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installing_programs
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| * Sometimes we are a little behind. If you need the latest version you can ask me to upgrade. I usually check with people I know use the program to see if they are OK with upgrading. | * Sometimes we are a little behind. If you need the latest version you can ask me to upgrade. I usually check with people I know use the program to see if they are OK with upgrading. | ||
| - | You are encouraged to install the software that you need into your own home directory (or possibly into a shared directory for the project you are working on). This gives you control of the versions of the software you are using, and when upgrades are made. This is good for reproducibility of results. You can use Conda to install specific versions of Python or R, and associated packages into your own home directory. You can also look at using a (Singularity) container to encapsulate a project or software pipeline - see [[Using Singularity]]. | + | **Since we have moved to using Environment Modules on the cluster, the point about versions is less valid. Once a version of a piece of software is installed as a module it will not be removed, and will therefore remain available to you.** |
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| + | You are encouraged to install the software that you need into your own home directory (or possibly into a shared directory for the project you are working on). This gives you control of the versions of the software you are using, and when upgrades are made. This is good for reproducibility of results. You can use Conda to install specific versions of Python or R, and associated packages into your own home directory. Conda can also install many bioinformatics programs (e.g. STAR, bwa etc.) through the bioconda channel. You can also look at using a (Singularity) container to encapsulate a project or software pipeline - see [[Using Singularity]]. | ||
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| + | You can install miniconda by downloading the installation script here: https:// | ||
| === Installing Ubuntu Packages Locally === | === Installing Ubuntu Packages Locally === | ||
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| make | make | ||
| </ | </ | ||
| + | |||
| + | This first style will build the application in the current directory. You can then run it from where it is, or copy it to a directory from where you usually run locally installed programs (a location that is in your PATH). | ||
| < | < | ||
| - | ./configure -prefix=$HOME | + | ./ |
| make install | make install | ||
| </ | </ | ||
| + | |||
| + | This second style will install the program into $HOME/bin. You can also give a prefix that points to a subdirectory of your home directory, e.g. $HOME/ | ||
| + | |||
| + | If you do not specify the " | ||
| === Installing a Source Package === | === Installing a Source Package === | ||
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| * Perl modules | * Perl modules | ||
| - | * If you have problems you can ask me (chris@statgen.ncsu.edu). | + | |
| + | * In this case you can send e-mail to the system administrators to get the dependency installed using the OS package manager, or possibly from a direct download and install. | ||
| + | | ||
| === Conda === | === Conda === | ||
| Line 72: | Line 85: | ||
| ... | ... | ||
| conda activate r-test | conda activate r-test | ||
| + | </ | ||
| + | |||
| + | To install R 4.0.2 inside a conda environment you can use the command: | ||
| + | |||
| + | < | ||
| + | conda install -c conda-forge r-base=4.0.2 | ||
| </ | </ | ||
installing_programs.1594680490.txt.gz · Last modified: 2020/07/13 18:48 by root
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