v3.4 (2021-03-30)
-----------------
* :issue:`481`: An experimental single-file Windows executable of Cutadapt
is `available for download on the GitHub "releases"
page <https://github.com/marcelm/cutadapt/releases>`_.
* :issue:`517`: Report correct sequence in info file if read was reverse complemented
* :issue:`517`: Added a column to the info file that shows whether the read was
reverse-complemented (if ``--revcomp`` was used)
* :issue:`320`: Fix (again) "Too many open files" when demultiplexing
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.
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.
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.
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.
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
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.
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
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.
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.
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.
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.
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.
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
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
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.
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.
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
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
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.
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).
