The CyVerse App Store is currently being restructured, and apps are being moved to an HPC environment. During this transition, users may occasionally be unable to locate or use apps that are listed in our tutorials. In many cases, these apps can be located by searching them using the search bar at the top of the Apps window in the DE. To increase the chance for search success, try not searching the entire app name and version number but only the portion that refers to the app's function or origin (e.g. 'SOAPdenovo' instead of 'SOAPdenovo-Trans 1.01').
Also, as part of the 2.8 app categorization, a number of apps were deprecated and are no longer available, and there is no longer an Archive category. You can search for a suitable replacement in the List of Applications in this window, or search on an app name or tool used for an app in the Apps window search field. If you need an app reinstated, please contact firstname.lastname@example.org.
The DE Quick Start tutorial provides an introduction to basic DE functionality and navigation.
Please work through the tutorial and add your comments on the bottom of this page. Or send comments per email to email@example.com. Thank you.
This app accepts a folder as an input and generates a table that consists of mapped, unmapped and total mapped reads using samtools command
- A CyVerse account. (Register for an CyVerse account here - user.cyverse.org)
- Input file(s)
- Input folder name: A folder consisting of sorted bam files
The test data for testing QUAST in here : /iplant/home/shared/iplantcollaborative/example_data/samtools_mapping_stats
- Input file: samtools_mapping_stats
Successful execution of the Samtools_mapping_stats-1.0 will create a output file - "bam_stats.txt"