Trinity
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
Availability and Restrictions
The following versions of Trinity are available on OSC clusters:
Cardinal
Steps on How to Submit Jobs
How to Submit Interactive jobs
There are different ways to submit interactive jobs.
Using sinteractive
You can use the custom tool sinteractive as:
How to Submit, Monitor and Manage Jobs
Submit Jobs
| Use | Torque/Moab Command | Slurm Equivalent |
|---|---|---|
| Submit batch job | qsub <jobscript> |
sbatch <jobscript> |
| Submit interactive job | qsub -I [options] |
|
HOWTO: Use Cron and OSCusage for Regular Emailed Reports
It is possible to utilize Cron and the OSCusage command to send regular usage reports via email
Cron
It is easy to create Cron jobs on the Cardinal and Pitzer clusters at OSC. Cron is a Linux utility which allows the user to schedule a command or script to run automatically at a specific date and time. A cron job is the task that is scheduled.
Shell scripts run as a cron job are usually used to update and modify files or databases; however, they can perform other tasks, for example a cron job can send an email notification.
HOWTO: Manage Access Control List (ACLs)
An ACL (access control list) is a list of permissions associated with a file or directory. These permissions allow you to restrict access to a certain file or directory by user or group.
OSC supports NFSv4 ACL on our home directory and POSIX ACL on our project and scratch file systems. Please see the how to use NFSv4 ACL for home directory ACL management and how to use POSIX ACL for managing ACLs in project and scratch file systems.
Manage profile information
Edit profile
Profile information can be changed by logging in with valid OSC credentials at MyOSC, navigating to the profile page by clicking the display name in the upper right corner of the page, and selecting Edit my profile.
Accessing Parallel R tutorial
This document will guide you on how to launch Rstudio App and acess Parallel R workshop material through OSC onDemand.
Step 1: Log on to https://ondemand.osc.edu. Please see this guide on how to use OnDemand service.
Step 2: Launch Rstudio App
Connectome Workbench
Connectome Workbench is an open source, freely available visualization and analysis tool for neuroimaging data, especially data generated by the Human Connectome Project.
Availability and Restrictions
Versions
Connectome Workbench is available on Pitzer and Cardinal clusters. These are the versions currently available:
LS-PrePost
LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA.
Availability and Restrictions
Versions
The following versions of ls-prepost are available on OSC clusters:
Gaussian
Gaussian is a very popular general purpose electronic structure program. Recent versions can perform density functional theory, Hartree-Fock, Möller-Plesset, coupled-cluster, and configuration interaction calculations among others. Geometry optimizations, vibrational frequencies, magnetic properties, and solution modeling are available. It performs well as black-box software on closed-shell ground state systems.
