Created attachment 194628 [details] svn diff HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads to a population of genomes as well as to a single reference. HISAT2 is a successor to HISAT and TopHat2, both of which are spliced alignment program for mapping RNA-seq reads; additionally, HISAT2 is designed to map sequencing reads from genomic DNA of generic human population having SNPs. WWW: https://ccb.jhu.edu/software/hisat2/ HISAT2 requires SSE2 instructions as often other modern alignment programs do. We can build it on i386 machines; however, CPUTYPE must be appropriately defined in /etc/make.conf It will detect POPCNT instruction runtime and use for acceleration, but the code is able to build only for amd64 architecture. NOTE: HISAT2 has SRA data access ability but it requires NCBI's NGS/VDB libraries, which port is currently pending (bug #223273). Tested by: poudriere testport (amd64/i386 11.1/10.4)
ping!
biology/hisat2 already exists. Sorry if I overlooked this PR, but it had been pending in my wip collection since 2017. It's a good idea to look there before creating any biology ports: https://github.com/outpaddling/freebsd-ports-wip/tree/master/hisat2 The SRA Tools issue is a complicated one. Currently SRA Tools can only download *some* files, while others require Aspera (closed-source but the ascp command it includes should work on FreeBSD) or Fusera. It appears that SRA Tools will still play a role in processing data downloaded by other means, but the documentation is very confusing. I'm currently working on a TOPMed project and dealing with this directly. Maybe this PR can be closed and we can revisit the SRA features after SRA Tools is commmitted?