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This article is about how to install the Conda package management tool under Linux. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

Conda is a package, dependency and environmental management tool for multiple languages, such as: Python, R, Scala, Java, Javascript, C / C clients, FORTRAN.

Conda download

Search conda Tsinghua directly in the search engine and enter Anaconda | help using mirror station | Open source software image station of Tsinghua University | Tsinghua … Find the "Miniconda installation package can be downloaded from https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/." Click the download page, download the software and install it (miniconda is a lightweight alternative to anaconda, and if you install it, you don't have to install anaconda,miniconda. It's enough for us to install software later, and we don't need to install both.) I installed miniconda. Choose to install the corresponding version according to your own Linux system

Miniconda installation

Install the latest version of the linux version of the example: bash Miniconda2-latest-Linux-x86_64.sh, you may encounter the following prompt:

Please, press ENTER to continue > # Click enter directly here and you can click the spacebar several times until the following line Do you accept the license terms appears. [yes | no] [no] > # enter yes here and click enter#. If you enter an error, such as yess, but cannot delete it, you should press enter and re-enter yes [/ home/you/miniconda2] > # when you encounter this, you can enter directly # the absolute path here refers to the installation path installation finished.Do you wish the installer to initialize Miniconda2in your / home/you/.bashrc of miniconda2? [yes | no] [no] > > # enter yes# here. People who are just beginning to learn had better enter yes. The aim is to let conda automatically configure your environment variable # enter yes. The result is: ~ / .bashrc the configuration information of conda is added in the last few lines of the file here # less ~ / .bashrc. The first line of the extra configuration information is as follows: # added by Miniconda2 4.5.12 installer.Thank you for installing Miniconda2 configuration # this indicates a successful installation # execute the following statement source ~ / .bashrc # after execution There is no prompt for conda-help# has conda help documentation information, which indicates that conda has been installed successfully # it is important to check whether the installation is successful or not, no matter what software is installed! # usage as follows: conda [- h] [- V] command... conda is a tool for managing and deploying applications, environments and packages.Options:.# continues to call the help documentation of the Conda subcommand, such as conda create-- helpconda install-- helpminiconda configuration image.

Because the conda installation software is similar to the R installation package that needs to be installed from the nearest image, the image must be configured after the software installation is successful, but unlike the R installation package, the software is installed once and only needs to be set up once, and then there is no need to set up the image again!

Of course, R language can also write configuration files to achieve the purpose of once setting and permanent use of mirrors.

Conda config-add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/freeconda config-add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgeconda config-add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biocondaconda config-set show_channel_urls yes

Run the above sentence on the linux command line one by one, that is, copy a sentence and press enter, in principle, the setting is successful without any prompt; the configuration information is saved in ~ / .condarc and can be viewed by cat ~ / .condarc!

Create a small environment

Before installing the software, set up a small environment. Do not install the software directly in the current environment of your account.

How do you understand this sentence? For example, you put something An in the storeroom at home, but you can also put in another cabinet, which can continue to store things. This cabinet is like a small storeroom, a small environment, and the environment of the storeroom includes the environment of the cabinet.

You can create a lot of small environment names, some of which are broken, and you can just don't want them, just like if the cabinet is broken, you can throw it away, but if you mess up your account environment, like the storeroom, the cost of recovery will be high.

Conda create-n rna# create a small environment named rnaconda install python=2# install python 2 version # the above two sentences can be equated with one command: conda create-n rna python=2

View the mini environment

Conda info-econda info-- envsconda env list# are all used to view the existing mini-environment name # after running as follows: rna is the newly established mini-environment name $conda info-e # conda environments:#base * / home/you/miniconda2rna / home/you/miniconda2/envs/rna after creating the mini-environment, be sure to enter / activate the mini-environment before installing the software Otherwise, it will be installed in the current account environment. Source activate rna: activate the mini-environment named rna. The successful activation of the environment is shown as: (rna) you 16:49:30 ~, with more user names (rna), enter the mini-environment.

After creating the mini-environment, be sure to enter / activate the mini-environment before installing the software, otherwise it will be installed in the current account environment.

Source activate rna: activate the environment of the small environment named rna

The success of the activation is shown as: (rna) you 16:49:30 ~, with more user names in front of (rna)

Find softwar

Find from within the conda page: http://bioconda.github.io/conda-recipe_index.html

Conda search PACKAGENAME: run the command to find out if it exists

Recommend the first one

Install softwar

Step 1: first check what the software name is from the bioconda image. Not a single letter can be wrong.

Step 2: conda install software name

Step 3: successfully retrieve the software help documentation = = make sure the installation is successful

This is similar to the installation of R package. After installation, you need to library () to confirm that the installation is successful.

Installation method: conda install-y sra-tools trim-galore

Parameter explanation:-y can be either, is to ask whether you agree to install, do not need to manually enter a y, I try to understand the meaning of this sentence; sra-tools trim-galore installation of two software, the default installation of the latest version; note that trim-galore a word can not be wrong, a word can not be wrong, important things said three times!

Specify the software installation version

Conda install numpy=1.11: that is, the installation can vaguely match to numpy version 1.11

Conda install numpy==1.11: that is, to install the exact version with numpy 1.11

Constraint typeSpecificationResult

Fuzzynumpy=1.111.11.0, 1.11.1, 1.11.2, 1.11.18 etc.

Exactnumpy==1.111.11.0

Greater than or equal to "numpy > = 1.11" 1.11.0 or higher

OR "numpy=1.11.11.11.3" 1.11.1, 1.11.3AND "numpy > = 1.8, 1.9, not 2.0

Update softwar

Conda update conda: update conda

Conda update bwa: update bwa; only if bwa has been successfully installed

View installed softwar

Conda list: in the current mini-environment, list all the installed software.

Example:

Source activate rna

Conda list

List all the software installed in the rna Mini Environment

Exit the mini-environment

Conda deactivate: conda exit mini-environment command under linux

Remove the small environment

Conda env remove-name bio-env: delete the mini environment and its contents

Other attention content pip installation

Install python before you can use pip to install python software, such as pip install multiqc

Miniconda installation failed to delete the installation directory. If the installation is in / home/you/miniconda2, execute rm-r / home/you/miniconda2 to delete the information written by conda in the last few lines of ~ / .bashrc (usually the following lines of # added by Miniconda2 4.5.12 installer). If there is no # added by Miniconda2 4.5.12 installer, it means that the information of conda configuration has not been written successfully.

Then follow the above steps to reinstall!

Conda network error

The error is as follows

CondaHTTPError: HTTP 000000 CONNECTION FAILED for url 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.

Actually, I've already set up the mirror image.

Conda config-add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/freeconda config-add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgeconda config-add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biocondaconda config-set show_channel_urls yesconda config-showconda install-y-c bioconda homer

Artificially specified channel can solve bug

Conda install-y-c https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda homerconda installation software often conflicts

In fact, there can not be a perfect tool, conda is very easy to manage multiple software processes, then there must be things that can not be solved, it will be embarrassing that two python software of the same process are based on different versions of python packages.

Solving environment: failedUnsatisfiableError: The following specifications were found to be in conflict:-rsemUse "conda info" to see the dependencies for each package.

There is no good way to install conflicting tools into different subenvironments.

Solving environment: failedPackagesNotFoundError: The following packages are not available from current channels:-salmon-boost=1.64-salmon-libcxx==4.0.0 configuration image error conda: command not found# indicates that conda cannot be found in the environment variable. # error reason: .bashrc does not have PATH configured for conda or source ~ / .bashrc # check method: run echo $PATH Check to see if there is a conda installation path Warning: 'https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge' already in' channels' list. Moving to the top# indicates that this code has been run before. When copying the image configuration statement, there is a replication error. When you need to reconfigure, you need to delete the image configuration file rm ~ / .image # and then reconfigure it. Refer to miniconda configuration image summary.

Install conda and configure a ngs group learning environment in one step

Wget-c https://mirrors.tuna.tsinghua.edu.cn/anaconda/miniconda/Miniconda2-latest-Linux-x86_64.sh# miniconda2 software downloaded successfully bash Miniconda2-latest-Linux-x86_64.sh# encountered yes/no input yes, other direct enter fixed source ~ / .bashrcconda-- help# miniconda2 installed successfully And successfully configured the environment variable conda config-- add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/freeconda config-- add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forgeconda config-- add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/biocondaconda config-- set show_channel_urls yes# configuration image successfully conda create-n rna python=2# successfully created the mini-environment And successfully install the python2 version # every time you set up a mini environment, you have to install a python=2 software that relies on source activate rna# to activate successfully and enter the mini environment. You can install the software conda install-y fastqc# with three done, that is, the installation is successful, otherwise the resubmit command fastqc-help# successfully appears the help document, and the fastqc software is successfully installed with conda install-y sra-tools# with three done, which means the installation is successful. Otherwise, resubmit command prefetch-help# successfully appears help documentation, sra-tools software installation successfully # what software is installed does not mean calling any command-helpsource deactivate# successfully exits the rna Mini Environment # or directly exits the current account Thank you for your reading! This is the end of this article on "how to install Conda package management tools under Linux". I hope the above content can be of some help to you, so that you can learn more knowledge. if you think the article is good, you can share it for more people to see!

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