guides:application-installation
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guides:application-installation [14.03.2020 14:03] Teemu Kuulasmaa |
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| - | # How to install applications | ||
| - | There are four different methods to get your favorite application installed on Bioinformatics Center' | ||
| - | |||
| - | ## 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/ | ||
| - | |||
| - | ## 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: | ||
| - | |||
| - | ``` | ||
| - | tar xzf APPLICATION.tar.gz # extract source code | ||
| - | cd APPLICATION # move into the source code directory | ||
| - | ./configure # generate makefiles before compilation | ||
| - | make # compile application | ||
| - | ``` | ||
| - | |||
| - | ## Use conda and configure Bioconda channel | ||
| - | |||
| - | Follow instructions from [[https:// | ||
| - | |||
| - | **The first install Miniconda** | ||
| - | |||
| - | ``` | ||
| - | wget https:// | ||
| - | sh Miniconda3-latest-Linux-x86_64.sh | ||
| - | ``` | ||
| - | |||
| - | **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). | ||
| - | |||
| - | ``` | ||
| - | conda config --add channels defaults | ||
| - | conda config --add channels bioconda | ||
| - | conda config --add channels conda-forge | ||
| - | ``` | ||
| - | |||
| - | **The third install packages** | ||
| - | Any packages from any configured channels can be installed into the current conda environment: | ||
| - | ``` | ||
| - | conda search bwa | ||
| - | conda install bwa | ||
| - | ``` | ||
| - | |||
| - | Or create a new environment and install packages: | ||
| - | |||
| - | ``` | ||
| - | 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.1584187437.txt.gz · Last modified: 14.03.2020 14:03 by Teemu Kuulasmaa