- CPT Dockerized GMOD Stack Demoed at GMOD2016 July 18, 2016 - At GMOD2016, Eric Rasche demoed the CPT’s completely dockerized GMOD stack. Up" @Eric_Rasche on Docker Compose for #usegalaxy, @apollo_bbop, Chado, and @usejbrowse all in a single docker image. #livedemo #GMOD2016— The Tweet Of GMOD (@gmodproject) July 1, 2016 The demo covered the use of “Docker” images which encapsulate complex services and dependencies and networking intoLearn More...
- Beta for Phage Annotation Pipeline July 13, 2016 - We’d like to announce a beta for the Phage Annotation Pipeline! If you are interested, please email esr@tamu.edu to get started! The documentation is available online, but we are granting access on a one-by-one basis during the beta, in order that we can have get in touch to find and fix any bugs you encounter. TheLearn More...
- Galaxy Tool News: JBrowse-in-Galaxy v0.5 released March 23, 2016 - The latest version of my JBrowse Galaxy wrapper (TAMU, Public) has been released. It is a smaller release, adding support for updating existing JBrowse instances with new data. Additionally a couple more configuration options have been exposed to end users. You can read more about it in the GitHub Pull Request.
- Analysis with PAUSE3 – 2016 Edition February 18, 2016 - How to Analyze Your Data with PAUSE3 Once you’ve run your analysis in PAUSE, you may be wondering how to interpret the plots you receive. This short guide should assist you in just that. Good Results After running PAUSE Plotter on raw sequencing data, good quality data will produce output that looks like the following:Learn More...
- Galaxy Tool News: JBrowse-in-Galaxy v0.4 released January 4, 2016 - The latest version of my JBrowse Galaxy wrapper (TAMU, Public) has been released! It features lots of exciting new features: Support for dataset collectionSupport for all coding tablesAdvanced styling options for colouring and colour coding your tracksMultiple file selections (easily select + style a whole group of tracks at once)Simplified tool interface (in places. MoreLearn More...
- Galaxy Tool News: Codon Optimizer, Gff3 Filters December 10, 2015 - Some exciting new tool updates; a couple of tools to help you filter GFF3 files in your analyses based on Shine Dalgarno sequences and “Phage Start Codons”, and an update to the CPT’s own Codon Optimizer Sometimes in your analyses you find yourself producing a gff3 file of naive gene calls, and have thousands ofLearn More...
- Scheduled Downtime – November 6 November 4, 2015 - Summary of Changes Swapping out hardware Expected Improvements Galaxy should be significantly more responsive even during heavy loads. Extenent of Downtime Friday, November 6th 0900 CST to Saturday, November 7th at 1700 CST Affected Services cpt.tamu.edu (CPT Server): All services will be down. Galaxy, WordPress, etc. cpt-fs.tamu.edu (CPT file server) will be completely unaffected.
- Fasta Ligation and DNA Digestion Tools October 28, 2015 - Howdy Phage Galaxy Users! We’ve recently updated our Digestion Toolkit, originally built by our BICH491 student Stephen Crosby, to take advantage of the new plasmid visualization library angularplasmid. This was built into a small workflow which handles ligating all of the sequences in a fasta file with a 5′ adapter, a 3′ adapter, andLearn More...
- Codon Optimisation Now Available October 28, 2015 - The CPT wanted to include a Codon Optimisation tool in Galaxy, but none of the existing ones are open source or willing to release their source. So, we wrote our own! We were able to add some extra, nice features as a result of this. We have an extensive library of bacterial codon usage dataLearn More...
- CPT Galaxy Updated to 15.10 October 13, 2015 - Howdy Y’all, We updated the CPT Galaxy today to the latest version (15.10 pre-release.) Soon we will begin rolling out access to the new Galaxy Interactive Environments for all registered TAMU users.