[Bug 229330] [NEW PORT] biology/hisat2: Graph-based alignment of sequencing reads to genomes

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[Bug 229330] [NEW PORT] biology/hisat2: Graph-based alignment of sequencing reads to genomes

bugzilla-noreply
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=229330

            Bug ID: 229330
           Summary: [NEW PORT] biology/hisat2: Graph-based alignment of
                    sequencing reads to genomes
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Some People
          Priority: ---
         Component: Individual Port(s)
          Assignee: [hidden email]
          Reporter: [hidden email]

Created attachment 194628
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=194628&action=edit
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)

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[Bug 229330] [NEW PORT] biology/hisat2: Graph-based alignment of sequencing reads to genomes

bugzilla-noreply
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=229330

Motomichi Matsuzaki <[hidden email]> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         Depends on|                            |223273


Referenced Bugs:

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=223273
[Bug 223273] [NEW PORT] biology/sra-tools: NCBI's toolkit for handling data in
INSDC Sequence Read Archives
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[Bug 229330] [NEW PORT] biology/hisat2: Graph-based alignment of sequencing reads to genomes

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In reply to this post by bugzilla-noreply
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=229330

Yuri Victorovich <[hidden email]> changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |[hidden email]
           Assignee|[hidden email]      |[hidden email]
             Status|New                         |In Progress

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