通过conda安装纯净环境的velocyto

发布于 2022-05-01  127 次阅读


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 <Cell Ranger>
  • wget <References>
  • 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 [email protected] sitecheck.txt
  • cellranger testrun --id=tiny
  • cellranger upload [email protected] tiny/tiny.mri.tgz

velocyto

http://velocyto.org/

http://velocyto.org/velocyto.py/install/index.html#install

  • 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

一枚爱好探索的医学生