Questions tagged [conda]

Major method for Python package installation and management associated with Anaconda data science framework.

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Bioconductor Conda release delay

How long does it take for the latest Bioconductor to end up on Conda? I think I saw a blog post about the challenges with this process, but I cannot find it. For example, Bioconductor 3.13 was ...
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0answers
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How to run conda/mono jobs in docker-compose container with celery job control?

I am looking for examples of how to set up biological data processing pipelines with docker-compose and celery. The standard celery docker image does not have all dependencies. What is the best way to ...
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1answer
42 views

downloaded software in Conda environment does not show in ls command

I installed gzip package in Conda environment, then to make sure the software was there, I used "ls" command, it was not in the list. Tried to install again, system says all the packages ...
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2answers
538 views

Can't install snakemake v5.15.0 from conda

I'm trying to install the latest version of snakemake from conda into a conda env, following the instructions here. I.e. ...
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1answer
35 views

How to run a one-time 'setup' step for amrfinder in snakemake using conda

I'm trying to add amrfinder running within conda to a snakemake workflow, working on a slurm HPC. The first time you run amrfinder, you have to run ...
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1answer
220 views

conda doesn't install latest version of snakemake

I would like to use the --default-resources parameter for profiles which is available in later versions of snakemake. To install snakemake, I created a new conda ...
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1answer
94 views

Use a specific python.exe instance with PyMOL/Windows?

I want to use RDKit with a python script in PyMOL. RDKit requires a conda environment, so I think I need to be able to specify that the instance of python that I want to use would be in that ...
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2answers
49 views

Installing a package on Mac

I am trying to instll sigproextractor package on my Mac I tried ...
7
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2answers
1k views

Getting the licenses of all conda installed packages

I would like to get a list of the licenses of all packages I installed using Conda. pip has what I need in the form of pip-licenses, is there a similar thing for conda?
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2answers
2k views

How to use busco installed through conda?

I have installed busco on my Mac computer using conda install --channel bioconda busco=3.0.2 into an environment called ...
3
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1answer
1k views

snakemake with --conda-prefix, can I use a pre-built conda environment?

I have read this question (Running Snakemake in one single conda env) but still have some doubt. I am using the '--conda-prefix /some/dir' option and I have a rule in my snakemake file with the ...
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1answer
2k views

Using `install.packages` with conda-managed R

I have R installed and managed by conda (miniconda) on my MacBook Pro. The version of R I use most frequently (3.5.1) is installed on the base environment and I have other version-specific ...
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1answer
140 views

UCSC packages/tools ucsc-netchainsubset and ucsc-fatotwobit not working on GNU/Linux

I have installed some ucsc tools on my Mac computer and it worked fine: Installation ...