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Port details
kallisto Quantify abundances of transcripts from RNA-Seq data
0.46.0 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
0.45.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-12-02 20:44:35
Last Update: 2019-06-12 16:24:55
SVN Revision: 504011
License: BSD2CLAUSE
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.

WWW: https://pachterlab.github.io/kallisto/about.html
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (5 items)
  1. bin/kallisto
  2. bin/kallisto-test
  3. /usr/local/share/licenses/kallisto-0.46.0/catalog.mk
  4. /usr/local/share/licenses/kallisto-0.46.0/LICENSE
  5. /usr/local/share/licenses/kallisto-0.46.0/BSD2CLAUSE
  6. Collapse this list.
Dependency lines:
  • kallisto>0:biology/kallisto

To install the port: cd /usr/ports/biology/kallisto/ && make install clean
To add the package: pkg install kallisto

PKGNAME: kallisto

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1560352294
SHA256 (pachterlab-kallisto-v0.46.0_GH0.tar.gz) = af4778cf121cdb9f732b355fc0ce44c6708caddf22d9560ba7f4b5d5b9795be1
SIZE (pachterlab-kallisto-v0.46.0_GH0.tar.gz) = 2252729


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. cmake : devel/cmake
Library dependencies:
  1. libhdf5.so : science/hdf5
  2. libsz.so : science/szip
  3. libhts.so : biology/htslib
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for kallisto-0.46.0:
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings

USES:
cmake:noninja compiler:c++11-lang

Master Sites:
  1. https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.46.0?dummy=/

Number of commits found: 8

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
12 Jun 2019 15:24:55
Original commit files touched by this commit  0.46.0
Revision:504011
jwb search for other commits by this committer
biology/kallisto: Upgrade to 0.46.0

Reported by:    portscout
24 Feb 2019 20:32:20
Original commit files touched by this commit  0.45.1
Revision:493810
jwb search for other commits by this committer
kallisto: Upgrade to 0.45.1, unbundle hstlib
05 Jan 2019 22:46:54
Original commit files touched by this commit  0.43.1_4
Revision:489412
sunpoet search for other commits by this committer
Update science/hdf5 to 1.10.4

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes
PR:		233070
Submitted by:	wen
12 Dec 2018 01:35:36
Original commit files touched by this commit  0.43.1_3
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
05 Sep 2018 22:05:23
Original commit files touched by this commit  0.43.1_2
Revision:479046
sunpoet search for other commits by this committer
Update science/hdf5 to 1.10.2

- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://portal.hdfgroup.org/display/support/HDF5%201.10.2#releasenotes
		https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.2/src/hdf5-1.10.2-RELEASE.txt
PR:		231009
Exp-run by:	antoine
29 Jul 2018 22:18:46
Original commit files touched by this commit  0.43.1_1
Revision:475857
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
02 Jun 2018 19:40:59
Original commit files touched by this commit  0.43.1
Revision:471400
linimon search for other commits by this committer
Adjust USES to fix building on gcc-based archs (in particular, powerpc64).

On the clang architectures, these changes have no effect: the baser
compiler already includes the needed features.

While here, remove now-redundant CXXFLAGS statements and pet portlint
(no other content change).

Tested on both powerpc64 and amd64.

Approved by:	portmgr (tier-2 blanket)
02 Dec 2017 20:44:28
Original commit files touched by this commit  0.43.1
Revision:455382
jwb search for other commits by this committer
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data

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

Number of commits found: 8

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