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Questions tagged [conda]

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

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3 votes
1 answer
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Unable to install prokka using homebrew or conda

I have tried to install prokka using homebrew using the code brew install prokka (I also tried brew install brewsci/bio/prokka) ...
Lucy Kelly's user avatar
2 votes
2 answers
84 views

problem with running Kallisto on single cell data

I am totally new to bioinformatics, therefore apologies if the terminology is not correct or the question is dumb :) I have been trying the following: installed miniconda create an environment called ...
Simon's user avatar
  • 31
2 votes
0 answers
25 views

Trouble Running VEP in Conda Environment Due to Perl DBD::mysql Error

Hello StackExchange Community, I am currently facing issues with running the Variant Effect Predictor (VEP) and vcf2maf in a Conda environment due to a Perl-related error. Installation Steps: I ...
qiuting Zhang's user avatar
0 votes
0 answers
88 views

Error in snakemake when running conda envs in container

I am facing an issue when running snakemake with a container and conda. Let me explain better. I am developing a workflow (locally) in snakemake, where some rules use a conda env (defined in /envs/env....
DavideBrex's user avatar
1 vote
1 answer
90 views

Snakemake MissingRuleException

I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference genome. I'm not too sure what I'm doing wrong based on this error message. ...
Hua Yuan's user avatar
1 vote
1 answer
1k views

Warning message related to tensorflow package when trying to run deepbgc bioinformatics tool

I have come across some related issues pertaining to this tensorflow warning but none related specifically to deepbgc I have created a conda environment and have installed onto it the bioinformatics ...
Joe_G's user avatar
  • 101
2 votes
1 answer
759 views

pip installation within conda env: Error downgrading scikit-learn - WARNING: No metadata

I am trying to get the bioinformatics tool deepbgc up and running. Now I have created a conda environment and have currently ...
Joe_G's user avatar
  • 101
0 votes
0 answers
204 views

set -euo pipefail in Snakemake wrapper

I have snakemake script doing fastqc with a wrapper but it errors out saying ...
5ko.brat's user avatar
2 votes
2 answers
76 views

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 ...
burger's user avatar
  • 2,199
1 vote
1 answer
114 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 ...
user9196's user avatar
1 vote
2 answers
913 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. ...
flashton's user avatar
  • 217
0 votes
1 answer
78 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 ...
flashton's user avatar
  • 217
4 votes
1 answer
312 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 ...
mrhd's user avatar
  • 363
0 votes
1 answer
218 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 ...
preyingmanti5's user avatar
0 votes
2 answers
68 views

Installing a package on Mac

I am trying to instll sigproextractor package on my Mac I tried ...
Zizogolu's user avatar
  • 2,160
4 votes
1 answer
2k 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 ...
guibar's user avatar
  • 143
4 votes
1 answer
3k 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 ...
Ram RS's user avatar
  • 2,330
0 votes
1 answer
214 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 ...
Biomagician's user avatar
  • 2,459
3 votes
2 answers
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 ...
Biomagician's user avatar
  • 2,459
8 votes
3 answers
2k 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?
Freek's user avatar
  • 563