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We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Port details
kallisto Quantify abundances of transcripts from RNA-Seq data
0.48.0_2,1 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 Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: BSD2CLAUSE
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
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-0.48.0_2,1/catalog.mk
  4. /usr/local/share/licenses/kallisto-0.48.0_2,1/LICENSE
  5. /usr/local/share/licenses/kallisto-0.48.0_2,1/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, run one of these commands:
  • pkg install biology/kallisto
  • pkg install kallisto
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: kallisto
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
kallisto
ABIlatestquarterly
FreeBSD:11:aarch640.43.1_20.46.2_1
FreeBSD:11:amd640.46.1,10.46.1,1
FreeBSD:11:armv6pkg-fallout0.46.2_1
FreeBSD:11:i3860.46.1,10.46.1,1
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch640.43.1_20.48.0_2,1
FreeBSD:12:amd640.48.0_2,10.48.0_2,1
FreeBSD:12:armv60.43.1_20.46.1,1
FreeBSD:12:armv70.43.1_20.46.1,1
FreeBSD:12:i3860.48.0_2,10.48.0_2,1
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-fallout0.46.1,1
FreeBSD:13:aarch640.48.0_2,10.48.0_2,1
FreeBSD:13:amd640.48.0_2,10.48.0_2,1
FreeBSD:13:armv60.46.1,10.48.0_1,1
FreeBSD:13:armv7pkg-fallout0.48.0_2,1
FreeBSD:13:i3860.48.0_2,10.48.0_2,1
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc640.46.1,10.48.0_2,1
FreeBSD:13:riscv64pkg-fallout0.48.0_1,1
FreeBSD:14:aarch640.48.0_2,1pkg-fallout
FreeBSD:14:amd640.48.0_2,1pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i3860.48.0_2,1pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc640.48.0_2,1pkg-fallout
FreeBSD:14:riscv640.46.1,1pkg-fallout
 
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-core
  3. gmake>=4.3 : devel/gmake
Library dependencies:
  1. libhdf5.so : science/hdf5
  2. libsz.so : science/libaec
  3. libhts.so : biology/htslib
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/rna-seq

Configuration Options:
Options name:
USES:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.48.0?dummy=/
Collapse this list.

Number of commits found: 21

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
0.48.0_2,1
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.48.0_2,1
20 Jul 2022 14:35:24
commit hash:5564b3b420db29745d2d4981d1963200ddf53e35commit hash:5564b3b420db29745d2d4981d1963200ddf53e35commit hash:5564b3b420db29745d2d4981d1963200ddf53e35commit hash:5564b3b420db29745d2d4981d1963200ddf53e35 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
science/hdf5: bump PORTREVISION of consumers

The SO-version increased in the update to 1.12.2 in
a43418b81530f7e897abfbe18dd59f44265a1a0f .

Reported by:	VVD <vvd@unislabs.com>
0.48.0_1,1
16 Jun 2022 15:13:01
commit hash:328ae4074233a5b85e0e38efece1af5dcc218160commit hash:328ae4074233a5b85e0e38efece1af5dcc218160commit hash:328ae4074233a5b85e0e38efece1af5dcc218160commit hash:328ae4074233a5b85e0e38efece1af5dcc218160 files touched by this commit
Po-Chuan Hsieh (sunpoet) search for other commits by this committer
*/*: Replace science/szip with science/libaec

- Bump PORTREVISION of dependent ports for dependency change

szip does not allow redistribution in binary form without proper commercial
license. Its LICENSE_PERMS should be set to no-auto-accept which blocks building
this port, therefore building dependent ports are also blocked. Switch all
dependent ports to science/libaec to avoid conflicts and license issue.

PR:		228743, 246097, 250165
0.48.0,1
19 Jan 2022 13:57:36
commit hash:c9bd01bdf4c1dae17b53482e9dabe000d310cf50commit hash:c9bd01bdf4c1dae17b53482e9dabe000d310cf50commit hash:c9bd01bdf4c1dae17b53482e9dabe000d310cf50commit hash:c9bd01bdf4c1dae17b53482e9dabe000d310cf50 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
0.46.1,1
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.46.1,1
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.46.1,1
26 Jan 2021 01:34:21
Revision:562627Original commit files touched by this commit
jwb search for other commits by this committer
biology/kallisto: Add -lz for pending hdf5 upgrade

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

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

Minor bug fixes and enhancements

Reported by:    portscout
0.46.0_1
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
0.46.0
12 Jun 2019 15:24:55
Revision:504011Original commit files touched by this commit
jwb search for other commits by this committer
biology/kallisto: Upgrade to 0.46.0

Reported by:    portscout
0.45.1
24 Feb 2019 20:32:20
Revision:493810Original commit files touched by this commit
jwb search for other commits by this committer
kallisto: Upgrade to 0.45.1, unbundle hstlib
0.43.1_4
05 Jan 2019 22:46:54
Revision:489412Original commit files touched by this commit
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
0.43.1_3
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
0.43.1_2
05 Sep 2018 22:05:23
Revision:479046Original commit files touched by this commit
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
0.43.1_1
29 Jul 2018 22:18:46
Revision:475857Original commit files touched by this commit
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
0.43.1
02 Jun 2018 19:40:59
Revision:471400Original commit files touched by this commit
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)
0.43.1
02 Dec 2017 20:44:28
Revision:455382Original commit files touched by this commit
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: 21