Day3——庚帅博方便面
2019-12-18 本文已影响0人
lconan
1.下载miniconda
1.1 确定Linux版本
uname[option]: print certain system information -a: print all information
bio01@VM-0-10-ubuntu:~$ uname -a
Linux VM-0-10-ubuntu 4.15.0-54-generic #58-Ubuntu SMP Mon Jun 24 10:55:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
1.2 在biosoft目录下使用wget命令下载安装脚本
bio01@VM-0-10-ubuntu:~$ cd ~/biosoft
bio01@VM-0-10-ubuntu:~/biosoft$ ls
bio01@VM-0-10-ubuntu:~/biosoft$ wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
--2019-12-18 14:03:49-- https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda3-latest-Linux-x86_64.sh
Resolving mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)... 101.6.8.193, 2402:f000:1:408:8100::1
Connecting to mirrors.tuna.tsinghua.edu.cn (mirrors.tuna.tsinghua.edu.cn)|101.6.8.193|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 71785000 (68M) [application/octet-stream]
Saving to: ‘Miniconda3-latest-Linux-x86_64.sh’
Miniconda3-latest-Linux-x86_64.sh 100%[===========================================================>] 68.46M 3.54MB/s in 40s
1.3 安装
bio01@VM-0-10-ubuntu:~/biosoft$ bash Miniconda3-latest-Linux-x86_64.sh
Welcome to Miniconda3 4.7.12
In order to continue the installation process, please review the license
agreement.
Please, press ENTER to continue
>>>
===================================
Miniconda End User License Agreement
===================================
Copyright 2015, Anaconda, Inc.
All rights reserved under the 3-clause BSD License:
//.......省略
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> For changes to take effect, close and re-open your current shell. <==
If you'd prefer that conda's base environment not be activated on startup,
set the auto_activate_base parameter to false:
conda config --set auto_activate_base false
Thank you for installing Miniconda3!
提示也说了需要重启shell
这里按照教程重新加载.bashrc
bio01@VM-0-10-ubuntu:~/biosoft$ source ~/.bashrc
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda
usage: conda [-h] [-V] command ...
并且经验证，前面出现（base）【默认环境？】并出现帮助信息说明已经可以使用
1.4 添加channels
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda config --set show_channel_urls yes
2. 使用conda
2.1 查看已安装软件conda list
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda list
# packages in environment at /home/bio01/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
asn1crypto 1.2.0 py37_0 defaults
ca-certificates 2019.10.16 0 defaults
certifi 2019.9.11 py37_0 defaults
cffi 1.13.0 py37h2e261b9_0 defaults
chardet 3.0.4 py37_1003 defaults
conda 4.7.12 py37_0 defaults
conda-package-handling 1.6.0 py37h7b6447c_0 defaults
cryptography 2.8 py37h1ba5d50_0 defaults
idna 2.8 py37_0 defaults
libedit 3.1.20181209 hc058e9b_0 defaults
libffi 3.2.1 hd88cf55_4 defaults
libgcc-ng 9.1.0 hdf63c60_0 defaults
libstdcxx-ng 9.1.0 hdf63c60_0 defaults
ncurses 6.1 he6710b0_1 defaults
openssl 1.1.1d h7b6447c_3 defaults
pip 19.3.1 py37_0 defaults
pycosat 0.6.3 py37h14c3975_0 defaults
pycparser 2.19 py37_0 defaults
pyopenssl 19.0.0 py37_0 defaults
pysocks 1.7.1 py37_0 defaults
python 3.7.4 h265db76_1 defaults
readline 7.0 h7b6447c_5 defaults
requests 2.22.0 py37_0 defaults
ruamel_yaml 0.15.46 py37h14c3975_0 defaults
setuptools 41.4.0 py37_0 defaults
six 1.12.0 py37_0 defaults
sqlite 3.30.0 h7b6447c_0 defaults
tk 8.6.8 hbc83047_0 defaults
tqdm 4.36.1 py_0 defaults
urllib3 1.24.2 py37_0 defaults
wheel 0.33.6 py37_0 defaults
xz 5.2.4 h14c3975_4 defaults
yaml 0.1.7 had09818_2 defaults
zlib 1.2.11 h7b6447c_3 defaults
2.2 搜索软件 conda search '软件名'
Q:
search的范围，是否是存在于channels中的？
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda search fastqc
Loading channels: done
# Name Version Build Channel
fastqc 0.10.1 0 anaconda/cloud/bioconda
fastqc 0.10.1 1 anaconda/cloud/bioconda
fastqc 0.11.2 1 anaconda/cloud/bioconda
fastqc 0.11.2 pl5.22.0_0 anaconda/cloud/bioconda
fastqc 0.11.3 0 anaconda/cloud/bioconda
fastqc 0.11.3 1 anaconda/cloud/bioconda
fastqc 0.11.4 0 anaconda/cloud/bioconda
fastqc 0.11.4 1 anaconda/cloud/bioconda
fastqc 0.11.4 2 anaconda/cloud/bioconda
fastqc 0.11.5 1 anaconda/cloud/bioconda
fastqc 0.11.5 4 anaconda/cloud/bioconda
fastqc 0.11.5 pl5.22.0_2 anaconda/cloud/bioconda
fastqc 0.11.5 pl5.22.0_3 anaconda/cloud/bioconda
fastqc 0.11.6 2 anaconda/cloud/bioconda
fastqc 0.11.6 pl5.22.0_0 anaconda/cloud/bioconda
fastqc 0.11.6 pl5.22.0_1 anaconda/cloud/bioconda
fastqc 0.11.7 4 anaconda/cloud/bioconda
fastqc 0.11.7 5 anaconda/cloud/bioconda
fastqc 0.11.7 6 anaconda/cloud/bioconda
fastqc 0.11.7 pl5.22.0_0 anaconda/cloud/bioconda
fastqc 0.11.7 pl5.22.0_2 anaconda/cloud/bioconda
fastqc 0.11.8 0 anaconda/cloud/bioconda
fastqc 0.11.8 1 anaconda/cloud/bioconda
fastqc 0.11.8 2 anaconda/cloud/bioconda
2.3 安装/删除
安装软件
conda install (软件名)
安装特定版本软件
conda install '软件名'='版本号'
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda install fastqc=0.11.7 -y
Collecting package metadata (current_repodata.json): done
Solving environment: done
##省略..........
Verifying transaction: done
Executing transaction: done
删除软件
conda remove (software name)
3. conda 环境
查看存在的环境
conda info --envs或者conda env list
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio01/miniconda3
看到只有一个环境，"*"指示默认环境
（Q：还是current activated环境，待查，倾向于current activated env）
建立一个名叫rnaseq的conda环境，指定python版本是3，安装软件fastqc、trimmomatic
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda create -n rna-seq python=3 fastqc trimmomatic -y
Collecting package metadata (current_repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /home/bio01/miniconda3/envs/rna-seq
added / updated specs:
- fastqc
- python=3
- trimmomatic
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | main 2 KB https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
certifi-2019.11.28 | py38_0 148 KB
#省略.......
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate rna-seq
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda info --envs
# conda environments:
#
base * /home/bio01/miniconda3
rna-seq /home/bio01/miniconda3/envs/rna-seq
此时默认环境还是base
conda activate rna-seq *会指向rna-seq；prompt也由base变为rna-seq
(base) bio01@VM-0-10-ubuntu:~/biosoft$ conda activate rna-seq
(rna-seq) bio01@VM-0-10-ubuntu:~$ conda env list
# conda environments:
#
base /home/bio01/miniconda3
rna-seq * /home/bio01/miniconda3/envs/rna-seq
运行fastqc
(rna-seq) bio01@VM-0-10-ubuntu:~$ fastqc
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208)
at java.desktop/java.awt.Window.<init>(Window.java:548)
at java.desktop/java.awt.Frame.<init>(Frame.java:423)
at java.desktop/java.awt.Frame.<init>(Frame.java:388)
at java.desktop/javax.swing.JFrame.<init>(JFrame.java:180)
at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63)
at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:332)
报错待解决
