conda

安装好后，先安装

conda install gcc_linux-64

conda install gxx_linux-64

conda install gfortran_linux-64

安装R

conda install r

#添加bioconda软件源和国内软件源

conda config --add channels conda-forge

conda config --add channels defaults

conda config --add channels r

conda config --add channels bioconda

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/

conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/

conda config --add channels https://mirrors.ustc.edu.cn/anaconda/pkgs/free/

conda config --add channels https://mirrors.ustc.edu.cn/anaconda/cloud/bioconda/

conda config --set show_channel_urls yes

# 创建环境

conda create -n bioinfo

# To activate this environment, use:

source activate bioinfo

conda create --name py27 python=2.7

#

# To deactivate an active environment, use:

source deactivate

#

##

###

conda install -y pysam ucsc-blat bedtools star  star-fusion tophat circexplorer2 bwa bowtie bowtie2 samtools

conda install -y bioconductor-tcgabiolinks bioconductor-clusterprofiler bioconductor-org.hs.eg.db

-bash-4.1$ conda install -y ucsc-blat

Solving environment: failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/r/linux-64/repodata.json.bz2>

Elapsed: -

An HTTP error occurred when trying to retrieve this URL.

HTTP errors are often intermittent, and a simple retry will get you on your way.

If your current network has https://www.anaconda.com blocked, please file

a support request with your network engineering team.

ConnectTimeout(MaxRetryError("HTTPSConnectionPool(host='repo.anaconda.com', port=443): Max retries exceeded with url: /pkgs/r/linux-64/repodata.json.bz2 (Caused by ConnectTimeoutError(<urllib3.connection.VerifiedHTTPSConnection object at 0x2adfe4215630>, 'Connection to repo.anaconda.com timed out. (connect timeout=9.15)'))"))

解决方案：

-bash-4.1$ vi .condarc

channels:

  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/

  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/

  - https://mirrors.ustc.edu.cn/anaconda/pkgs/free/

  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/

 - defaults (将这一行删除)

show_channel_urls: true

conda install -y soapdenovo2 prinseq kmergenie krona wtdbg abyss