通过conda安装纯净环境的velocyto.md 1.9 KB
title: 通过conda安装纯净环境的velocyto tags: [] id: '1779' categories:
- - 拟时序
- - 生信 date: 2022-05-01 15:54:51 ---
cellranger
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation
https://www.jianshu.com/p/1e7acde1a318
https://mp.weixin.qq.com/s/TJsdj7qesZGlvmEkNLAy0A
GRCh38_rmsk.gtf.gz：https://genome.ucsc.edu/cgi-bin/hgTables
- cd /opt/cellranger
- wget
- wget
- tar -xzvf cellranger-6.1.2.tar.gz
- tar -xzvf refdata-gex-GRCh38-2020-A.tar.gz
- 下载 GRCh38_rmsk.gtf.gz 上传阿里云盘
- ./aliyunpan
- login
- d GRCh38_rmsk.gtf.gz -saveto /opt/cellranger
- gunzip GRCh38_rmsk.gtf.gz
- export PATH=/opt/cellranger/cellranger-6.1.2:$PATH
- cellranger sitecheck > sitecheck.txt
- cellranger upload xxx@fudan.edu.cn sitecheck.txt
- cellranger testrun --id=tiny
- cellranger upload xxx@fudan.edu.cn tiny/tiny.mri.tgz
- conda create -n velocyto -c conda-forge python=3.7 -y
- conda activate velocyto
- conda install numpy scipy cython numba matplotlib scikit-learn h5py click -y
- pip install pysam
- pip install velocyto
- velocyto --help
- conda install -c bioconda samtools=1.15.1 -y
velocyto
http://velocyto.org/velocyto.py/install/index.html#install