./biology/kallisto, Quantify abundances of transcripts from RNA-Seq data

[ CVSweb ] [ Homepage ] [ RSS ] [ Required by ] [ Add to tracker ]

Branch: CURRENT, Version: 0.51.1, Package name: kallisto-0.51.1, Maintainer: bacon

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
data, or more generally of target sequences using high-throughput sequencing
reads. It is based on the novel idea of pseudoalignment for rapidly determining
the compatibility of reads with targets, without the need for alignment.


Required to run:
[devel/hdf5] [biology/htslib] [archivers/libaec]

Required to build:
[pkgtools/cwrappers]

Master sites:

Filesize: 5814.697 KB

Version history: (Expand)

CVS history: (Expand)


   2023-11-04 15:35:07 by Jason Bacon | Files touched by this commit (13) 
Log message:
biology/kallisto: Update to 0.50.1

Update kallisto index version to 13
A few other new features
Changes: https://github.com/pachterlab/kallisto/releases
   2022-12-28 16:27:18 by Jason Bacon | Files touched by this commit (20) 
Log message:
Change MAINTAINER= to OWNER= on mission-critical packages
   2022-02-27 02:57:27 by Jason Bacon | Files touched by this commit (6) 
Log message:
biology/kallisto: Update to 0.48.0

Long awaited bug fix release
Also unbundled htslib
Changes: https://github.com/pachterlab/kallisto/tags
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Remove SHA1 hashes for distfiles
   2020-07-30 09:59:19 by Thomas Klausner | Files touched by this commit (2) | Package updated
Log message:
kallisto: remove patches that were removed from distinfo during update
   2020-07-23 21:22:00 by Jason Bacon | Files touched by this commit (3) 
Log message:
biology/kallisto: Upgrade to 0.46.1

Minor enhancements since 0.45
0.46.2 is available, but has serious regressions.
Reverted to bundled htslib 1.4.1, since kallisto source contains modified
htslib files that are incompatible with the current 1.10.2 package.
   2019-05-01 14:38:54 by Jason Bacon | Files touched by this commit (1) 
Log message:
biology/kallisto: Switch from archivers/szip to archivers/libaec

libaec is a BSD-licensed drop-in replacement for the non-redistributable szip