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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 ...
Devon Ryan's user avatar
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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 ...
Devon Ryan's user avatar
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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, ...
Devon Ryan's user avatar
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4 votes
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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 ...
Daniel Standage's user avatar
4 votes
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Installing a package on Mac

maybe you could try python3 -m pip install package
TANGLi83's user avatar
  • 128
4 votes
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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 ...
Devon Ryan's user avatar
  • 19.6k
3 votes

Unable to install prokka using homebrew or conda

Prokka's github page github page has: conda install -c conda-forge -c bioconda -c defaults prokka edit Seems that there may be another way to do it: stepwise ...
darked89's user avatar
  • 358
3 votes
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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 ...
Devon Ryan's user avatar
  • 19.6k
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 ...
James Hawley's user avatar
  • 1,384
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__'s user avatar
  • 12.5k
2 votes

problem with running Kallisto on single cell data

created another environment called "kb", where I installed Kallisto-bustools This is known to work well. What about installing bustools in the same env as Kallisto? Alternatively you can ...
M__'s user avatar
  • 12.5k
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-...
Ram RS's user avatar
  • 2,330
1 vote

problem with running Kallisto on single cell data

Well, it's embarassing to say but...I didn't have Autotools, CMake, and Make installed! Once I installed them, I could run the command. However, I am running now in another problem: even though the ...
Simon's user avatar
  • 31
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__'s user avatar
  • 12.5k
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__'s user avatar
  • 12.5k
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__'s user avatar
  • 12.5k
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 ...
Devon Ryan's user avatar
  • 19.6k
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 ...
Matteo Ferla's user avatar
  • 4,234
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: ...
Tom Sproul's user avatar
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/) ...
Luuk Peters's user avatar
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 ...
Biomagician's user avatar
  • 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.
Kamil S Jaron's user avatar

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