7
votes
Getting the licenses of all conda installed packages
To my knowledge there's no single listing of the licenses, but you can:
conda list | awk '{if(NR>3) printf("%s=%s", $1, $2)}' | xargs conda info | grep license
...
- 19.5k
4
votes
Accepted
conda doesn't install latest version of snakemake
Python (whether installed with conda or not) will prefer packages installed in your home directory unless you tell it not to. This is a little known secret about using a virtualenv, actually, since ...
- 19.5k
4
votes
Accepted
4
votes
Accepted
How to use busco installed through conda?
From the README, it looks like the command-line entry point is not busco but run_BUSCO.py. This seems to agree with the bioconda ...
- 5,060
4
votes
Accepted
Can't install snakemake v5.15.0 from conda
This is an example of the conda solver behaving incorrectly. In this case, it's choosing to pick a version that minimizes the number of dependencies required. Version 5.3.0 has 25 fewer dependencies, ...
- 19.5k
3
votes
Accepted
Bioconductor Conda release delay
I started the roll-out on the 30th in the evening. There's not much of a delay for the October Bioconductor release, but for the summer release we first have to build the newest R version and then ...
- 19.5k
3
votes
Using `install.packages` with conda-managed R
Installing packages outside of an R session is arguably the point of using conda. Package management isn't something that should be done within scripts, only the ...
- 1,364
2
votes
Installing a package on Mac
At a guess you don't have python3 installed and hence pip3
https://stackoverflow.com/questions/17271319/how-do-i-install-pip-on-macos-or-os-x
Personally I would install via Anaconda3 and skip a ...
M__♦
- 11.3k
2
votes
Accepted
snakemake with --conda-prefix, can I use a pre-built conda environment?
If the environment already exists it will simply be used. You cannot, however, tell it to use an environment with a normal name (e.g., "my_env").
I assume you mean, "where the heck does the random ...
- 19.5k
2
votes
Snakemake MissingRuleException
You're not using wildcards the way snakemake is equipped to work with them. See:
FAQs such as https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-run-my-rule-on-all-files-of-a-...
- 1,993
1
vote
Warning message related to tensorflow package when trying to run deepbgc bioinformatics tool
The 'blunderbus' way to do this is as follows (not recommended in this instance :-) ),
...
M__♦
- 11.3k
1
vote
pip installation within conda env: Error downgrading scikit-learn - WARNING: No metadata
pip and conda don't mix and good advice is don't ever mix them. Thus to avoid this delete your old environment, create a new <...
M__♦
- 11.3k
1
vote
downloaded software in Conda environment does not show in ls command
Just type
conda list gzip
OR
conda list | grep gzip
OR if its installed in a given environment
...
M__♦
- 11.3k
1
vote
Accepted
How to run a one-time 'setup' step for amrfinder in snakemake using conda
There are two approaches you can take:
There's a --conda-create-envs-only option that you can use to exit after creating the envs. You should get information about ...
- 19.5k
1
vote
Use a specific python.exe instance with PyMOL/Windows?
So it is really hard to make a given python instance run a library from a different instance. It is not just one dist-packages library folder, but multiple that you ...
- 4,174
1
vote
UCSC packages/tools ucsc-netchainsubset and ucsc-fatotwobit not working on GNU/Linux
Short answer: respect the case of the tool name
Longer story below
Thanks to terdon, I printed the PATH when the conda environment was active and listed what was in the folder where conda installed ...
- 2,459
1
vote
How to use busco installed through conda?
The new version of busco (v4) has the user entry point called busco (it's still a python script). BUSCO v4 is available at conda, note it's a very fresh update.
- 5,497
1
vote
Getting the licenses of all conda installed packages
I can't comment, but here's an improvement for the top answer to list more information:
...
- 19
1
vote
Getting the licenses of all conda installed packages
This one uses JQ for parsing and querying conda generated json output (https://stedolan.github.io/jq/)
...
- 11
Only top scored, non community-wiki answers of a minimum length are eligible