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* biology/unikmer: Update 0.18.4 -> 0.18.8Yuri Victorovich2021-09-262-7/+7
| | | | Reported by: portscout
* biology/vcftools: Add CPE informationBernhard Froehlich2021-09-251-1/+3
| | | | Approved by: portmgr (blanket)
* biology/ucsc-userapps: Add "kent" command in ${PREFIX}/binJason W. Bacon2021-09-243-0/+63
| | | | | | | | | | | | 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]
* biology/emboss: Add "emboss" command in ${LOCALBASE}/binJason W. Bacon2021-09-244-2/+66
| | | | | | | | | | | | 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]
* biology/bioparser: Update 3.0.12-2 -> 3.0.15Yuri Victorovich2021-09-212-5/+4
| | | | Reported by: portscout
* */Makefile: Sort SUBDIRsPo-Chuan Hsieh2021-09-211-2/+2
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* biology/py-PySCeS: Update 0.9.8a -> 1.0.0Yuri Victorovich2021-09-202-9/+8
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* biology/py-libsedml: New port: SED-ML library for PythonYuri Victorovich2021-09-197-0/+89
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* biology/libsedml: New port: C++ SED-ML libraryYuri Victorovich2021-09-195-0/+149
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* biology/py-libnuml: Fix typoYuri Victorovich2021-09-191-1/+1
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* biology/py-libnuml: New port: Numerical Markup Language for PythonYuri Victorovich2021-09-196-0/+68
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* biology/libnuml: New port: C++ library for Numerical Markup LanguageYuri Victorovich2021-09-195-0/+80
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* biology/seqkit: Update 0.16.1 -> 2.0.1Yuri Victorovich2021-09-182-7/+7
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* biology/jellyfish: Switch to static tarball and update license infoJoseph Mingrone2021-09-172-10/+11
| | | | | | | | | | | | | 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>
* biology/biolibc: Update to 0.2.0.11Jason W. Bacon2021-09-172-5/+5
| | | | | Regenerate man pages with improved auto-c2man Adds missing return value sections and improves formatting
* biology/ugene: update Unipro UGENE to version 40.0.Alexey Dokuchaev2021-09-164-19/+15
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* biology/py-PySCeS: Update 0.9.8post1 -> 0.9.8aYuri Victorovich2021-09-143-5/+19
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* biology/hhsuite: Fix build on aarch64Mikael Urankar2021-09-131-1/+3
| | | | Approved by: portmgr (build fix blanket)
* biology/mmseqs2: disable on 32-bitsPiotr Kubaj2021-09-121-1/+1
| | | | 32-bits are not supported per https://github.com/soedinglab/MMseqs2/issues/460
* biology/jellyfish: Fix unused open mode variableJason W. Bacon2021-09-112-0/+12
| | | | | PR: 258397 Reported by: dim
* 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
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