TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. WWW: http://transdecoder.github.io/ Dependency for upcoming Trinity genomics pipeline. portlint: OK (looks fine.) testport: OK (poudriere: {10.1,9.3}-RELEASE {amd64,i386})
Created attachment 168259 [details] Shar archive
testbuild@work
A commit references this bug: Author: pi Date: Wed Mar 16 20:12:33 UTC 2016 New revision: 411246 URL: https://svnweb.freebsd.org/changeset/ports/411246 Log: New port: biology/p5-transdecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. WWW: http://transdecoder.github.io/ PR: 207993 Submitted by: Jason Bacon <bacon4000@gmail.com> Changes: head/biology/Makefile head/biology/p5-transdecoder/ head/biology/p5-transdecoder/Makefile head/biology/p5-transdecoder/distinfo head/biology/p5-transdecoder/pkg-descr head/biology/p5-transdecoder/pkg-plist
Committed, thanks! Please note that I updated to 2.1.0.
Thanks, Kurt! The upgrade should be OK in this case. It would be better to ask before upgrading ports, though. Many of the genomics apps we use are very sensitive to specific versions of dependencies, since they depend on specific algorithms and command line flags that can change. They often bundle dependencies as a defensive move for that reason, but I unbundle them wherever it seems reasonable. Cheers, Jason
As this was a new port, I assumed that upgrading it from the start would not be a big problem 8-}