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Questions tagged [mamba]

Mamba is a Python-based CLI conceived as a drop-in replacement for conda, offering higher speed and more reliable environment solutions.

Mamba is a fast, robust, and cross-platform package manager.

It runs on Windows, OS X and Linux (ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda’s commands.

https://github.com/mamba-org/mamba

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Accessing Anaconda Channels from Mamba

I am building my Python environment around micromamba. I was wondering how can I use the Anaconda channels to download packages as described in conda channels: https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/channels.html. By…
Mark
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Unable to install snakemake via conda

I am trying to install snakemake as instructed by the tutorial: conda install -n base -c conda-forge mamba conda activate base mamba create -c conda-forge -c bioconda -n snakemake snakemake But after the third line I get this error: Traceback (most…
mrad
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conda and mamba were broken (segmentation fault) after installing "conda install -c asmeurer glibc"

I am a Thai microbiologist try to use command line. I installed "Ubuntu 20.04 on Windows" then bowtie2 by conda: conda install -c bioconda bowtie2 and then check version of the bowtie2. it is 2.2.5 but I need 2.4.5. the con labels is weird like…
Chooseel Bunsuwansakul
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Workflow with Snakemake & Conda: Placeholder of length '80' too short in package

I have followed the Snakemake best practices here to create a workflow, where different steps activate different Conda environments. For example, a rule that collects statistics: rule per_samp_stats: input: …
ksw
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How to install h3-py (from uber) with mamba?

I have recently switched to mamba as a package installer and am now trying to install h3-py into an environment. I have tried several ways, first using: mamba install h3-py but then it says encountered problems while solving: - nothing provides…
jchristiaanse
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How can I use mamba/conda packages in rstudio server

I am trying to write to dockerfile to install conda environments from a yaml and to run rstudio server from within my project directories. I am aware of rstudio-server-conda but would like to be able to use a single dockerfile to create an…
Noah_Seagull
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Is it possible to have mamba aggregate a list of yaml files during the create command?

I have a process where envs are created and then multiple env files are used to update the env via mamba env update . The problem is that I'm running commands in parallel and the lockfile doesn't appear to work with mamba env update only for mamba…
red888
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How to add local tar.gz package in conda meta.yaml requierement?

I have a meta.yaml recipe for conda, to build a package. (we will call it mypackage) I want this package to use a local (tar.bz2) file in his requirement section (build&run) (we will call it locapackagedep) Here is an example of what I would like to…
Skapin
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mamba install of FASTBOOK leading to provider install issue

While trying to run command below mamba install -y fastbook I am receiving the problem/error below Looking for: ['fastbook'] fastai/linux-64 [====================] (00m:00s) Done fastchan/linux-64 [====================] (00m:00s)…
Judy007
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Mamba can't create env giving 'nothing provides' but pip sees such version of opencv-python

I need to create env with mamba create --name tf1_12__HDR Tensorflow==1.12.0 Keras==2.2.4 opencv-python==3.4.4.19 anaconda It provides mamba (0.7.3) supported by @QuantStack ... Looking for: ['tensorflow==1.12.0', 'keras==2.2.4',…
MosQuan
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With Mamba, pypy cannot find modules installed using pip?

I'm testing using pypy for speeding up the execution time of a Python script I wrote. To install the dependencies of the script, I used both pip (some modules I need are not available via anaconda) and Mamba. When I run the script using pypy…
albus_c
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Can't import WinPty in Mamba/Conda Environment

I'll try to outline what the issue I'm facing in this post: Issue For some reason, the winpty module cannot be imported in the base mamba/conda environment on an AWS virtual machine I have running Windows Server 2016 running on an EC2 instance on…
blue2609
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Mamba installing a package into wrong environment

The background is, I'm responsible for maintaining a fancy Docker image that is used by our team for analytics. It uses a Jupyter notebook image as the base, and then adds various customisations, extra packages, etc. One of the team members recently…
Hong Ooi
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Snakemake takes forever to create conda envs

I am using the --use-conda option to create separate environments for some rules. Whether I am using my own yaml files or snakemake wrappers that download the relevant yaml file, snakemake always gets stuck at creating the first…
justinian482
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Mamba stalls on creating environment from yaml on Ubuntu 22 EC2 instance that works perfectly on local machine

I am trying to spin up a Python web application on an AWS EC2 instance running Ubuntu 22. I am using mamba as a package manager and have the packages written into an environment.yml file. Running mamba env create --file=environment.yml works…
stat_is_quo
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