Created attachment 194628 [details]
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.
HISAT2 requires SSE2 instructions as often other modern alignment programs do.
We can build it on i386 machines; however, CPUTYPE must be appropriately defined
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)
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:
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?