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
