kpriv/freebsd-ports
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity
561385 commits 42 branches 80 tags 2.7 GiB
Commit graph

3155 commits

Author SHA1 Message Date
Wen Heping
112c183adc biology/py-biopython: Update to 1.79 
PR:		259046
Reported by:	wen@
Approved by:	maintainer
 2021-10-12 14:43:04 +08:00
Piotr Kubaj
b6994dfc3e biology/diamond: enable on powerpc64le 2021-10-09 13:49:00 +00:00
Piotr Kubaj
096fef40c5 biology/diamond: enable on powerpc64 2021-10-08 18:19:23 +00:00
Yuri Victorovich
c38052dfd6 biology/libneurosim: New port: Common interfaces for neuronal simulators 2021-10-08 10:20:27 -07:00
Mikael Urankar
46ed8da916 biology/hyphy: Enable on aarch64. 2021-10-08 18:27:33 +02:00
Mikael Urankar
63de6c3db6 biology/diamond: Enable on aarch64. 2021-10-08 18:25:09 +02:00
Piotr Kubaj
0716ab6599 biology/pooler: fix build on powerpc 
In file included from bit-common.c:63:
In file included from ./bit-choice.h:23:
In file included from ./triangle.h:44:
./openmp.h:19:10: fatal error: 'omp.h' file not found
 2021-10-06 20:52:30 +00:00
Fernando Apesteguía
07fb2d5e9d */*: Remove compiler:openmp from Mk/Uses/compiler.mk 
The option implied a dependency on gcc but clang got openmp support long ago.

Remove compiler:openmp from Mk/Uses/compiler.mk

For ports using USE=compiler:openmp, just remove it and make them build with
clang.
Fix conditionals when necessary
Bump PORTREVISION where appropriate

If problem arises, they can be addressed by using USE_GCC=yes

An update to the Porter's Handbook will follow.

Approved by: portmgr (bapt)
Differential Revision: https://reviews.freebsd.org/D31971
 2021-10-03 19:47:27 +02:00
Yuri Victorovich
a3d97bcf09 biology/ncbi-cxx-toolkit: Update 25.0.0 -> 25.2.0 
Reported by:	upstream ML notification
 2021-10-01 00:14:37 -07:00
Rene Ladan
620968a43a cleanup: drop support for EOL FreeBSD 11.X 
Search criteria used:
- 11.4
- OSREL*
- OSVER*
- *_FreeBSD_11

Input from:
- adridg: devel/qca-legacy
- jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds
- sunpoet: security/p5-*OpenSSL*

Reviewed by:	doceng, kde, multimedia, perl, python, ruby, rust
Differential Revision: https://reviews.freebsd.org/D32008
Test Plan: make index
 2021-09-30 23:23:30 +02:00
Jason W. Bacon
96d32d8118 biology/biostar-tools: Add biology/kallisto run depend to metaport 
Also clean up other deps for consistency
 2021-09-27 07:14:45 -05:00
Yuri Victorovich
a138a5bcb4 biology/unikmer: Update 0.18.4 -> 0.18.8 
Reported by:	portscout
 2021-09-26 01:54:07 -07:00
Bernhard Froehlich
311f6fb1d3
biology/vcftools: Add CPE information 
Approved by:	portmgr (blanket)
 2021-09-25 20:28:38 +00:00
Jason W. Bacon
d94f19ab9f biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin 
Standard kent userapps commands are installed under ${PREFIX}/userapps
because of multiple conflicts.  The kent command turns the standard
commands into subcommands, so no special PATH is needed.

    /usr/local/ucsc-userapps/bin/bigWigToBedGraph [args]

can be run as

    kent bigWigToBedGraph [args]
 2021-09-24 16:53:30 -05:00
Jason W. Bacon
c68b6dc644 biology/emboss: Add "emboss" command in ${LOCALBASE}/bin 
Standard emboss commands are installed under a special prefix because
of multiple conflicts.  The emboss command turns the standard commands
into subcommands, so no special PATH is needed.

    /usr/local/emboss/bin/needle [args]

can be run as

    emboss needle [args]
 2021-09-24 16:34:20 -05:00
Yuri Victorovich
e681b89328 biology/bioparser: Update 3.0.12-2 -> 3.0.15 
Reported by:	portscout
 2021-09-21 09:41:49 -07:00
Po-Chuan Hsieh
6e0aa01726
*/Makefile: Sort SUBDIRs 2021-09-21 11:35:06 +08:00
Yuri Victorovich
01e5dfaad7 biology/py-PySCeS: Update 0.9.8a -> 1.0.0 2021-09-20 14:34:22 -07:00
Yuri Victorovich
d8c851df59 biology/py-libsedml: New port: SED-ML library for Python 2021-09-19 11:15:36 -07:00
Yuri Victorovich
dd804e9871 biology/libsedml: New port: C++ SED-ML library 2021-09-19 11:15:35 -07:00
Yuri Victorovich
b20ce0d061 biology/py-libnuml: Fix typo 2021-09-19 11:15:35 -07:00
Yuri Victorovich
74c998634a biology/py-libnuml: New port: Numerical Markup Language for Python 2021-09-18 23:47:03 -07:00
Yuri Victorovich
ad2bdb6508 biology/libnuml: New port: C++ library for Numerical Markup Language 2021-09-18 23:47:02 -07:00
Yuri Victorovich
cd48d9beaf biology/seqkit: Update 0.16.1 -> 2.0.1 2021-09-18 10:48:26 -07:00
Joseph Mingrone
3b937ad738
biology/jellyfish: Switch to static tarball and update license info 
The GitHub-generated tarballs require reautoconf and more dependencies
including gettext, regardless whether the NLS knob is turned off.
https://github.com/gmarcais/Jellyfish/issues/138#issuecomment-463272029

This update also fixes a build issue when the NLS knob was turned off.
http://pkg.ftfl.ca/data/13amd64-default/2021-09-16_13h45m55s/logs/errors/Jellyfish-2.3.0_1.log

Differential Revision:	https://reviews.freebsd.org/D31984

Co-authored-by: Jason W. Bacon <jwb@FreeBSD.org>
 2021-09-17 15:01:35 -03:00
Jason W. Bacon
623975bcb4 biology/biolibc: Update to 0.2.0.11 
Regenerate man pages with improved auto-c2man
Adds missing return value sections and improves formatting
 2021-09-17 11:33:57 -05:00
Alexey Dokuchaev
299862ff2a biology/ugene: update Unipro UGENE to version 40.0. 2021-09-16 09:48:26 +00:00
Yuri Victorovich
e53b99b2dc biology/py-PySCeS: Update 0.9.8post1 -> 0.9.8a 2021-09-14 02:21:07 -07:00
Mikael Urankar
e9f35d7e41 biology/hhsuite: Fix build on aarch64 
Approved by:	portmgr (build fix blanket)
 2021-09-13 17:47:57 +02:00
Piotr Kubaj
031ddba476 biology/mmseqs2: disable on 32-bits 
32-bits are not supported per https://github.com/soedinglab/MMseqs2/issues/460
 2021-09-12 21:05:53 +00:00
Jason W. Bacon
696f6acf5d biology/jellyfish: Fix unused open mode variable 
PR:             258397
Reported by:    dim
 2021-09-11 07:29:47 -05:00
Bernhard Froehlich
8522c8336e
biology/htslib: Add CPE information 
Approved by:	portmgr (blanket)
 2021-09-10 21:18:20 +00:00
Jason W. Bacon
c73e3a89ec biology/biostar-tools: Add biology/sam2pairwise to run deps 
Displays pairwise alignments in a SAM file
 2021-09-07 15:41:10 -05:00
Jason W. Bacon
e61df5e464 biology/sam2pairwise: Show pairwise alignment for each read in a SAM file 
sam2pairwise takes a SAM file and uses the CIGAR and MD tag to
reconstruct the pairwise alignment of each read.
 2021-09-07 15:32:29 -05:00
Jason W. Bacon
e47c577da6 biology/emboss: Put emboss-shell in default PATH 
PREFIX is overridden by default in the port Makefile, so PREFIX/bin
is not normally in PATH.  The purpose of emboss-shell is to prepend
PREFIX/bin to PATH to give access to emboss tools.

Also fix tcsh detection.

PR:             258316
 2021-09-06 10:13:03 -05:00
Jason W. Bacon
0ec8be4158 biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps 
Short-read alignment related tools
 2021-09-06 09:27:20 -05:00
Jason W. Bacon
fa2e0b8c66 biology/emboss: Add emboss-shell: Run subshell with proper PATH 
Also silence portlint and stage-qa warnings

PR:             258316
Approved by:    wen
 2021-09-06 09:21:44 -05:00
Jason W. Bacon
c085af1e81 biology/py-pywgsim: Modified wgsim genomic data simulator 
pywgsim is a modified version of the wgsim short read simulator.  The
code for wgsim has been modified to allow visualizing the simulated
mutations as a GFF file.
 2021-09-06 07:55:49 -05:00
Yuri Victorovich
4fac1dac10 biology/ncbi-cxx-toolkit: Broken on 11 
Reported by:	fallout
 2021-09-03 20:58:21 -07:00
Tobias Kortkamp
310623bb97
*: Clean up some things 
- Fix typos
- Remove duplicate variables
- Remove nop or unreferenced variables
- Add missing ports to the build
- Clean up commented PORTREVISION
- Add missing USES

Reported by:	portscan
 2021-09-03 15:01:58 +02:00
Jason W. Bacon
7e94c6d1f8 biology/peak-classifier: Update to 0.1.1.21 
Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks
 2021-09-02 18:15:40 -05:00
Jason W. Bacon
df59313087 biology/biolibc: Update to 0.2.0.1 
Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks
 2021-09-02 18:10:21 -05:00
Yuri Victorovich
03cb17ef46 biology/mothur: Update 1.46.0 -> 1.46.1 
Reported by:	portscout
 2021-09-02 02:29:56 -07:00
Jason W. Bacon
904aa60469 biology/biolibc-tools: High-performance tools based on biolibc 
Biolibc-tools is a collection of simple fast, memory-efficient,
programs for processing biological data.  These are simple programs
built on biolibc that are not complex enough to warrant a separate
project.
 2021-08-30 08:09:23 -05:00
Jason W. Bacon
541454f993 biology/pooler: Update to 1.78 
Adds desktop file

PR:             258120
Reported by:    Silas S. Brown <silas-freebsd@flatline.org.uk>
 2021-08-28 09:35:01 -05:00
Jason W. Bacon
b16616b283 biology/peak-classifier: Update to 0.1.1.20 
Updates for libxtend and biolibc API changes
 2021-08-27 20:34:46 -05:00
Jason W. Bacon
dc651f0234 biology/vcf2hap: Update to 0.1.3.12 
Updates for libxtend and bioloibc API changes
 2021-08-27 20:32:51 -05:00
Jason W. Bacon
61ebfe4137 biology/vcf-split: Update to 0.1.2.14 
Updates for libxtend and biolibc API changes
 2021-08-27 20:30:52 -05:00
Jason W. Bacon
b30b9f1a1e biology/ad2vcf: Update to 0.1.3.31 
Updates for libxtend and biolibc API changes
Clean up and minor bug fixes
 2021-08-27 20:28:10 -05:00
Jason W. Bacon
9876430959 biology/biolibc: Update to 0.2.0 
Major API overhaul
New classes for FASTA and FASTQ
Generate accessor and mutator functions for all classes
Generate man pages for all functions and macros
Export delimiter-separated-value class to libxtend
 2021-08-27 20:21:02 -05:00