non port: biology/kallisto/Makefile |
Number of commits found: 25 |
Saturday, 4 Nov 2023
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13:15 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
8a2deae |
Monday, 24 Jul 2023
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15:44 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
ddc8126 |
Friday, 14 Jul 2023
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16:12 Jason W. Bacon (jwb)
biology/kallisto: Tag only for 64-bit architectures
Also patch out -march=native
Reported by: pkg-fallout
2b96a02 |
Friday, 7 Jul 2023
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18:00 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
cab5056 |
Sunday, 23 Apr 2023
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09:09 Gerald Pfeifer (gerald)
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
8d3e020 |
Wednesday, 7 Sep 2022
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21:10 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.
This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.
There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.
The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.
Approved by: portmgr (tcberner)
b7f0544 |
Wednesday, 20 Jul 2022
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14:35 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>
5564b3b |
Thursday, 16 Jun 2022
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15:13 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
328ae40 |
Wednesday, 19 Jan 2022
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13:57 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
c9bd01b |
Wednesday, 7 Apr 2021
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08:09 Mathieu Arnold (mat)
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
cf118cc |
Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Tuesday, 26 Jan 2021
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01:34 jwb
biology/kallisto: Add -lz for pending hdf5 upgrade
PR: 252965
Submitted by: thierry
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Monday, 3 Aug 2020
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15:45 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.
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Wednesday, 1 Apr 2020
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23:35 jwb
kallisto: Patch for build with GCC
PR: ports/245240
Submitted by: pkubaj
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Saturday, 15 Feb 2020
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23:09 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
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Wednesday, 6 Nov 2019
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00:18 jwb
biology/kallisto: Upgrade to 0.46.1
Minor bug fixes and enhancements
Reported by: portscout
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Friday, 26 Jul 2019
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20:46 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
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Wednesday, 12 Jun 2019
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15:24 jwb
biology/kallisto: Upgrade to 0.46.0
Reported by: portscout
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Sunday, 24 Feb 2019
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20:32 jwb
kallisto: Upgrade to 0.45.1, unbundle hstlib
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Saturday, 5 Jan 2019
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22:46 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
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Wednesday, 12 Dec 2018
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01:35 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
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Wednesday, 5 Sep 2018
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22:05 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
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Sunday, 29 Jul 2018
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22:18 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
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Saturday, 2 Jun 2018
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19:40 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)
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Saturday, 2 Dec 2017
|
20:44 jwb
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13328
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Number of commits found: 25 |