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2021-03-24biology/Makefile: Add vcf2hapbacon1-1/+2
2021-03-24biology/vcf2hap: import vcf2hap-0.1.2bacon4-0/+32
vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file is required by haplohseq. vcf2hap is extremely fast and requires a trivial amount of memory regardless of the size of the VCF file.
2021-03-24biology/Makefile: Add ad2vcfbacon1-1/+2
2021-03-24biology/ad2vcf: import ad2vcf-0.1.2bacon4-0/+30
ad2vdf extracts allelic depth info from a SAM stream and adds it to a corresponding single-sample VCF file.
2021-03-24biology/Makefile: Add biolibc, vcf-splitbacon1-1/+3
2021-03-24biology/vcf-split: import vcf-split-0.1.1bacon4-0/+31
Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF with bcftools takes two days, so extracting the 137,977 samples one at a time or using thousands of parallel readers of the same file is impractical. Vcf-split solves this by generating thousands of single-sample outputs during a single sweep through the multi-sample input.
2021-03-24biology/biolibc: import biolibc-0.1.1bacon5-0/+43
Biolibc is a library of fast, memory-efficient, low-level functions for processing biological data. Like libc, it consists of numerous disparate, general-purpose functions which could be used by a wide variety of applications. These include functions for streaming common file formats such as SAM and VCF, string functions specific to bioinformatics, etc.
2021-03-21biology/Makefile: Add generandbacon1-1/+2
2021-03-21biology/generand: import generand-0.1.2bacon4-0/+24
Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for small academic examples or test inputs of arbitrary size. Output can be piped directly to programs or redirected to a file and edited to taste.
2021-03-20biology/htslib: Update to 1.12bacon16-321/+53
biology/bcftools: Update to 1.12 biology/samtools: Update to 1.12 Numerous enhancements, performance improvements, and bug fixes since 1.10 Minimized pkgsrc patches in all three packages Moved htslib to custom tarball since Github-generated distfiles are incomplete
2021-03-17openbabel: make buildlink3.mk match Makefile and require eigen3prlw13-6/+6
The dependency is visible for packages using the LBFGS solver.
2021-03-09biology/molsketch: update to 0.7.1pin3-12/+15
Unfortunately, there were quite some unintended bugs in the last version (some of them older than that, however), which are being addressed by this version. Saving files and re-opening might have sometimes led to crashes due to inconsistencies in the drawing's data. This should now be fixed in, if not all at least most of the cases. Likewise, copying, cutting, and pasting is more robust now. The last version prematurely updated some code leading to incompatibilities with older versions of Qt (especially pre-5.14). These older versions should now work again; support for Qt 4, on the other hand is completely removed, as it is doubtful whether that still worked anyway. Translations should now really work throughout Molsketch (currently supported languages: Chinese, English, German, Greek). Finally, for Windows, an installer is provided, which will download from a repository hosted at github.
2021-03-08py-cutadapt: updated to 3.3adam2-7/+7
v3.3: * :issue:`504`: Fix a crash on Windows. * :issue:`490`: When ``--rename`` is used with ``--revcomp``, disable adding the ``rc`` suffix to reads that were reverse-complemented. * Also, there is now a ``{rc}` template variable for the ``--rename`` option, which is replaced with "rc" if the read was reverse-complemented (and the empty string if not). * :issue:`512`: Fix issue :issue:`128` once more (the “Reads written” figure in the report incorrectly included both trimmed and untrimmed reads if ``--untrimmed-output`` was used). * :issue:`515`: The report is now send to stderr if any output file is written to stdout
2021-03-04(biology/py-dnaio) +BUILD_DEPENDS+= py-setuptools_scm (other than 27 are fixed)mef1-1/+3
2021-02-24biology/Makefile: + igvwiz1-1/+2
2021-02-24biology/igv: import igv-2.9.2bacon5-0/+343
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
2021-02-12biology/Makefile: sort entriesgutteridge1-3/+3
2021-02-11py-cutadapt: fix CATEGORY, mark as not for 2.7 and 3.6, use ALTERNATIVESadam3-6/+11
2021-02-08biology/Makefile: Add py-cutadaptbacon1-1/+2
2021-02-08biology/py-cutadapt: import py38-cutadapt-3.2bacon4-0/+76
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
2021-02-08biology/Makefile: Add py-dnaiobacon1-1/+2
2021-02-08biology/py-dnaio: import py38-dnaio-0.5.0bacon4-0/+51
dnaio is a Python 3 library for fast input and output of FASTQ and FASTA files. It supports paired-end data in separate files, interleaved paired-end in a single file and compression using gzip, bzip, and xz.
2021-02-08biology/bedtools: Update to 2.30.0bacon7-20/+76
Some major performance improvements Numerous minor bug fixes and enhancements Added a do-test target to the pkgsrc Makefile
2021-01-22biology/Makefile: Add bedtoolsbacon1-1/+2
2021-01-22biology/bedtools: import bedtools-2.29.2bacon6-0/+159
The bedtools utilities are a suite of tools for performing a wide range of genomics analysis tasks. The most widely-used of these tools enable genome arithmetic, i.e., set theory on the genome. For example, with bedtools one can intersect, merge, count, complement, and shuffle genomic intervals from multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF. Although each individual utility is designed to do a relatively simple task, e.g., intersect two interval files, more sophisticated analyses can be conducted by stringing together multiple bedtools operations on the command line or in shell scripts.
2021-01-21biology/Makefile: Add bowtie2bacon1-1/+2
2021-01-21biology/bowtie2: import bowtie2-2.4.2bacon6-0/+131
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour.
2021-01-20biology/Makefile: Add fastqcbacon1-1/+2
2021-01-20biology/fastqc: import fastqc-0.11.9bacon4-0/+301
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
2021-01-01*: Recursive revbump from boost-1.75.0ryoon6-8/+12
2020-12-18Add biology/molsketchpin1-1/+2
2020-12-18biology/molsketch: import version 0.7.0pin4-0/+184
Originally packaged by Kamil Rytarowski (v0.6.0) on wip kindly responding to a request of mine. Molsketch is a 2D molecular editing tool. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats. Features: * open, save and import in all formats supported by the OpenBabel(tm) library * export to Scalable Vector Graphics (SVG) and a number of common used bitmap formats * print and export your document to PDF
2020-12-04Revbump packages with a runtime Python dep but no version prefix.nia5-10/+10
For the Python 3.8 default switch.
2020-11-05*: Recursive revbump from textproc/icu-68.1ryoon4-8/+8
2020-11-05*: Recursive revbump from textproc/icu-68.1ryoon2-4/+4
2020-11-04openbabel: do not download dependencies during buildbsiegert4-41/+43
Explicitly depend against maeparser, coordgenlibs and rapidjson, so that the build does not download the current version from github (!). Also fix the coordgenlibs detection logic -- this is also submitted upstream. Fixes PR pkg/55755
2020-11-03New package, coordgenlibs-1.4.2.bsiegert6-1/+76
Part of PR pkg/55755. This is Schroedinger, Inc's 2D coordinate generation. It was formerly proprietary code, but is now released under the BSD license. The emphasis of these algorithms are on quality of 2D coordinates rather than speed of generation. The algorithm distinguishes itself from many others by doing well with both macrocycles and metal complexes. It also does extremely well on typical drug-like small molecules, and has been validated on millions of compounds.
2020-11-03New package, maeparser-1.4.2.bsiegert6-1/+60
maeparser is a parser for Schrodinger Maestro files. Structure files (.mae,.maegz,.mae.gz) can contain multiple structures delimited by "f_m_ct". See MaeConstants.hpp for standard block and property names.
2020-11-01(biology/openbabel) Regen PLISTmef1-2/+2
2020-10-12math/blas, math/lapack: Install interchangeable BLAS systembacon4-10/+10
Install the new interchangeable BLAS system created by Thomas Orgis, currently supporting Netlib BLAS/LAPACK, OpenBLAS, cblas, lapacke, and Apple's Accelerate.framework. This system allows the user to select any BLAS implementation without modifying packages or using package options, by setting PKGSRC_BLAS_TYPES in mk.conf. See mk/blas.buildlink3.mk for details. This commit should not alter behavior of existing packages as the system defaults to Netlib BLAS/LAPACK, which until now has been the only supported implementation. Details: Add new mk/blas.buildlink3.mk for inclusion in dependent packages Install compatible Netlib math/blas and math/lapack packages Update math/blas and math/lapack MAINTAINER approved by adam@ OpenBLAS, cblas, and lapacke will follow in separate commits Update direct dependents to use mk/blas.buildlink3.mk Perform recursive revbump
2020-09-25gnome-chemistry-utils: fix buildsgutteridge1-2/+5
This requires scrollkeeper tools (as provided by textproc/rarian) in order to build. It should also depend on graphics/hicolor-icon-theme.
2020-09-06bioperl: update to 1.7.7.wiz3-26/+13
1.7.7 2019-12-07 13:41:36-06:00 America/Chicago * The program bp_chaos_plot has been removed. * GD is now no longer a dependency, suggestion or requirement. * #321 - GenBank format fix for un-quoted features, text wrapping * Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(), and a 'private' _sleep() function that mirror those from Bio::DB::WebDBSeqI, primarily for compliance with potential website restrictions for the number and frequency of queries (e.g. NCBI eUtils). * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation in last release. 1.7.6 2019-08-28 12:37:01+01:00 Europe/London * The program bp_classify_hits_kingdom has been removed and is now part of the examples documentation instead. * GD is now listed as a suggestion instead of a requirement. The bp_chaos_plot program will now work with the GD module. * New method Bio::Tree::Statistics::transfer_bootstrap_expectation to compute Transfer Bootstrap Expectation (TBE) for internal nodes based on the methods outlined in Lemoine et al, Nature, 2018. * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next sequence in the stream faster but not perfect. 1.7.5 2019-02-11 14:57:45+00:00 Europe/London * The following modules have been removed from the BioPerl distribution to be part of a separate distribution with independent development: Bio::Symbol::* * The Bio::Seq::SeqWithQuality module, which was deprecated since 2001, was finally removed. * The deprecated() method has been deprecated. It is recommended to use Carp::carp to warn. * The following methods have been deprecated for a long while and have now been removed: Bio::Align::AlignI->no_residues Bio::Align::AlignI->no_sequences Bio::LocatableSeq->no_gap Bio::LocatableSeq->no_sequences Bio::SeqFeature::Generic->slurp_gff_file Bio::SimpleAlign->no_residues Bio::SimpleAlign->no_sequences 1.7.4 2019-02-05 16:23:53+00:00 Europe/London * Fix Bio::Root::Test, and the testuite, to properly check for internet connection and the NO_NETWORK_TESTING environment variable. Previously, tests that required internet connection were not being skipped, causing tests to fail. 1.7.3 2019-01-30 13:30:34+00:00 Europe/London * The following modules have been removed from the BioPerl distribution to be part of a separate distribution. They have been integrated into other module distributions for independent development: Bio::Align::Graphics Bio::AlignIO::nexml Bio::AlignIO::stockholm Bio::Assembly::* Bio::Cluster::* Bio::ClusterI::* Bio::ClusterIO::* Bio::DB::Ace Bio::DB::BioFetch Bio::DB::CUTG Bio::DB::EMBL Bio::DB::EntrezGene Bio::DB::Expression::* Bio::DB::GFF Bio::DB::GFF::Adaptor::* Bio::DB::GFF::Aggregator::* Bio::DB::GFF::Featname Bio::DB::GFF::Feature Bio::DB::GFF::Homol Bio::DB::GFF::RelSegment Bio::DB::GFF::Segment Bio::DB::GFF::Typename Bio::DB::GenBank Bio::DB::GenPept Bio::DB::HIV::* Bio::DB::MeSH Bio::DB::NCBIHelper Bio::DB::Query::GenBank Bio::DB::Query::HIVQuery Bio::DB::RefSeq Bio::DB::SeqFeature::* Bio::DB::SeqVersion::* Bio::DB::SwissProt Bio::DB::TFBS::* Bio::DB::Taxonomy::entrez Bio::DB::Taxonomy::sqlite Bio::DB::Universal Bio::Draw::Pictogram Bio::Factory::MapFactoryI Bio::Index::Hmmer Bio::Index::Stockholm Bio::LiveSeq::* Bio::Map::* Bio::MapIO::* Bio::MolEvol::CodonModel Bio::Nexml::Factory Bio::NexmlIO Bio::Perl Bio::Phenotype::* Bio::PhyloNetwork::* Bio::PopGen::* Bio::Restriction::* Bio::Root::Build Bio::Search::HSP::HMMERHSP Bio::Search::HSP::HmmpfamHSP Bio::Search::Hit::HMMERHit Bio::Search::Hit::HmmpfamHit Bio::Search::Hit::hmmer3Hit Bio::Search::Result::HMMERResult Bio::Search::Result::HmmpfamResult Bio::Search::Result::hmmer3Result Bio::SearchDist Bio::SearchIO::hmmer Bio::SearchIO::hmmer2 Bio::SearchIO::hmmer3 Bio::SearchIO::hmmer_pull Bio::SeqEvolution::* Bio::SeqFeature::SiRNA::* Bio::SeqIO::abi Bio::SeqIO::agave Bio::SeqIO::alf Bio::SeqIO::chadoxml Bio::SeqIO::chaos Bio::SeqIO::chaosxml Bio::SeqIO::ctf Bio::SeqIO::entrezgene Bio::SeqIO::excel Bio::SeqIO::exp Bio::SeqIO::flybase_chadoxml Bio::SeqIO::lasergene Bio::SeqIO::nexml Bio::SeqIO::pln Bio::SeqIO::strider Bio::SeqIO::ztr Bio::Structure::* Bio::Taxonomy::* Bio::Tools::AlignFactory Bio::Tools::Analysis::* (except SimpleAnalysisBase) Bio::Tools::Gel Bio::Tools::HMMER::* Bio::Tools::Hmmpfam Bio::Tools::Phylo::Gumby Bio::Tools::Protparam Bio::Tools::Run::RemoteBlast Bio::Tools::SiRNA::* Bio::Tools::dpAlign Bio::Tools::pSW Bio::Tree::AlleleNode Bio::Tree::Draw::Cladogram Bio::TreeIO::nexml Bio::TreeIO::svggraph Bio::Variation::* * The following modules are new in the BioPerl distribution. They have been previously released in the BioPerl-Run distribution. This will enable smaller distributions that provide a Bio::Tool::Run interface, to be only dependent on the BioPerl distribution instead of the whole (very large) BioPerl-Run: Bio::Tools::Run::Analysis Bio::Tools::Run::AnalysisFactory Bio::Tools::Run::Phylo::PhyloBase Bio::Tools::Run::WrapperBase Bio::Tools::Run::WrapperBase::CommandExts * The following programs have been removed: bp_biofetch_genbank_proxy bp_blast2tree bp_bulk_load_gff bp_composite_LD bp_das_server bp_download_query_genbank bp_fast_load_gff bp_flanks bp_genbank2gff bp_generate_histogram bp_heterogeneity_test bp_hivq bp_hmmer_to_table bp_load_gff bp_meta_gff bp_netinstall bp_parse_hmmsearch bp_process_wormbase bp_query_entrez_taxa bp_remote_blast bp_seqfeature_delete bp_seqfeature_gff3 bp_seqfeature_load * Because of the move of so many modules and programs into separate distributions, the following modules are no longer prerequisites: Ace Ace::Sequence::Homol Algorithm::Munkres Apache::DBI Archive::Tar Array::Compare Bio::ASN1::EntrezGene Bio::Expression::Contact Bio::Expression::DataSet Bio::Expression::Platform Bio::Expression::Sample Bio::Ext::Align Bio::GMOD::CMap::Utils Bio::Phylo::Factory Bio::Phylo::Forest::Tree Bio::Phylo::IO Bio::Phylo::Matrices Bio::Phylo::Matrices::Datum Bio::Phylo::Matrices::Matrix Bio::SeqFeature::Annotated Bio::SeqIO::staden::read Bio::Tools::Run::Alignment::Clustalw Bio::Tools::Run::Ensembl Bio::Tools::Run::Phylo::Molphy::ProtML Bio::Tools::Run::Phylo::Phylip::Neighbor Bio::Tools::Run::Phylo::Phylip::ProtDist Bio::Tools::Run::Phylo::Phylip::ProtPars Bio::Tools::Run::Samtools CGI CPAN Cache::FileCache Config Convert::Binary::C DBD::Pg DBD::SQLite Data::Stag::XMLWriter Encode English ExtUtils::Install ExtUtils::Manifest File::Glob GD::Simple Getopt::Std Graph::Undirected GraphViz HTML::HeadParser HTML::TableExtract LWP LWP::Simple MIME::Base64 Memoize PostScript::TextBlock SVG SVG::Graph SVG::Graph::Data SVG::Graph::Data::Node SVG::Graph::Data::Tree Sort::Naturally Spreadsheet::ParseExcel Term::ReadLine Text::NSP::Measures::2D::Fisher2::twotailed Text::ParseWords Time::Local Tree::DAG_Node URI::Escape WWW::Mechanize XML::Simple * The following is a new prerequisite: Test::RequiresInternet * The deobfuscator has been removed. * The emacs bioperl minor mode is no longer distributed as part of the perl module distributions. See https://github.com/bioperl/emacs-bioperl-mode
2020-09-06p5-Bio-ASN1-EntrezGene: update to 1.73.wiz2-9/+9
1.73 2018-09-24 21:31:26-05:00 America/Chicago * Fix regex warnings for Perl 5.28. * New module 'Bio::SeqIO::entrezgene' imported from the BioPerl distribution. This means Bio-ASN1-Entrezgene now "Enhances" BioPerl's Bio::SeqIO instead of being a hard dependency of BioPerl.
2020-08-31*: bump PKGREVISION for perl-5.32.wiz16-30/+32
2020-08-17*: revbump after fontconfig bl3 changes (libuuid removal)leot5-8/+10
2020-08-10biology/R-popbio: import R-popbio-2.7brook4-1/+26
Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
2020-07-30kallisto: remove patches that were removed from distinfo during updatewiz2-58/+0
2020-07-27biology/bcftools: Upgrade to 1.10.2bacon6-36/+157
Numerous bug fixes, usability improvements and sanity checks were added since 1.9 to prevent common user errors.
2020-07-26biology/samtools: Upgrade to 1.10bacon4-20/+119
Numerous performance and feature improvements and several bug fixes since 1.9
2020-07-23biology/kallisto: Upgrade to 0.46.1bacon3-18/+15
Minor enhancements since 0.45 0.46.2 is available, but has serious regressions. Reverted to bundled htslib 1.4.1, since kallisto source contains modified htslib files that are incompatible with the current 1.10.2 package.
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-26 06:09:41 +0000