【QIIME2】服务器及本地安装QIIME2

服务器

安装包下载链接
https://pan.baidu.com/s/1Ikd_47HHODOqC3Rcx6eJ6Q?pwd=0315 其中db/conda/qiime2-2023.5.tar.gz

mkdir /public1/home/sch4625/.conda/envs/qiime2-2023.5
cd /public1/home/sch4625/.conda/envs/qiime2-2023.5
#新环境安装，将安装包存放于相应路径
tar -xzf /mnt/c/temp/qiime2-2023.5.tar.gz -C /public1/home/sch4625/.conda/envs/qiime2-2023.5
# 激活并初始化环境
conda activate qiime2-2023.5
conda unpack

安装最新版（2024.10）：

conda info
mkdir -p anaconda3/envs/qiime2-amplicon-2024.10
tar -zxvf /public1/home/sch4625/qiime2-amplicon-2024.10.tar.gz -C ./
conda activate qiime2-amplicon-2024.10
conda info --envs
conda activate qiime2-amplicon-2024.10
mv qiime2-amplicon-2024.10 /public/home/sch4625/.conda/emvs
conda activate qiime2-amplicon-2024.10
conda unpack
conda info --envs
qiime2 info
R
qiime --help

[sch4625@ln1%bscc-t6 qiime2-amplicon-2024.10]$ tar -zxvf /public1/home/sch4625/qiime2-amplicon-2024.10.tar.gz -C ./
...
lib/R/library/GenomeInfoDbData/Meta/package.rds
lib/R/library/GenomeInfoDbData/DESCRIPTION
lib/python3.10/site-packages/pynndescent/__pycache__/sparse.sparse_diff-201.py310.2.nbc
lib/python3.10/site-packages/pynndescent/__pycache__/utils.seed-13.py310.1.nbc
lib/python3.10/site-packages/pynndescent/__pycache__/rp_trees.euclidean_random_projection_split-309.py310.1.nbc
lib/python3.10/site-packages/pynndescent/__pycache__/utils.checked_flagged_heap_push-521.py310.nbi
lib/R/library/GenomeInfoDbData/data/specData.rda
lib/python3.10/site-packages/pynndescent/__pycache__/rp_trees.search_flat_bit_tree-1254.py310.nbi
bin/activate
bin/deactivate
bin/conda-unpack
[sch4625@ln1%bscc-t6 qiime2-amplicon-2024.10]$ conda activate qiime2-amplicon-2024.10

EnvironmentNameNotFound: Could not find conda environment: qiime2-amplicon-2024.10
You can list all discoverable environments with `conda info --envs`.

[sch4625@ln1%bscc-t6 qiime2-amplicon-2024.10]$ conda info --envs

# conda environments:
#
NHGNN-DTA              /public1/home/sch4625/.conda/envs/NHGNN-DTA
R                      /public1/home/sch4625/.conda/envs/R
R4.3.1                 /public1/home/sch4625/.conda/envs/R4.3.1
SSM                    /public1/home/sch4625/.conda/envs/SSM
SSR                    /public1/home/sch4625/.conda/envs/SSR
UniKP                  /public1/home/sch4625/.conda/envs/UniKP
af3                    /public1/home/sch4625/.conda/envs/af3
antismash              /public1/home/sch4625/.conda/envs/antismash
bigslice               /public1/home/sch4625/.conda/envs/bigslice
enzymecage             /public1/home/sch4625/.conda/envs/enzymecage
interproscan           /public1/home/sch4625/.conda/envs/interproscan
iprscan                /public1/home/sch4625/.conda/envs/iprscan
mash                   /public1/home/sch4625/.conda/envs/mash
py27                   /public1/home/sch4625/.conda/envs/py27
py36                   /public1/home/sch4625/.conda/envs/py36
py37                   /public1/home/sch4625/.conda/envs/py37
py376                  /public1/home/sch4625/.conda/envs/py376
py37_env               /public1/home/sch4625/.conda/envs/py37_env
python37_env           /public1/home/sch4625/.conda/envs/python37_env
python38               /public1/home/sch4625/.conda/envs/python38
qiime2-2023.5          /public1/home/sch4625/.conda/envs/qiime2-2023.5
qiime2-amplicon-2024.2   /public1/home/sch4625/.conda/envs/qiime2-amplicon-2024.2
r_431                  /public1/home/sch4625/.conda/envs/r_431
sch4625                /public1/home/sch4625/.conda/envs/sch4625
wuxm                   /public1/home/sch4625/.conda/envs/wuxm
                       /public1/home/sch4625/miniconda3
                       /public1/home/sch4625/miniconda3/envs/antismash-test
                       /public1/home/sch4625/miniconda3/envs/py38
base                   /public1/soft/miniforge/24.11
py310                  /public1/soft/miniforge/24.11/envs/py310

[sch4625@ln1%bscc-t6 qiime2-amplicon-2024.10]$ conda activate qiime2-amplicon-2024.10

EnvironmentNameNotFound: Could not find conda environment: qiime2-amplicon-2024.10
You can list all discoverable environments with `conda info --envs`.

[sch4625@ln1%bscc-t6 qiime2-amplicon-2024.10]$ cd ..
[sch4625@ln1%bscc-t6 envs]$ mv qiime2-
qiime2-2023.5/           qiime2-amplicon-2024.10/ 
[sch4625@ln1%bscc-t6 envs]$ mv qiime2-amplicon-2024.10 /public1/home/sch4625/.conda/envs/
[sch4625@ln1%bscc-t6 envs]$ conda activate qiime2-amplicon-2024.10
(qiime2-amplicon-2024.10) [sch4625@ln1%bscc-t6 envs]$ conda unpack
(qiime2-amplicon-2024.10) [sch4625@ln1%bscc-t6 envs]$ conda info --envs

# conda environments:
#
NHGNN-DTA              /public1/home/sch4625/.conda/envs/NHGNN-DTA
R                      /public1/home/sch4625/.conda/envs/R
R4.3.1                 /public1/home/sch4625/.conda/envs/R4.3.1
SSM                    /public1/home/sch4625/.conda/envs/SSM
SSR                    /public1/home/sch4625/.conda/envs/SSR
UniKP                  /public1/home/sch4625/.conda/envs/UniKP
af3                    /public1/home/sch4625/.conda/envs/af3
antismash              /public1/home/sch4625/.conda/envs/antismash
bigslice               /public1/home/sch4625/.conda/envs/bigslice
enzymecage             /public1/home/sch4625/.conda/envs/enzymecage
interproscan           /public1/home/sch4625/.conda/envs/interproscan
iprscan                /public1/home/sch4625/.conda/envs/iprscan
mash                   /public1/home/sch4625/.conda/envs/mash
py27                   /public1/home/sch4625/.conda/envs/py27
py36                   /public1/home/sch4625/.conda/envs/py36
py37                   /public1/home/sch4625/.conda/envs/py37
py376                  /public1/home/sch4625/.conda/envs/py376
py37_env               /public1/home/sch4625/.conda/envs/py37_env
python37_env           /public1/home/sch4625/.conda/envs/python37_env
python38               /public1/home/sch4625/.conda/envs/python38
qiime2-2023.5          /public1/home/sch4625/.conda/envs/qiime2-2023.5
qiime2-amplicon-2024.10 * /public1/home/sch4625/.conda/envs/qiime2-amplicon-2024.10
qiime2-amplicon-2024.2   /public1/home/sch4625/.conda/envs/qiime2-amplicon-2024.2
r_431                  /public1/home/sch4625/.conda/envs/r_431
sch4625                /public1/home/sch4625/.conda/envs/sch4625
wuxm                   /public1/home/sch4625/.conda/envs/wuxm
                       /public1/home/sch4625/miniconda3
                       /public1/home/sch4625/miniconda3/envs/antismash-test
                       /public1/home/sch4625/miniconda3/envs/py38
base                   /public1/soft/miniforge/24.11
py310                  /public1/soft/miniforge/24.11/envs/py310

(qiime2-amplicon-2024.10) [sch4625@ln1%bscc-t6 envs]$ qiime info
System versions
Python version: 3.10.14
QIIME 2 release: 2024.10
QIIME 2 version: 2024.10.1
q2cli version: 2024.10.1

Installed plugins
alignment: 2024.10.0
composition: 2024.10.0
cutadapt: 2024.10.0
dada2: 2024.10.0
deblur: 2024.10.0
demux: 2024.10.0
diversity: 2024.10.0
diversity-lib: 2024.10.0
emperor: 2024.10.0
feature-classifier: 2024.10.0
feature-table: 2024.10.0
fragment-insertion: 2024.10.0
longitudinal: 2024.10.0
metadata: 2024.10.0
phylogeny: 2024.10.0
quality-control: 2024.10.0
quality-filter: 2024.10.0
rescript: 2024.10.0
sample-classifier: 2024.10.0
stats: 0+unknown
taxa: 2024.10.0
types: 2024.10.0
vizard: 0.0.1.dev0
vsearch: 2024.10.0

Application config directory
/public1/home/sch4625/.conda/envs/qiime2-amplicon-2024.10/var/q2cli

Config
Config Source: /public1/home/sch4625/.conda/envs/qiime2-amplicon-2024.10/etc/qiime2_config.toml

Getting help
To get help with QIIME 2, visit https://qiime2.org
To get help with configuring and/or understanding QIIME 2 parallelization, visit https://use.qiime2.org/en/latest/references/parallel-configuration.html

(qiime2-amplicon-2024.10) [sch4625@ln1%bscc-t6 UNITE]$ R --version
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

(qiime2-amplicon-2024.10) [sch4625@ln1%bscc-t6 envs]$ qiime --help

本地WSL2

本地安装最新版（2024.10）：

conda deactivate
conda info
mkdir -p anaconda3/envs/qiime2-amplicon-2024.10
conda activate qiime2-amplicon-2024.10
R
qiime info
conda unpack
conda envs --envs
conda info --envs
conda envs --envs
conda unpack
conda envs --envs
conda info --envs
R
qiime --help

本地安装：

mkdir /home/yangzy/anaconda3/envs/qiime2-2024.2
cd /home/yangzy/anaconda3/envs/qiime2-2024.2
#新环境安装，将安装包存放于相应路径
tar -xzf /mnt/d/WSL/qiime2-amplicon-2024.2.tar.gz -C /home/yangzy/anaconda3/envs/qiime2-2024.2
tar -xzf /mnt/f/WSL_old/qiime2-2023.5.tar.gz -C /home/yangzy/anaconda3/envs/qiime2-2023.5
# 激活并初始化环境
conda activate qiime2-2024.2
conda unpack

参考：
[1]QIIME 2教程. 01简介和安装 Introduction & Install(2023.5)
[2]https://conda.github.io/conda-pack/
[3]conda-unpack