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Port details
kallisto Quantify abundances of transcripts from RNA-Seq data
0.46.1,1 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 View this port on Repology. pkg-fallout 0.46.1,1Version 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: 2021-01-26 01:34:21
SVN Revision: 562627
License: BSD2CLAUSE
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/kallisto
  2. bin/kallisto-test
  3. /usr/local/share/licenses/kallisto-0.46.1,1/catalog.mk
  4. /usr/local/share/licenses/kallisto-0.46.1,1/LICENSE
  5. /usr/local/share/licenses/kallisto-0.46.1,1/BSD2CLAUSE
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
Flavors: there is no flavor information for this port.
distinfo:
Packages: (move your mouse over the cells for more information)
kallisto
ABIlatestquarterly
FreeBSD:11:aarch640.43.1_20.46.2_1
FreeBSD:11:amd640.46.1,10.46.1,1
FreeBSD:11:armv6-0.46.2_1
FreeBSD:11:i3860.46.1,10.46.1,1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch640.43.1_20.46.1,1
FreeBSD:12:amd640.46.1,10.46.1,1
FreeBSD:12:armv60.43.1_20.46.1,1
FreeBSD:12:armv70.43.1_20.46.1,1
FreeBSD:12:i3860.46.1,10.46.1,1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-0.46.1,1
FreeBSD:13:aarch640.46.1,10.46.1,1
FreeBSD:13:amd640.46.1,10.46.1,1
FreeBSD:13:armv60.46.1,10.46.1,1
FreeBSD:13:armv70.46.1,10.46.1,1
FreeBSD:13:i3860.46.1,10.46.1,1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc640.46.1,10.46.1,1
FreeBSD:14:aarch640.46.1,1-
FreeBSD:14:amd640.46.1,1-
FreeBSD:14:armv60.46.1,1-
FreeBSD:14:armv70.46.1,1-
FreeBSD:14:i3860.46.1,1-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc640.46.1,1-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. autoconf>=0 : devel/autoconf
  2. cmake : devel/cmake
  3. gmake>=4.3 : devel/gmake
Library dependencies:
  1. libhdf5.so : science/hdf5
  2. libsz.so : science/szip
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.46.1?dummy=/
Collapse this list.

Number of commits found: 14

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Jan 2021 01:34:21
Original commit files touched by this commit  0.46.1,1
Revision:562627
jwb search for other commits by this committer
biology/kallisto: Add -lz for pending hdf5 upgrade

PR:             252965
Submitted by:   thierry
03 Aug 2020 15:45:22
Original commit files touched by this commit  0.46.1,1
Revision:544077
jwb search for other commits by this committer
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.
01 Apr 2020 23:35:38
Original commit files touched by this commit  0.46.2_1
Revision:530250
jwb search for other commits by this committer
kallisto: Patch for build with GCC

PR:             ports/245240
Submitted by:   pkubaj
15 Feb 2020 23:09:20
Original commit files touched by this commit  0.46.2
Revision:526244
jwb search for other commits by this committer
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
06 Nov 2019 00:18:14
Original commit files touched by this commit  0.46.1
Revision:516853
jwb search for other commits by this committer
biology/kallisto: Upgrade to 0.46.1

Minor bug fixes and enhancements

Reported by:    portscout
26 Jul 2019 20:46:57
Original commit files touched by this commit  0.46.0_1
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

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, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
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: 14

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