I am just trying to get my head around using conda environments.
I created a conda environment for a project containing plink2, plink, R and bcftools.
When I installed plink, using mamba install -n autozygosity -c conda-forge plink, I got the output:
Package Version Build Channel Size
────────────────────────────────────────────────────────────────────────────────
Install:
────────────────────────────────────────────────────────────────────────────────
+ plink 1.90b6.21 hec16e2b_2 bioconda/linux-64 7MB
Change:
────────────────────────────────────────────────────────────────────────────────
- curl 7.86.0 h7bff187_1 conda-forge
+ curl 7.86.0 h2283fc2_1 conda-forge/linux-64 Cached
- krb5 1.19.3 h3790be6_0 conda-forge
+ krb5 1.19.3 h08a2579_0 conda-forge/linux-64 Cached
- libcurl 7.86.0 h7bff187_1 conda-forge
+ libcurl 7.86.0 h2283fc2_1 conda-forge/linux-64 Cached
- libnghttp2 1.47.0 hdcd2b5c_1 conda-forge
+ libnghttp2 1.47.0 hff17c54_1 conda-forge/linux-64 Cached
- libssh2 1.10.0 haa6b8db_3 conda-forge
+ libssh2 1.10.0 hf14f497_3 conda-forge/linux-64 Cached
- python 3.11.0 h582c2e5_0_cpython conda-forge
+ python 3.11.0 ha86cf86_0_cpython conda-forge/linux-64 Cached
- r-openssl 2.0.4 r42hfaab4ff_0 conda-forge
+ r-openssl 2.0.4 r42h1f3e0c5_0 conda-forge/linux-64 Cached
Upgrade:
────────────────────────────────────────────────────────────────────────────────
- openssl 1.1.1s h166bdaf_0 conda-forge
+ openssl 3.0.7 h166bdaf_0 conda-forge/linux-64 Cached
Downgrade:
────────────────────────────────────────────────────────────────────────────────
- bcftools 1.16 hfe4b78e_1 bioconda
+ bcftools 1.8 h4da6232_3 bioconda/linux-64 794kB
- htslib 1.16 h6bc39ce_0 bioconda
+ htslib 1.9 h4da6232_3 bioconda/linux-64 1MB
Summary:
Install: 1 packages
Change: 7 packages
Upgrade: 1 packages
Downgrade: 2 packages
Total download: 9MB
This is kind of annoying since I would like to use some of the more recent features in htslib/bcftools and 1.8 is a pretty old version.
Are these kind of downgrades just a necessary part of using conda or is there something to be done? I guess one option is to create a new environment just for plink, but this seems like it could get messy quite quickly!
1 answer
Sometimes downgrades are neccessary. However, its perfectly possible to have both plink 1.90b2 and bcftools 1.16 in the same environment, so there must be something lese that is preventing this.
The only depedency of plink is libgcc-ng>=10.3.0, which is not even that recent.
However, in general it is usually easy to have as few tools as possible in each environment you use, to reduce the probability of things like this. Personally, I'm terrible at this, and like my whole pipeline for a given project to run in a single environment, but many people have a seperate env for each tool
No. You load one env. run the tool. Load the other env, run that tool etc.
THere is also now "conda run" I believe that will run a command in an env.
I think the most common thing is to have an env per commandline statement actually, rather than per tool.
Things like snakemake and Nextflow will even automate the building of an env for a particular step, and caching it for if its needed again.
I like my whole pipeline for a given project to run in a single environment
I agree with this. I create an environment for each project and create additional environments if incompatibilities arise. Specifically, for each project I have a requirements.txt where I list the packages I need and their version. As the project develops, I add or remove packages in requirements.txt and install them with mamba install --file requirements.txt -n my-project-env. One env per tool seems unmanageable to me but I'd like to hear other opinions...
can you load multiple environments at the same time
conda activate has a --stack option that could make that work but again, it seems messy to me.
It may be interesting to post one of such cases and see what people think... My projects usually have something like ~30 dependencies listed in requirements.txt. Sometimes envs break down and I need to rebuild them but it's usually a matter of minutes. Besides, I'm still not entirely settled on what should go in requirements.txt. For example, if you use ggplot2, do you also list R? (I don't)
Log in to answer this question.
