lefse安装笔记

ice-melt

lefse 安装

# lefse 安装依赖r>3.5和python>3.7环境，这里使用python3.8,r3.5
conda create -n lefse112 -y python=3.8 pip=22.0.4 r-base=3.5
conda activate lefse112
# 使用 conda 安装一直报环境错误，这里使用pip安装
pip install lefse==1.1.2

# 安装依赖的R包
conda install r-survival r-mvtnorm r-modeltools r-coin r-mass -y -c conda-forge

环境记录

~/.condarc
channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
  - defaults

~/.config/pip/pip.conf
[global]
index-url = https://mirrors.aliyun.com/pypi/simple/

[install]
trusted-host = mirrors.aliyun.com

# 更新conda
conda update -n base -c defaults conda

安装后验证R环境

(lefse) lx@anneng01[13:45:08]:~$R --version
R version 3.5.1 (2018-07-02) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-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
http://www.gnu.org/licenses/.

(lefse) lx@anneng01[13:45:08]:~$R

报错
/ceph_disk3/lx/miniconda3/envs/lefse/lib/R/bin/exec/R: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory

原因：libreadline.so.6 更新了，将7软连到6即可

cd /lib/x86_64-linux-gnu/
sudo ln -s libreadline.so.7.0 libreadline.so.6