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3123 commits

Author SHA1 Message Date
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
Jason W. Bacon
7813a6f1a1 biology/fastp: Update to 0.22.0 
Add support for deduplication
 2021-08-26 14:48:10 -05:00
Yuri Victorovich
2c2bb694d2 biology/mothur: Update 1.45.3 -> 1.46.0 
Reported by:	portscout
 2021-08-26 10:45:39 -07:00
Yuri Victorovich
cc5fdc14d9 biology/ncbi-cxx-toolkit: Update 22.0.0 -> 25.0.0 2021-08-25 13:28:23 -07:00
Yuri Victorovich
a8dd36546a biology/unikmer: Update 0.18.3 -> 0.18.4 
Reported by:	portscout
 2021-08-24 10:10:11 -07:00
Jason W. Bacon
1e0d8ce207 biostar-tools: Update to 1.4.0 
Add multiqc, flash, bfc, and jellyfish to metaport deps
 2021-08-24 11:46:30 -05:00
Jason W. Bacon
2e559ca48c biology/bfc: Correct sequencing errors from Illumina sequencing data 
BFC is a standalone high-performance tool for correcting sequencing
errors from Illumina sequencing data. It is specifically designed for
high-coverage whole-genome human data, though also performs well for
small genomes.
 2021-08-23 12:28:41 -05:00
Jason W. Bacon
615c521bb3 biology/flash: Fast Length Adjustment of SHort reads 
FLASH (Fast Length Adjustment of SHort reads) is a very fast and
accurate software tool to merge paired-end reads from next-generation
sequencing experiments. FLASH is designed to merge pairs of reads when
the original DNA fragments are shorter than twice the length of reads.
The resulting longer reads can significantly improve genome assemblies.
They can also improve transcriptome assembly when FLASH is used to
merge RNA-seq data.
 2021-08-23 12:26:47 -05:00
Jason W. Bacon
d09fdd5d58 biology/minimap2: Add pkg-plist to repo 2021-08-22 12:46:37 -05:00
Jason W. Bacon
4952cf637a biology/jellyfish: Update to 2.3.0 
Changelog:      https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0
 2021-08-22 12:44:17 -05:00
Jason W. Bacon
205fcac221 biology/minimap2: Update to 2.22 
Changelog: https://github.com/lh3/minimap2/releases/tag/v2.22

Reported by:    portscout
 2021-08-22 09:15:06 -05:00
Jason W. Bacon
c5efaea23b biology/bbmap: Update to 38.92 
Numerous small fixes and enhancements

Reported by:    portscout
 2021-08-22 08:59:58 -05:00
Jason W. Bacon
472c25aa5d biology/pooler: Update to 1.77 
Minor fixes and enhancements.

Reported by:    silas-freebsd@flatline.org.uk
 2021-08-21 17:12:35 -05:00
Yuri Victorovich
70ea3d2756 biology/igv: Broken on 11 
Reported by:	fallout
 2021-08-21 12:08:05 -07:00
Yuri Victorovich
9352bd72e0 biology/abyss: Broken on 11 
Reported by:	fallout
 2021-08-21 12:02:36 -07:00
Yuri Victorovich
d3e8f76131 biology/edlib: Update 1.2.6.20201202 -> 1.2.7 
Reported by:	portscout
 2021-08-21 10:12:15 -07:00
Joseph Mingrone
dab99da055
biology/hyphy: Update to 2.4.32 
https://github.com/veg/hyphy/releases/tag/2.5.32

Port changes:
- Remove USES=ssl since it's an indirect dependency from curl
- Remove patch that was upstreamed
 2021-08-20 10:56:52 -03:00
Yuri Victorovich
6f742da5a7 misc/: Update 0.99.6-2 -> 0.991 
Reported by:	portscout
 2021-08-18 10:17:45 -07:00
Yuri Victorovich
e231650c4a biology/ngs-sdk: Update 2.11.0-> 2.11.1 
Reported by:	portscout
 2021-08-18 10:17:44 -07:00
Yuri Victorovich
1c0e78eb4b biology/py-PySCeS: New port: Python Simulator for Cellular Systems 2021-08-17 14:30:08 -07:00
Yuri Victorovich
10875d93bb biology/py-python-libsbml: New port: LibSBML Python API 2021-08-17 14:30:07 -07:00
Yuri Victorovich
640855add1 biology/py-bx-python: Update 0.8.10 -> 0.8.11-6 2021-08-17 12:10:45 -07:00
wen heping
21c779f88e biology/py-resdk: Update 13.3.0 -> 13.4.0 2021-08-17 10:29:42 -07:00
Yuri Victorovich
aa9a35be04 biology/sigviewer: New port: Viewing application for biosignals 2021-08-17 00:05:37 -07:00
Yuri Victorovich
9bc5a1e99f biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX 2021-08-16 19:57:30 -07:00
Yuri Victorovich
df70b7efed biology/biosig: New port: Library for reading and writing different biosignal data format 2021-08-16 19:51:36 -07:00
Yuri Victorovich
6223eec380 biology/seqkit: Add 'test' target 2021-08-14 11:53:27 -07:00
Yuri Victorovich
c9c0132387 biology/unikmer: Add 'test' target 2021-08-14 11:35:11 -07:00
Alexey Dokuchaev
0ee21a35d1 biology/seaview: in preparation to FLTK update, unbreak the port 
Ensure there is only one variable definition per each object, as
the C (and C++) standards mandated for years and is now enforced
by modern toolchains.
 2021-08-14 08:58:03 +00:00
Yuri Victorovich
cea0bdfd08 biology/seqan3: Add the 'test' target (currently broken due to lacking clang support) 2021-08-13 10:08:56 -07:00
Jason W. Bacon
361278dd7c biostar-tools: Correct category for py-ont-fast5-api 2021-08-13 09:16:27 -05:00
Jason W. Bacon
3ed2dd540f biostar-tools: Add new deps to metaport 
csvkit, miller: Tools for working with comma-separated data
py-ont-fast5-api: Library and tools for Oxford Nanopore fast5 files
 2021-08-13 08:37:48 -05:00
Jason W. Bacon
5797d6a329 biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files 
The ont_fast5_api is a simple interface to HDF5 files of the Oxford
Nanopore .fast5 file format. It provides:

    o Implementation of the fast5 file schema using h5py library
    o Methods to interact with and reflect the fast5 file schema
    o Tools to convert between multi_read and single_read formats
    o Tools to compress/decompress raw data in files
 2021-08-13 08:34:09 -05:00