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installing_programs
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| * You may want to stick with a specific version. | * You may want to stick with a specific version. | ||
| * 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. | ||
| + | |||
| + | **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.** | ||
| 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]]. | 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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| * Sometimes R (or Python, or Perl) packages depend on software libraries that are not other R (or Python, or Perl) packages. | * Sometimes R (or Python, or Perl) packages depend on software libraries that are not other R (or Python, or Perl) packages. | ||
| * 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. | * 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. | ||
| - | * If you have problems with an install you can ask me (chris@statgen.ncsu.edu). Send e-mail describing what you have tried and what happened. | + | * If you have problems with an install you can ask send a help request to help@sciences.ncsu.edu). Send e-mail describing what you have tried and what happened. |
| === Conda === | === Conda === | ||
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| ... | ... | ||
| 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.1600280772.txt.gz ยท Last modified: 2020/09/16 14:26 by root
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