13:15 Jason W. Bacon (jwb) 

biology/kallisto: Update to 0.50.1,1

Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases

Reported by:    portscout

    8a2deae

18:00 Jason W. Bacon (jwb) 

biology/kallisto: Update to 0.50.0

New, more memory-efficient index
Several other new features and enhancements
End of support for bulk RNASeq features

changes: https://github.com/pachterlab/kallisto/releases

Reported by:    portscout

    cab5056

13:57 Jason W. Bacon (jwb) 

biology/kallisto: Update to 0.48.0

Fixes segfault with --genomebam in 0.46.2
Unbundle htslib
A few new features and performance improvements

Changes:        https://github.com/pachterlab/kallisto/tags

    c9bd01b

15:45 jwb 

biology/kallisto: Revert to 0.46.1

0.46.2 has long-standing regressions that are not being addressed, including
a seg fault when using --genomebam.
Also revert to bundled htslib in preparation for biology/htslib upgrade
to 1.10.  Kallisto source contains modified bits of htslib 1.4.1 that are
incompatible with htslib > 1.9.

 

23:09 jwb 

biology/kallisto: Upgrade to 0.46.2

Kallisto no longer builds in hdf5 by default, but it is still required
for some downstream tools like Sleuth.  Forcing it ON for now, but will
disable it in a future upgrade.

Reported by:    portscout

 

00:18 jwb 

biology/kallisto: Upgrade to 0.46.1

Minor bug fixes and enhancements

Reported by:    portscout

 

15:24 jwb 

biology/kallisto: Upgrade to 0.46.0

Reported by:    portscout

 

20:32 jwb 

kallisto: Upgrade to 0.45.1, unbundle hstlib

 

20:44 jwb 

[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13328