
• tpmcalculator-0.0.4-2
• transposon_annotation_tools_env
• TransposonUltimate
• truvari
• trycycler
• ttclust_v4.10.1_py3.7
• unifunc-1.4.5
• wgddetector_v1.1_py2.7
• wiggletools
• winnowmap

Documentation

https://github.com/conda/conda

Homepage

https://docs.conda.io/en/latest/