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7

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 Allegedly conda info --license should work, but at least in conda 4.6.3 it doesn't show any license information. It unfortunate that there's no convenient way to get a tabular list of package:...


4

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 internally those tell python to ignore everything in your home directory. Within conda, there's long been a debate about whether python (and also R) should ...


4

maybe you could try python3 -m pip install package


4

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 recipe, where run_BUSCO.py and run_busco are listed among the commands.


4

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, so if you let conda choose the version that's what it will pick. There's nothing you can really do about this other than specifying the version of snakemake ...


3

Devon will probably add a more precise answer, until then I just link his Tweet from last week: https://twitter.com/dpryan79/status/1394714988720308226 Edit: 31.5.21 Rollout started yesterday, should take a week to complete: https://twitter.com/dpryan79/status/1399273322601459712


3

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 loading of packages. Doing so ensures that your environment setup is somewhat robust, which should be set before you perform actual calculations. Using conda install ... is the best way to ensure ...


2

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 direct Python3 installation altogether. The answer above recommends using homebrew, again personally I wouldn't touch it and go straight for a full Anaconda3 ...


2

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 looking conda environment name come from?!?", which is a very good question. The answer to that is that it's a hash of the --conda-prefix setting and the contents ...


2

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 rebuild all conda CRAN packages. It's probably not widely known, but Bioconductor packages are only compatible with a single R version. For example, the ones being ...


1

Just type conda list gzip OR conda list | grep gzip OR if its installed in a given environment conda activate myenv or else just activate myenv system depending followed by either of the first two commands. It is better to use conda-navigate a very nice and under used GUI, and would work in this particular instance. The details are found in an earlier ...


1

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 where the envs are so you can run amrfinder -u. Add a new rule called "amr_setup" or something like that that runs: . amrfinder -u touch amrfinder.setup Then put amrfinder.setup into your ...


1

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 would need to link, and all that assuming they use the same version of python. So the best bet is to install a new instance of pymol the python module. The module can be installed in a python ...


1

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 the UCSC tool. ls /mnt/home2/miska/cr517/anaconda3/envs/ucsc-netchainsubset377/bin c_rehash libpng-config mysql_config openssl pngfix libpng16-...


1

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.


1

This one uses JQ for parsing and querying conda generated json output (https://stedolan.github.io/jq/) conda list | awk '{if(NR>3) printf("%s=%s\n", $1, $2)}' | xargs -I{} conda search --info --json "{}" | jq --raw-output '.[][0] | "\(.name)\t\(.version)\t\(.license)"' builds the list, asks conda search for all info on package as json, feeds json to JQ, ...


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