Comments (6)
gmgitx
commented on July 30, 2024
安装😊
#通过使用conda安装（Miniconda已经安装，装的3），解决软解依赖问题
#要求通过Miniconda安装Python 3 ，okay先查看目前环境所用python版本
conda search "^python$"
#此处省去上上边现实的很多，part:
python 3.6.4 hc3d631a_1 pkgs/main
python 3.6.4 hc3d631a_3 pkgs/main
python 3.6.5 hc3d631a_0 pkgs/main
python 3.6.5 hc3d631a_1 pkgs/main
python 3.6.5 hc3d631a_2 pkgs/main
python 3.6.6 hc3d631a_0 pkgs/main
python 3.7.0 hc3d631a_0 pkgs/main
#1是要求，2是现有，so, 准备装个3.7的虚拟环境。一定要指定python版本，否则直接global python版本。:confused:那其它的呢？并且把安装的依赖包全部放在global env下面，不利于你对python虚拟环境的隔离？？？
#创建环境
conda create --name EnvPy37 python=3.7 #安装3.7是因为亚版本
#检查已有环境
conda info --envs
#激活环境
source activate EnvPy37
#安装Snakemake
conda install -c bioconda -c conda-forge snakemake
😕安装过程中需要确认更新一些包，有pip，我需要换个确定一下是否影响到了另一个环境的版本
The following packages will be UPDATED:_
ca-certificates: 2018.03.07-0 --> 2018.8.24-ha4d7672_0 conda-forge
certifi: 2018.8.24-py37_1 --> 2018.8.24-py36_1 conda-forge
openssl: 1.0.2p-h14c3975_0 --> 1.0.2p-h470a237_0 conda-forge
pip: 10.0.1-py37_0 --> 18.0-py36_1 conda-forge
setuptools: 40.2.0-py37_0 --> 40.2.0-py36_0 conda-forge
wheel: 0.31.1-py37_0 --> 0.31.1-py36_1 conda-forge
The following packages will be DOWNGRADED:_
python: 3.7.0-hc3d631a_0 --> 3.6.6-h5001a0f_0 conda-forge
Proceed ([y]/n)? y
验证得知，这种情况下，虚拟环境之间，互不影响:stuck_out_tongue:
#退出环境
source deactivate
使用😊
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gmgitx
commented on July 30, 2024
Writing a RNA-Seq workflow with snakemake
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gmgitx
commented on July 30, 2024
Snakemake是用Python3写的一个工具，模仿makefile的格式，注意各个步骤的依赖关系，先后顺序。
三个重要概念：
- input files， 定义了输入文件
- output files， 定义了输出文件
- rules，定义了输入文件生成输出文件过程
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gmgitx
commented on July 30, 2024
如何半路使用？
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gmgitx
commented on July 30, 2024
Snakemake Pipelines
#snakeparse
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gmgitx
commented on July 30, 2024
Snakemake—a scalable bioinformatics workflow engine
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