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most of these simply extend matching from "aarch64" to "aarch64eb"
in various forms of code. most remaining uses in pkgsrc of
"MACHINE_ARCH == aarch64" are because of missing aarch64eb support,
such as most of the binary-bootstrap requiring languages like rust,
go, and java.
no pkg-bump because this shouldn't change packages on systems that
could already build all of these.
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-This is just a small release to fix some issues with the (possibly) renamed
*.so/*.dll files after removing Qt5 support. In case you were using Molsketch
prior to version 0.7.1, it will ask you to update the corresponding settings at
start up.
For Windows users, there will be an online installer, as in version 0.7.1, but
this will now reside in a separate folder and not be updated as frequently as
Molsketch itself. Updates will instead be made available in the online
repository at github from which the installer will fetch them. Just start the
installer and select the update option
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v3.4 (2021-03-30)
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* :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
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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.
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ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file.
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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.
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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.
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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.
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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
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The dependency is visible for packages using the LBFGS solver.
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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.
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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
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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.
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Cutadapt finds and removes adapter sequences, primers, poly-A tails and other
types of unwanted sequence from your high-throughput sequencing reads.
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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.
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Some major performance improvements
Numerous minor bug fixes and enhancements
Added a do-test target to the pkgsrc Makefile
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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.
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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.
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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.
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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
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For the Python 3.8 default switch.
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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
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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.
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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.
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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
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This requires scrollkeeper tools (as provided by textproc/rarian) in
order to build. It should also depend on graphics/hicolor-icon-theme.
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