mamba 基本使用
1 mamba 介紹
Note
現代生物資訊工作流程（特別是 nf-core）已全面建議使用 mamba 取代 conda 進行求解，沒接觸過 conda 的人可參閱 conda教學。
mamba 是一個高效、與 conda 完全相容的套件與環境管理工具，由 QuantStack 開發。它的目標是提供比 conda 更快、更穩定、更具可預測性的套件求解（dependency solving）能力，同時保留所有 conda 的使用方式與指令格式。
1.1 為什麼需要 mamba？
傳統的 conda 在進行環境建立或安裝套件時，常因依賴衝突（dependency conflicts）導致求解時間很長（數分鐘到數十分鐘）
mamba 使用 C++ 實作的高速依賴求解器（libsolv），大幅提升速度與穩定性，使許多原本需要 1–10 分鐘的 conda 操作縮短到 數秒完成。
| 功能 | conda | mamba |
|---|---|---|
| 依賴求解速度 | 慢（Python solver） | 極快（libsolv） |
| 下載方式 | 單線程 | 多線程並行下載 |
| 相容性 | 完全支援 | 100% 相容 conda |
| 生信 pipeline 推薦度 | 普通 | 強烈推薦（nf-core / Snakemake） |
1.2 mamba 的核心特色
- 超高速的依賴求解器
- 與 conda 指令相同，僅需將
conda換成mamba - 支援與 conda 共存（Miniforge 已預設內建 mamba）
- 多線程下載（parallel downloads）
- 更清楚的錯誤訊息
2 mamba 安裝（直接安裝 Miniforge）
直接安裝 Miniforge，即包含 mamba，也可查閱 mamba 官方下載指南
3 mamba –version (版本)
使用 --version 參數確認 conda 是否成功安裝，並顯示版本號。
mamba --version2.4.04 mamba create (建立環境)
-n 代表創建環境名稱， -y 代表直接確認下載 (yes)
mamba create -n myenv python=3.10 -y5 mamba activate (啟動環境)
mamba activate myenv6 mamba install (安裝套件)
mamba install numpy -y7 mamba remove (移除套件)
mamba remove numpy -y8 mamba deactivate (離開環境)
mamba deactivate9 mamba env (環境相關指令)
查看環境相關指令
mamba env --helpClick to expand
See `mamba/micromamba env --help`
/home/benson/miniforge3/bin/mamba env [OPTIONS] [SUBCOMMANDS]
OPTIONS:
-h, --help Print this help message and exit
Configuration options:
--rc-file FILE1 FILE2...
Paths to the configuration files to use
--no-rc Disable the use of configuration files
--no-env Disable the use of environment variables
Global options:
-v, --verbose Set verbosity (higher verbosity with multiple -v, e.g. -vvv)
--log-level ENUM:value in {critical->5,debug->1,error->4,info->2,off->6,trace->0,warning->3} OR {5,1,4,2,6,0,3}
Set the log level
-q, --quiet Set quiet mode (print less output)
-y, --yes Automatically answer yes on prompted questions
--json Report all output as json
--offline Force use cached repodata
--dry-run Only display what would have been done
--download-only Only download and extract packages, do not link them into
environment.
--experimental Enable experimental features
--use-uv Whether to use uv for installing pip dependencies. Defaults to
false.
Prefix options:
-r, --root-prefix PATH Path to the root prefix
-p, --prefix PATH Path to the target prefix
--relocate-prefix PATH
Path to the relocation prefix
-n, --name NAME Name of the target prefix
SUBCOMMANDS:
list List known environments
create Create new environment (pre-commit.com compatibility alias for
'micromamba create')
export Export environment
remove Remove an environment
update Update an environment9.1 mamba env export (匯出環境YAML)
mamba env export > output.yaml9.2 mamba env create (由YAML檔建立環境)
-f 指定檔名，創建環境名稱為 YAML 中 name 參數
mamba env create -f ./mamba/mamba-envs.yaml -y9.3 mamba env remove (刪除環境)
mamba env remove -n myenv -y9.4 mamba env list (列出所有環境)
* 為目前環境
mamba env list Name Active Path
─────────────────────────────────────────────────────────────────────────
base /home/benson/miniforge3
bio-tools * /home/benson/miniforge3/envs/bio-tools10 mamba list
列出套件相關資源
10.1 mamba list (查看套件來源)
mamba listList of packages in environment: "/home/benson/miniforge3/envs/bio-tools"
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_python_abi3_support 1.0 hd8ed1ab_2 conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.15.1 hb03c661_0 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
anyio 4.12.0 pyhcf101f3_0 conda-forge
argon2-cffi 25.1.0 pyhd8ed1ab_0 conda-forge10.2 mamba list –explicit (詳細套件url)
列出詳細 url
mamba list --explicitList of packages in environment: "/home/benson/miniforge3/envs/bio-tools"
https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
https://conda.anaconda.org/conda-forge/noarch/_python_abi3_support-1.0-hd8ed1ab_2.conda
https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2
https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.1-hb03c661_0.conda
https://conda.anaconda.org/conda-forge/noarch/annotated-types-0.7.0-pyhd8ed1ab_1.conda
https://conda.anaconda.org/conda-forge/noarch/anyio-4.12.0-pyhcf101f3_0.conda
https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-25.1.0-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/linux-64/argon2-cffi-bindings-25.1.0-py314h5bd0f2a_2.conda
https://conda.anaconda.org/conda-forge/noarch/arrow-1.4.0-pyhcf101f3_0.conda
https://conda.anaconda.org/conda-forge/noarch/asttokens-3.0.1-pyhd8ed1ab_0.conda
https://conda.anaconda.org/conda-forge/noarch/async-lru-2.0.5-pyh29332c3_0.conda11 環境資訊
完整記錄當前執行的 Conda 環境，有助於分析重現、版本追蹤與錯誤排查。
echo "======================================="
echo "Mamba Environment: $(mamba env list | grep '*' | awk '{print $1}')"
echo "======================================="
mamba list=======================================
Mamba Environment: bio-tools
=======================================
List of packages in environment: "/home/benson/miniforge3/envs/bio-tools"
Name Version Build Channel
───────────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_python_abi3_support 1.0 hd8ed1ab_2 conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
alsa-lib 1.2.15.1 hb03c661_0 conda-forge
annotated-types 0.7.0 pyhd8ed1ab_1 conda-forge
anyio 4.12.0 pyhcf101f3_0 conda-forge
argon2-cffi 25.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 25.1.0 py314h5bd0f2a_2 conda-forge12 mamba –help
顯示 mamba 的主要參數與使用說明，適合作為快速查詢用途。
mamba --helpClick to expand
Version: 2.4.0
/home/benson/miniforge3/bin/mamba [OPTIONS] [SUBCOMMAND]
OPTIONS:
-h, --help Print this help message and exit
--version
Configuration options:
--rc-file FILE1 FILE2...
Paths to the configuration files to use
--no-rc Disable the use of configuration files
--no-env Disable the use of environment variables
Global options:
-v, --verbose Set verbosity (higher verbosity with multiple -v, e.g. -vvv)
--log-level ENUM:value in {critical->5,debug->1,error->4,info->2,off->6,trace->0,warning->3} OR {5,1,4,2,6,0,3}
Set the log level
-q, --quiet Set quiet mode (print less output)
-y, --yes Automatically answer yes on prompted questions
--json Report all output as json
--offline Force use cached repodata
--dry-run Only display what would have been done
--download-only Only download and extract packages, do not link them into
environment.
--experimental Enable experimental features
--use-uv Whether to use uv for installing pip dependencies. Defaults to
false.
Prefix options:
-r, --root-prefix PATH Path to the root prefix
-p, --prefix PATH Path to the target prefix
--relocate-prefix PATH
Path to the relocation prefix
-n, --name NAME Name of the target prefix
SUBCOMMANDS:
shell Generate shell init scripts
create Create new environment
install Install packages in active environment
update Update packages in active environment
repoquery Find and analyze packages in active environment or channels
remove, uninstall Remove packages from active environment
list List packages in active environment
package Extract a package or bundle files into an archive
clean Clean package cache
config Configuration of micromamba
info Information about micromamba
constructor Commands to support using micromamba in constructor
env See `mamba/micromamba env --help`
activate Activate an environment
run Run an executable in an environment
ps Show, inspect or kill running processes
auth Login or logout of a given host
search Find packages in active environment or channels
This is equivalent to `repoquery search` command