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* biology/htslib: Add CPE informationBernhard Froehlich2021-09-101-1/+1
| | | | Approved by: portmgr (blanket)
* biology/biostar-tools: Add biology/sam2pairwise to run depsJason W. Bacon2021-09-072-3/+4
| | | | Displays pairwise alignments in a SAM file
* biology/sam2pairwise: Show pairwise alignment for each read in a SAM fileJason W. Bacon2021-09-075-0/+67
| | | | | sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.
* biology/emboss: Put emboss-shell in default PATHJason W. Bacon2021-09-064-4/+5
| | | | | | | | | | 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
* biology/biostar-tools: Add mafft, clustal-omega, pywgsim depsJason W. Bacon2021-09-062-3/+6
| | | | Short-read alignment related tools
* biology/emboss: Add emboss-shell: Run subshell with proper PATHJason W. Bacon2021-09-067-17/+47
| | | | | | | Also silence portlint and stage-qa warnings PR: 258316 Approved by: wen
* biology/py-pywgsim: Modified wgsim genomic data simulatorJason W. Bacon2021-09-064-0/+26
| | | | | | 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.
* biology/ncbi-cxx-toolkit: Broken on 11Yuri Victorovich2021-09-041-0/+2
| | | | Reported by: fallout
* *: Clean up some thingsTobias Kortkamp2021-09-031-3/+2
| | | | | | | | | | | - 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
* biology/peak-classifier: Update to 0.1.1.21Jason W. Bacon2021-09-022-5/+5
| | | | | Fix regression: Replace BL_BED_SET_STRAND() macro with bl_bed_set_strand(), which performs sanity checks
* biology/biolibc: Update to 0.2.0.1Jason W. Bacon2021-09-022-4/+5
| | | | | Fix regression: Replace BL_BED_SET_STRAND() macro with bl_bed_set_strand(), which performs sanity checks
* biology/mothur: Update 1.46.0 -> 1.46.1Yuri Victorovich2021-09-022-4/+4
| | | | Reported by: portscout
* biology/biolibc-tools: High-performance tools based on biolibcJason W. Bacon2021-08-305-0/+45
| | | | | | | 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.
* biology/pooler: Update to 1.78Jason W. Bacon2021-08-282-5/+5
| | | | | | | Adds desktop file PR: 258120 Reported by: Silas S. Brown <silas-freebsd@flatline.org.uk>
* biology/peak-classifier: Update to 0.1.1.20Jason W. Bacon2021-08-282-4/+5
| | | | Updates for libxtend and biolibc API changes
* biology/vcf2hap: Update to 0.1.3.12Jason W. Bacon2021-08-282-4/+5
| | | | Updates for libxtend and bioloibc API changes
* biology/vcf-split: Update to 0.1.2.14Jason W. Bacon2021-08-282-4/+5
| | | | Updates for libxtend and biolibc API changes
* biology/ad2vcf: Update to 0.1.3.31Jason W. Bacon2021-08-282-4/+5
| | | | | Updates for libxtend and biolibc API changes Clean up and minor bug fixes
* biology/biolibc: Update to 0.2.0Jason W. Bacon2021-08-284-22/+553
| | | | | | | | 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
* biology/fastp: Update to 0.22.0Jason W. Bacon2021-08-262-4/+4
| | | | Add support for deduplication
* biology/mothur: Update 1.45.3 -> 1.46.0Yuri Victorovich2021-08-262-11/+10
| | | | Reported by: portscout
* biology/ncbi-cxx-toolkit: Update 22.0.0 -> 25.0.0Yuri Victorovich2021-08-252-10/+21
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* biology/unikmer: Update 0.18.3 -> 0.18.4Yuri Victorovich2021-08-242-6/+6
| | | | Reported by: portscout
* biostar-tools: Update to 1.4.0Jason W. Bacon2021-08-242-2/+6
| | | | Add multiqc, flash, bfc, and jellyfish to metaport deps
* biology/bfc: Correct sequencing errors from Illumina sequencing dataJason W. Bacon2021-08-236-0/+76
| | | | | | | 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.
* biology/flash: Fast Length Adjustment of SHort readsJason W. Bacon2021-08-235-0/+57
| | | | | | | | | | 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.
* biology/minimap2: Add pkg-plist to repoJason W. Bacon2021-08-221-0/+10
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* biology/jellyfish: Update to 2.3.0Jason W. Bacon2021-08-226-58/+4
| | | | Changelog: https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0
* biology/minimap2: Update to 2.22Jason W. Bacon2021-08-223-10/+16
| | | | | | Changelog: https://github.com/lh3/minimap2/releases/tag/v2.22 Reported by: portscout
* biology/bbmap: Update to 38.92Jason W. Bacon2021-08-223-8/+22
| | | | | | Numerous small fixes and enhancements Reported by: portscout
* biology/pooler: Update to 1.77Jason W. Bacon2021-08-212-4/+6
| | | | | | Minor fixes and enhancements. Reported by: silas-freebsd@flatline.org.uk
* biology/igv: Broken on 11Yuri Victorovich2021-08-211-0/+2
| | | | Reported by: fallout
* biology/abyss: Broken on 11Yuri Victorovich2021-08-211-0/+1
| | | | Reported by: fallout
* biology/edlib: Update 1.2.6.20201202 -> 1.2.7Yuri Victorovich2021-08-212-5/+5
| | | | Reported by: portscout
* biology/hyphy: Update to 2.4.32Joseph Mingrone2021-08-204-32/+6
| | | | | | | | 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
* misc/: Update 0.99.6-2 -> 0.991Yuri Victorovich2021-08-181-0/+1
| | | | Reported by: portscout
* biology/ngs-sdk: Update 2.11.0-> 2.11.1Yuri Victorovich2021-08-184-29/+10
| | | | Reported by: portscout
* biology/py-PySCeS: New port: Python Simulator for Cellular SystemsYuri Victorovich2021-08-174-0/+45
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* biology/py-python-libsbml: New port: LibSBML Python APIYuri Victorovich2021-08-175-0/+32
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* biology/py-bx-python: Update 0.8.10 -> 0.8.11-6Yuri Victorovich2021-08-172-5/+10
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* biology/py-resdk: Update 13.3.0 -> 13.4.0wen heping2021-08-172-5/+5
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* biology/sigviewer: New port: Viewing application for biosignalsYuri Victorovich2021-08-174-0/+39
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* biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIXYuri Victorovich2021-08-171-1/+1
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* biology/biosig: New port: Library for reading and writing different ↵Yuri Victorovich2021-08-178-0/+460
| | | | biosignal data format
* biology/seqkit: Add 'test' targetYuri Victorovich2021-08-141-0/+4
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* biology/unikmer: Add 'test' targetYuri Victorovich2021-08-141-0/+13
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* biology/seaview: in preparation to FLTK update, unbreak the portAlexey Dokuchaev2021-08-142-3/+74
| | | | | | 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.
* biology/seqan3: Add the 'test' target (currently broken due to lacking clang ↵Yuri Victorovich2021-08-131-0/+8
| | | | support)
* biostar-tools: Correct category for py-ont-fast5-apiJason W. Bacon2021-08-131-1/+1
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* biostar-tools: Add new deps to metaportJason W. Bacon2021-08-132-4/+7
| | | | | csvkit, miller: Tools for working with comma-separated data py-ont-fast5-api: Library and tools for Oxford Nanopore fast5 files
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