Questions tagged [conda]
Major method for Python package installation and management associated with Anaconda data science framework.
17
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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....
- 123
1
vote
1
answer
58
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.
...
- 11
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vote
1
answer
453
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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 ...
- 101
2
votes
1
answer
621
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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 ...
- 101
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0
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186
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set -euo pipefail in Snakemake wrapper
I have snakemake script doing fastqc with a wrapper but it errors out saying
...
- 1
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vote
2
answers
72
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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 ...
- 2,169
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1
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102
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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 ...
- 11
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2
answers
892
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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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- 217
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67
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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 ...
- 217
4
votes
1
answer
310
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 ...
- 363
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1
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202
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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2
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63
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Installing a package on Mac
I am trying to instll sigproextractor package on my Mac
I tried
...
- 1,981
3
votes
1
answer
2k
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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 ...
- 133
4
votes
1
answer
3k
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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 ...
- 2,086
0
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1
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199
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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
...
- 2,459
3
votes
2
answers
2k
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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 ...
- 2,459
8
votes
3
answers
2k
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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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