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| ====== Cluster Software ====== | ====== Cluster Software ====== | ||
| - | Operating System: Ubuntu 16.04 LTS | + | Environment Modules are used to allow multiple versions of pieces of software to be installed " |
| - | * Installed on the nodes using PXE and preseeding. | + | To get a list of installed software, issue one of these commands: |
| - | * “Hands-free” install for a new node. | + | |
| + | < | ||
| + | module avail | ||
| + | ml avail | ||
| + | </ | ||
| + | |||
| + | Or take a look in /opt where the naming convention for directories is: | ||
| + | |||
| + | < | ||
| + | / | ||
| + | </ | ||
| + | |||
| + | More details on environment modules can be found on the [[Environment Modules]] page. | ||
| Cluster Resource Management | Cluster Resource Management | ||
| Line 12: | Line 24: | ||
| * From Lawrence Livermore National Laboratory | * From Lawrence Livermore National Laboratory | ||
| * [[https:// | * [[https:// | ||
| - | * Version | + | * Version |
| - | + | ||
| - | Software Available on the Cluster | + | |
| - | + | ||
| - | This is an incomplete list. Look in /usr/local and / | + | |
| In general, and where possible, we recommend that you install the software you want in your own home directory. This gives you complete control over the versions of software and associated packages that you are using. You can use **conda** to manage specific software versions within different environments, | In general, and where possible, we recommend that you install the software you want in your own home directory. This gives you complete control over the versions of software and associated packages that you are using. You can use **conda** to manage specific software versions within different environments, | ||
| - | |||
| - | If you need a later version of these tools, first look at installing the version you want yourself either directly in your home directory or using conda. If that is not possible, or if you have difficulty installing the software you need, please contact one of the system administrators. | ||
| - | |||
| - | * R currently 3.5.1 | ||
| - | * Python 2.7.12 and Python 3.5.2 | ||
| - | * Use python3 to run python 3.5.2 | ||
| - | * Use conda to install a specific version of python for yourself. | ||
| - | * ABYSS | ||
| - | * agalma | ||
| - | * augustus | ||
| - | * bedtools | ||
| - | * blast | ||
| - | * bowtie | ||
| - | * bowtie2 | ||
| - | * bwa | ||
| - | * cufflinks | ||
| - | * eigenstrat | ||
| - | * falcon | ||
| - | * fastqc | ||
| - | * hmmer | ||
| - | * HYPHYMP | ||
| - | * jgil | ||
| - | * matlab | ||
| - | * merlin | ||
| - | * mothur | ||
| - | * plink | ||
| - | * samtools | ||
| - | * SAS | ||
| - | * tophat | ||
| - | * vcftools | ||
cluster_software.1623865589.txt.gz · Last modified: 2021/06/16 13:46 by root
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