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Author SHA1 Message Date
Jimmy Olgeni
4460cf727a *: fix tab vs. space issues, and comments according to the guide. 2021-10-16 11:51:39 +02:00
Yuri Victorovich
c16b145a0f biology/treekin: Unbreak 
Recent Lapack API changes broke it.

PR:		259179
 2021-10-15 08:50:24 -07:00
Jason W. Bacon
9d1d409f42 biology/biostar-tools: Add py-deeptools to metaport deps 2021-10-14 06:53:52 -05:00
Jason W. Bacon
799d4cc2cf biology/py-deeptools: User-friendly tools for exploring deep-sequencing data 
deepTools contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard
bedGraph and bigWig file formats, that allow comparison between
different files (for example, treatment and control). Finally, using
such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for
functional annotations of the genome.
 2021-10-14 06:51:12 -05:00
Alexey Dokuchaev
e409be37a8 biology/ugene: update UniPro UGENE to version 40.1 (bugfix release). 2021-10-14 11:23:37 +00:00
Jan Beich
818989d766 biology/py-crossmap: chase ad5a0604c4 
make_index: biology/py-crossmap: no entry for biology/py-bigwig

Reported by:	indexbuild
 2021-10-14 00:53:16 +00:00
Jason W. Bacon
ad5a0604c4 biology/py-bigwig: Rename to biology/py-pybigwig 
Fully match upstream name
 2021-10-13 16:21:32 -05:00
Antoine Brodin
6a226290f3 biology/py-pybigwig: remove, duplicate of biology/py-bigwig 2021-10-13 18:57:58 +00:00
Jason W. Bacon
06e26353b2 biology/py-deeptoolsintervals: Python interface for deepTools interval trees 
Deeptools_intervals is an interval tree backend designed to interface
with deepTools, supporting metadata associated with each interval.
 2021-10-13 11:02:13 -05:00
Jason W. Bacon
646f3fc381 biology/py-py-pybigwig: Patch out setup.py warning 
Neglected to add this file during previous commit
 2021-10-13 11:02:12 -05:00
Jason W. Bacon
c69e97e63a biology/py-pybigwig: Fix poudriere build 
Typo in post-install
 2021-10-13 11:02:12 -05:00
Jason W. Bacon
904a889fd1 biology/py-pybigwig: Python access to bigWig files using libBigWig 
py-bigwig is a python extension, written in C, for quick access to
bigBed files and access to and creation of bigWig files. This extension
uses libBigWig for local and remote file access.
 2021-10-13 08:03:21 -05:00
Jason W. Bacon
d92344039b biology/py-py2bit: Python interface for 2bit packed nucleotide files 
py2bit is a python extension, written in C, for quick access to 2bit
files for randomly accessible, packed nucleotide sequences. The
extension uses lib2bit for file access.
 2021-10-13 07:53:53 -05:00
Jason W. Bacon
2e8996e43d biology/biostar-tools: Add biology/bamutil to metaport deps 2021-10-12 11:43:08 -05:00
Jason W. Bacon
cdf2ff2f68 biology/bamutil: Utilities for working with SAM/BAM files 
Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health.  It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc.
 2021-10-12 11:40:35 -05:00
Joseph Mingrone
523d2537b4
biology/diamond: Update to 2.0.12 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.12
 2021-10-12 12:40:55 -03:00
Tobias Kortkamp
ae22a7846a
*: Clean up some things 
- Fix typos
- Fix overwritten variables with focus on master/slave ports
- Remove unreferenced variables
- Sort categories
- Remove redundant option descriptions
- Clean up commented PORTREVISION
- Add missing USES

Reported by:	portscan
 2021-10-12 17:01:38 +02:00
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