Port details |
- kallisto Quantify abundances of transcripts from RNA-Seq data
- 0.51.1,1 biology
=2 0.51.1,1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
 - Port Added: 2017-12-02 20:44:35
- Last Update: 2024-09-19 22:46:47
- Commit Hash: c449c3e
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: BSD2CLAUSE
- WWW:
- https://pachterlab.github.io/kallisto/about.html
- Description:
- 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.
¦ ¦ ¦ ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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.
- ONLY_FOR_ARCHS: aarch64 amd64 powerpc64 powerpc64le riscv64
- distinfo:
- TIMESTAMP = 1726658334
SHA256 (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = a8bcc23bca6ac758f15e30bb77e9e169e628beff2da3be2e34a53e1d42253516
SIZE (pachterlab-kallisto-v0.51.1_GH0.tar.gz) = 5954250
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- cmake : devel/cmake-core
- gmake>=4.4.1 : devel/gmake
- Library dependencies:
-
- libhdf5.so : science/hdf5
- libsz.so : science/libaec
- libhts.so : biology/htslib
- This port is required by:
- for Run
-
- biology/biostar-tools
- biology/rna-seq
Configuration Options:
- ===> The following configuration options are available for kallisto-0.51.1,1:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_kallisto
- USES:
- cmake:noninja compiler:c++11-lang gmake localbase:ldflags
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
0.51.1,1 19 Sep 2024 22:46:47
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Jason W. Bacon (jwb)  |
biology/kallisto: Update to 0.51.1,1
Enhancements to ir-kallisto and pseudoalignments
Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout |
0.51.0,1 27 Jul 2024 12:02:57
    |
Jason W. Bacon (jwb)  |
biology/kallisto: Update to 0.51.0,1
Add support for long reads to kallisto bus and kallisto quant-tcc
Changes: https://github.com/pachterlab/kallisto/releases
Reported by: portscout |
0.50.1_1,1 05 May 2024 14:47:05
    |
Jason W. Bacon (jwb)  |
biology/kallisto: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
Reduces I/O during builds
PR: 278739
Reported by: diizzy |
0.50.1,1 04 Nov 2023 13:15:25
    |
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 |
0.50.0_2,1 24 Jul 2023 15:44:58
    |
Jason W. Bacon (jwb)  |
biology/kallisto: Clean up build
Silence warnings due to detected compiler standards
Enable BAM support in cmake
Patch out remaining aggressive optimizations |
0.50.0_1,1 14 Jul 2023 16:12:06
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Jason W. Bacon (jwb)  |
biology/kallisto: Tag only for 64-bit architectures
Also patch out -march=native
Reported by: pkg-fallout |
0.50.0,1 07 Jul 2023 18:00:11
    |
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 |
0.48.0_3,1 23 Apr 2023 09:09:58
    |
Gerald Pfeifer (gerald)  |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
07 Sep 2022 21:58:51
    |
Stefan Eßer (se)  |
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
    |
Stefan Eßer (se)  |
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 ) |
0.48.0_2,1 20 Jul 2022 14:35:24
    |
Tobias C. Berner (tcberner)  |
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
    |
Po-Chuan Hsieh (sunpoet)  |
*/*: 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
    |
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 |
0.46.1,1 07 Apr 2021 08:09:01
    |
Mathieu Arnold (mat)  |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.46.1,1 06 Apr 2021 14:31:07
    |
Mathieu Arnold (mat)  |
Remove # $FreeBSD$ from Makefiles. |
0.46.1,1 26 Jan 2021 01:34:21
  |
jwb  |
biology/kallisto: Add -lz for pending hdf5 upgrade
PR: 252965
Submitted by: thierry |
0.46.1,1 03 Aug 2020 15:45:22
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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. |
0.46.2_1 01 Apr 2020 23:35:38
  |
jwb  |
kallisto: Patch for build with GCC
PR: ports/245240
Submitted by: pkubaj |
0.46.2 15 Feb 2020 23:09:20
  |
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 |
0.46.1 06 Nov 2019 00:18:14
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jwb  |
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
  |
gerald  |
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
  |
jwb  |
biology/kallisto: Upgrade to 0.46.0
Reported by: portscout |
0.45.1 24 Feb 2019 20:32:20
  |
jwb  |
kallisto: Upgrade to 0.45.1, unbundle hstlib |
0.43.1_4 05 Jan 2019 22:46:54
  |
sunpoet  |
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
  |
gerald  |
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
  |
sunpoet  |
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
  |
gerald  |
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
  |
linimon  |
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
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jwb  |
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13328 |