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guides:application-installation [24.09.2019 17:45]
Teemu Kuulasmaa created 		guides:application-installation [14.03.2020 14:03] (current)
Teemu Kuulasmaa
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 # How to install applications # How to install applications
  
-There are four different methods to get your favorite application installed on servers. +There are four different methods to get your favorite application installed on Bioinformatics Center's servers. The three first options doesn't require system administrator privileges and can be carried out by user.
  
-# 1. Download binaries+## Download binaries
  
 You can always download already compiled binaries from Internet. All you need to do is extract downloaded archive file (e.g. *.gz, *.zip) files to any directory (e.g. $HOME/bin/). Please make sure that the binaries have been compiled for appropriate platform e.g. "linux 64-bit", "linux x64".  You can always download already compiled binaries from Internet. All you need to do is extract downloaded archive file (e.g. *.gz, *.zip) files to any directory (e.g. $HOME/bin/). Please make sure that the binaries have been compiled for appropriate platform e.g. "linux 64-bit", "linux x64". 
  
-# 2. Download source code and compile+## Download source code and compile
  
 Always ready-made binaries are not available or you need to recompile application from the source code again. In this case download the source code to the server, extract source code and follow installation instructions. Normally you will find compilation and installation instructions from among the downloaded files (search for README or INSTALLATION files). The most often you just need to do something like this: Always ready-made binaries are not available or you need to recompile application from the source code again. In this case download the source code to the server, extract source code and follow installation instructions. Normally you will find compilation and installation instructions from among the downloaded files (search for README or INSTALLATION files). The most often you just need to do something like this:
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 ./configure # generate makefiles before compilation ./configure # generate makefiles before compilation
 make # compile application make # compile application
-´´´+```
  
-# 3. Use conda and configure Bioconda channel+## Use conda and configure Bioconda channel
  
 Follow instructions from [[https://bioconda.github.io/user/install.html#install-conda|Bioconda]]. In short this procedure requires Miniconda installation, channels configuration and application installation. Follow instructions from [[https://bioconda.github.io/user/install.html#install-conda|Bioconda]]. In short this procedure requires Miniconda installation, channels configuration and application installation.
  
 **The first install Miniconda**  **The first install Miniconda** 
 +
 ``` ```
 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
 sh Miniconda3-latest-Linux-x86_64.sh sh Miniconda3-latest-Linux-x86_64.sh
-´´´+```
  
 **The second set up channels** **The second set up channels**
 After installing conda you will need to add the bioconda channel as well as the other channels bioconda depends on. It is important to add them in this order so that the priority is set correctly (that is, conda-forge is highest priority). After installing conda you will need to add the bioconda channel as well as the other channels bioconda depends on. It is important to add them in this order so that the priority is set correctly (that is, conda-forge is highest priority).
 +
 ``` ```
 conda config --add channels defaults conda config --add channels defaults
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 conda install bwa conda install bwa
 ``` ```
 +
 Or create a new environment and install packages: Or create a new environment and install packages:
 +
 ``` ```
 conda create -n aligners bwa  conda create -n aligners bwa 
 ``` ```
 +
 +## Request system wide install
 +
 +If you prefer to have system wide installation of you favorite application you need to send software installation request to bioinformatics@uef.fi. The system wide installation requires system administrator privileges. 
guides/application-installation.1569336302.txt.gz · Last modified: 29.10.2019 15:10 (external edit)

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