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libomp.
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Point to the proper includedir.
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Upstream changelog
==================
Open Babel 3.0.0
@ghutchis ghutchis released this on 10 Oct - 29 commits to master since this release
This release represents a major update and is strongly recommended for all users.
It also removes deprecated components and breaks the API in a few places. For information on migrating from the previous version, please see:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#migrating-to-3-0
We intend to move to semi-annual releases in Spring and Fall, with bug fix releases as needed.
A sample of major new features:
Code for handling implicit hydrogens and kekulization has been entirely replaced. As well as being accurate, the new approach is much faster.
Speed of reading and writing SMILES has been improved by more than 50-fold.
Removal of the old 'babel' binary in favor of the newer 'obabel' command-line tool.
New improved fragment-based 3D coordinate generation code as part of Google Summer of code 2018/2019. Significantly faster and more accurate: https://doi.org/10.1186/s13321-019-0372-5
(Please cite J. Cheminf. (2019) v11, article 49 if you use the new 3D coordinate generation.)
New API for handling reactions stored as molecules (e.g. Reaction InChI, etc.)
New API for copying part of an OBMol as a substructure
Support for Maestro file format, contributed by Patrick Lorton of Schrodinger
There are an incredible number of improvements, minor features and many bug fixes.
For a full list of changes and to download source packages (and eventually binaries)
https://open-babel.readthedocs.io/en/latest/ReleaseNotes/ob300.html
https://github.com/openbabel/openbabel/releases
Thanks to a cast of many for this release, particularly including Noel O'Boyle;
aandi, adalke (Andrew Dalke), adamjstewart (Adam J. Stewart), afonari (Alexandr Fonari), artoria2e5 (Mingye Wang), baoilleach (Noel O'Boyle), barrymoo (Barry Moore), bbucior (Ben Bucior), boryszef (Borys Szefczyk), camannguyen (An Nguyen), cmanion (Charles A. Manion), cowsandmilk (David Hall), cstein (Casper Steinmann), derekharmon (Derek Harmon), djhogan (Daniel Hogan), dkoes (David Koes), e-kwsm (Eisuke Kawashima), eloyfelix (Eloy Felix), fredrikw (Fredrik Wallner), ghutchis (Geoff Hutchison), hille721 (Christoph Hille), hseara (Hector Martinez-Seara), jasonychuang (Jason Huang), jeffjanes (Jeff Janes), johnmay (John Mayfield), katrinleinweber (Katrin Leinweber), keipertk (Kristopher Keipert), kyle-roberts-arzeda, langner (Karol M. Langner), lorton (Pat Lorton), mcs07 (Matt Swain), merkys (Andrius Merkys), mkrykunov, mmghahremanpour (Mohammad Ghahremanpour), mwojcikowski (Maciej Wojcikowski), n-yoshikawa (Naruki Yoshikawa), nakatamaho (Nakata Maho), nsoranzo (Nicola Soranzo), oititov (Titov Oleg), orex (Kirill Okhotnikov), pbecherer (Paul Becherer), peawagon (Jen), philthiel (Philipp Thiel), psavery (Patrick Avery), rmeli (Rocco Meli), serval2412 (Julien Nabet), sunoru, susilehtola (Susi Lehtola), tgaudin (Theophile Gaudin), theavey (Thomas Heavey), timvdm (Tim Vandermeersch), torcolvin (Tor Colvin), wojdyr (Marcin Wojdyr), xomachine (Dmitriy Fomichev), yishutu (Yi-Shu Tu)
Open Babel 2.4.0 (2016-9-21)
This release represents a major update and should be a stable upgrade, strongly recommended for all users.
Note that this release deprecates the babel executable in favor of obabel. A future release will remove babel entirely. For information on the differences, please see the documentation.
New file formats
DALTON output files (read only) and DALTON input files (read/write) (Casper Steinmann)
JSON format used by ChemDoodle (read/write) (Matt Swain)
JSON format used by PubChem (read/write) (Matt Swain)
LPMD's atomic configuration file (read/write) (Joaquin Peralta)
The format used by the CONTFF and POSFF files in MDFF (read/write) (Kirill Okhotnikov)
ORCA output files (read only) and ORCA input files (write only) (Dagmar Lenk)
ORCA-AICCM's extended XYZ format (read/write) (Dagmar Lenk)
Painter format for custom 2D depictions (write only) (Noel O'Boyle)
Siesta output files (read only) (Patrick Avery)
Smiley parser for parsing SMILES according to the OpenSMILES specification (read only) (Tim Vandermeersch)
STL 3D-printing format (write only) (Matt Harvey)
Turbomole AOFORCE output (read only) (Mathias Laurin)
A representation of the VDW surface as a point cloud (write only) (Matt Harvey)
New file format capabilities and options
AutoDock PDBQT: Options to preserve hydrogens and/or atom names (Matt Harvey)
CAR: Improved space group support in .car files (kartlee)
CDXML: Read/write isotopes (Roger Sayle)
CIF: Extract charges (Kirill Okhotnikov)
CIF: Improved support for space-groups and symmetries (Alexandr Fonari)
DL_Poly: Cell information is now read (Kirill Okhotnikov)
Gaussian FCHK: Parse alpha and beta orbitals (Geoff Hutchison)
Gaussian out: Extract true enthalpy of formation, quadrupole, polarizability tensor, electrostatic potential fitting points and potential values, and more (David van der Spoel)
MDL Mol: Read in atom class information by default and optionally write it out (Roger Sayle)
MDL Mol: Support added for ZBO, ZCH and HYD extensions (Matt Swain)
MDL Mol: Implement the MDL valence model on reading (Roger Sayle)
MDL SDF: Option to write out an ASCII depiction as a property (Noel O'Boyle)
mmCIF: Improved mmCIF reading (Patrick Fuller)
mmCIF: Support for atom occupancy and atom_type (Kirill Okhotnikov)
Mol2: Option to read UCSF Dock scores (Maciej Wojcikowski)
MOPAC: Read z-matrix data and parse (and prefer) ESP charges (Geoff Hutchison)
NWChem: Support sequential calculations by optionally overwriting earlier ones (Dmitriy Fomichev)
NWChem: Extract info on MEP(IRC), NEB and quadrupole moments (Dmitriy Fomichev)
PDB: Read/write PDB insertion codes (Steffen Moller)
PNG: Options to crop the margin, and control the background and bond colors (Fredrik Wallner)
PQR: Use a stored atom radius (if present) in preference to the generic element radius (Zhixiong Zhao)
PWSCF: Extend parsing of lattice vectors (David Lonie)
PWSCF: Support newer versions, and the 'alat' term (Patrick Avery)
SVG: Option to avoid addition of hydrogens to fill valence (Lee-Ping)
SVG: Option to draw as ball-and-stick (Jean-Noel Avila)
VASP: Vibration intensities are calculated (Christian Neiss, Mathias Laurin)
VASP: Custom atom element sorting on writing (Kirill Okhotnikov)
Other new features and improvements
2D layout: Improved the choice of which bonds to designate as hash/wedge bonds around a stereo center (Craig James)
3D builder: Use bond length corrections based on bond order from Pyykko and Atsumi (http://dx.doi.org/10.1002/chem.200901472) (Geoff Hutchison)
3D generation: "--gen3d", allow user to specify the desired speed/quality (Geoff Hutchison)
Aromaticity: Improved detection (Geoff Hutchison)
Canonicalisation: Changed behaviour for multi-molecule SMILES. Now each molecule is canonicalized individually and then sorted. (Geoff Hutchison/Tim Vandermeersch)
Charge models: "--print" writes the partial charges to standard output after calculation (Geoff Hutchison)
Conformations: Confab, the systematic conformation generator, has been incorporated into Open Babel (David Hall/Noel O'Boyle)
Conformations: Initial support for ring rotamer sampling (Geoff Hutchison)
Conformer searching: Performance improvement by avoiding gradient calculation and optimising the default parameters (Geoff Hutchison)
EEM charge model: Extend to use additional params from http://dx.doi.org/10.1186/s13321-015-0107-1 (Tomas Racek)
FillUnitCell operation: Improved behavior (Patrick Fuller)
Find duplicates: The "--duplicate" option can now return duplicates instead of just removing them (Chris Morley)
GAFF forcefield: Atom types updated to match Wang et al. J. Comp. Chem. 2004, 25, 1157 (Mohammad Ghahremanpour)
New charge model: EQeq crystal charge equilibration method (a speed-optimized crystal-focused charge estimator, http://pubs.acs.org/doi/abs/10.1021/jz3008485) (David Lonie)
New charge model: "fromfile" reads partial charges from a named file (Matt Harvey)
New conversion operation: "changecell", for changing cell dimensions (Kirill Okhotnikov)
New command-line utility: "obthermo", for extracting thermochemistry data from QM calculations (David van der Spoel)
New fingerprint: ECFP (Geoff Hutchison/Noel O'Boyle/Roger Sayle)
OBConversion: Improvements and API changes to deal with a long-standing memory leak (David Koes)
OBAtom::IsHBondAcceptor(): Definition updated to take into account the atom environment (Stefano Forli)
Performance: Faster ring-finding algorithm (Roger Sayle)
Performance: Faster fingerprint similarity calculations if compiled with -DOPTIMIZE_NATIVE=ON (Noel O'Boyle/Jeff Janes)
SMARTS matching: The "-s" option now accepts an integer specifying the number of matches required (Chris Morley)
UFF: Update to use traditional Rappe angle potential (Geoff Hutchison)
Language bindings
Bindings: Support compiling only the bindings against system libopenbabel (Reinis Danne)
Java bindings: Add example Scala program using the Java bindings (Reinis Danne)
New bindings: PHP (Maciej Wojcikowski)
PHP bindings: BaPHPel, a simplified interface (Maciej Wojcikowski)
Python bindings: Add 3D depiction support for Jupyter notebook (Patrick Fuller)
Python bindings, Pybel: calccharges() and convertdbonds() added (Patrick Fuller, Bjorn Gruning)
Python bindings, Pybel: compress output if filename ends with .gz (Maciej Wojcikowski)
Python bindings, Pybel: Residue support (Maciej Wojcikowski)
Development/Build/Install Improvements
Version control: move to git and GitHub from subversion and SourceForge
Continuous integration: Travis for Linux builds and Appveyor for Windows builds (David Lonie and Noel O'Boyle)
Python installer: Improvements to the Python setup.py installer and "pip install openbabel" (David Hall, Matt Swain, Joshua Swamidass)
Compilation speedup: Speed up compilation by combining the tests (Noel O'Boyle)
MacOSX: Support compiling with libc++ on MacOSX (Matt Swain)
Cast of contributors
Alexandr Fonari, Anders Steen Christensen, Andreas Kempe, arkose, Benoit Leblanc, Bjorn Gruning, Casper Steinmann, Chris Morley, Christoph Willing, Craig James, Dagmar Lenk, David Hall, David Koes, David Lonie, David van der Spoel, Dmitriy Fomichev, Fulvio Ciriaco, Fredrik Wallner, Geoff Hutchison, Heiko Becker, Itay Zandbank, Jean-Noel Avila, Jeff Janes, Joaquin Peralta, Joshua Swamidass, Julien Nabet, Karol Langner, Karthik Rajagopalan, Katsuhiko Nishimra, Kevin Horan, Kirill Okhotnikov, Lee-Ping, Matt Harvey, Maciej Wojcikowski, Marcus Hanwell, Mathias Laurin, Matt Swain, Mohamad Mohebifar, Mohammad Ghahremanpour, Noel O'Boyle, Patrick Avery, Patrick Fuller, Paul van Maaren, Peng Bai, Philipp Thiel, Reinis Danne, Roger Sayle, Ronald Cohen, Scott McKechnie, Stefano Forli, Steve Roughley, Steffen Moeller, Tim Vandermeersch, Tomas Racek, Tomas Trnka, Tor Colvin, Torsten Sachse, Yi-Shu Tu, Zhixiong Zhao
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pkglint -Wall -F --only aligned --only indent -r
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From Eric A. Borisch in pull request NetBSD/pkgsrc#52.
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future Python 3.8
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Start building FreeGLUT with GLUT compatibility on.
- GLUT's maintainance state is much worse than FreeGLUT's, with no
substanital commits since 2011.
- GLUT can no longer be consider a core component of Mesa or X11.
- Nobody except us seems to be using it...
Other vendors still shipping GLUT:
- GoboLinux, T2 SDE, PLD Linux
Revbump packages using GLUT or freeglut by default.
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The biopython license is _very_ similar, but not identical, to many
other open source licenses used throughout pkgsrc. The gratuitous
differences are being addressed by the project through an effort to
relicense all files to the 3-clause BSD license. In the meantime,
Debian has accepted that the current biopython license meets the DFSG
and includes the package in their main distribution. Consequently,
rename the license file and add it to DEFAULT_ACCEPTABLE_LICENSES.
See http://mail-index.netbsd.org/pkgsrc-changes/2019/08/13/msg195804.html.
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The Biopython package contains high-quality, reusable modules and
scripts written in Python to make it as easy as possible to use Python
for bioinformatics. The Biopython includes the follwing: the ability
to parse bioinformatics files into python utilizable data structures,
including support for the formats such as Blast output, Clustalw,
FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP,
Rebase, UniGene, and SwissProt.
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The former now redirects to the latter.
This covers the most simple cases where http://search.cpan.org/dist/name
can be changed to https://metacpan.org/release/name.
Reviewed by hand to hopefully make sure no unwanted changes sneak in.
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Configure script does not support --enable-option-checking
Also add perl to USE_TOOLS
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Reviewed by hand.
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pkgsrc patches incorporated into upstream release
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VSEARCH supports de novo and reference based chimera detection,
clustering, full-length and prefix dereplication, rereplication,
reverse complementation, masking, all-vs-all pairwise global
alignment, exact and global alignment searching, shuffling,
subsampling and sorting. It also supports FASTQ file analysis,
filtering, conversion and merging of paired-end reads.
The aim of this project is to create an alternative to the USEARCH
tool developed by Robert C. Edgar (2010).
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fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
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libaec is a BSD-licensed drop-in replacement for the non-redistributable szip
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python 3.4 / 3.5 removal commit.
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- Includes some whitespace changes, to be handled in a separate commit.
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This is a semi-manual PKGREVISION bump.
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Upstream build does not use LDFLAGS canonically.
Makefile.in will require restructuring to eliminate workaround.
This patch fixes build on CentOS and build with RELRO on NetBSD.
Also add LICENSE and fig2dev runtime dependency.
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Fixes build on CentOS 7 minimal.
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Resolves build failures on CentOS
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HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as to a single reference genome).
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jwbacon@tds.net ==> bacon@NetBSD.org
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Support for new BLAST database format
Increased makeblastdb output file size limit to 4GB
Other minor bug fixes and enhancements
OK wiz@
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Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
Canu is a hierarchical assembly pipeline which runs in four steps:
Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences
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Stacks is a software pipeline for building loci from short-read sequences, such
as those generated on the Illumina platform. Stacks was developed to work with
restriction enzyme-based data, such as RAD-seq, for the purpose of building
genetic maps and conducting population genomics and phylogeography.
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Kallisto is a program for quantifying abundances of transcripts from RNA-Seq
data, or more generally of target sequences using high-throughput sequencing
reads. It is based on the novel idea of pseudoalignment for rapidly determining
the compatibility of reads with targets, without the need for alignment.
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From Eric A. Borisch in pull request NetBSD/pkgsrc#40.
- Do not derive Dataset from dict (#767)
- fixes side effects from initializing with another dataset
- Added missing dict methods that are passed to the tags dict
- Adapted documentation to Dataset changes
- Make sure that the retry order config is reset in the test (#772)
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BCFtools is a program for variant calling and manipulating files in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
In order to avoid tedious repetion, throughout this document we will use "VCF"
and "BCF" interchangeably, unless specifically noted.
Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.
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Release 1.9:
* Samtools mpileup VCF and BCF output is now deprecated. It is still
functional, but will warn. Please use bcftools mpileup instead.
* Samtools mpileup now handles the '-d' max_depth option differently. There
is no longer an enforced minimum, and '-d 0' is interpreted as limitless
(no maximum - warning this may be slow). The default per-file depth is
now 8000, which matches the value mpileup used to use when processing
a single sample. To get the previous default behaviour use the higher
of 8000 divided by the number of samples across all input files, or 250.
* Samtools stats new features:
- The '--remove-overlaps' option discounts overlapping portions of
templates when computing coverage and mapped base counting.
- When a target file is in use, the number of bases inside the
target is printed and the percentage of target bases with coverage
above a given threshold specified by the '--cov-threshold' option.
- Split base composition and length statistics by first and last reads.
* Samtools faidx new features:
- Now takes long options.
- Now warns about zero-length and truncated sequences due to the
requested range being beyond the end of the sequence.
- Gets a new option (--continue) that allows it to carry on
when a requested sequence was not in the index.
- It is now possible to supply the list of regions to output in a text
file using the new '--region-file' option.
- New '-i' option to make faidx return the reverse complement of
the regions requested.
- faidx now works on FASTQ (returning FASTA) and added a new
fqidx command to index and return FASTQ.
* Samtools collate now has a fast option '-f' that only operates on
primary pairs, dropping secondary and supplementary. It tries to write
pairs to the final output file as soon as both reads have been found.
* Samtools bedcov gets a new '-j' option to make it ignore deletions (D) and
reference skips (N) when computing coverage.
* Small speed up to samtools coordinate sort, by converting it to use
radix sort.
* Samtools idxstats now works on SAM and CRAM files, however this
isn't fast due to some information lacking from indices.
* Compression levels may now be specified with the level=N
output-fmt-option. E.g. with -O bam,level=3.
* Various documentation improvements.
* Bug-fixes:
- Improved error reporting in several places.
- Various test improvements.
- Fixed failures in the multi-region iterator (view -M) when regions
provided via BED files include overlaps
- Samtools stats now counts '=' and 'X' CIGAR operators when
counting mapped bases.
- Samtools stats has fixes for insert size filtering (-m, -i).
- Samtools stats -F now longer negates an earlier -d option.
- Fix samtools stats crash when using a target region.
- Samtools sort now keeps to a single thread when the -@ option is absent.
Previously it would spawn a writer thread, which could cause the CPU
usage to go slightly over 100%.
- Fixed samtools phase '-A' option which was incorrectly defined to take
a parameter.
- Fixed compilation problems when using C_INCLUDE_PATH.
- Fixed --version when built from a Git repository.
- Use noenhanced mode for title in plot-bamstats. Prevents unwanted
interpretation of characters like underscore in gnuplot version 5.
- blast2sam.pl now reports perfect match hits (no indels or mismatches).
- Fixed bug in fasta and fastq subcommands where stdout would not be flushed
correctly if the -0 option was used.
- Fixed invalid memory access in mpileup and depth on alignment records
where the sequence is absent.
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1.9:
If ./configure fails, make will stop working until either configure is re-run successfully, or make distclean is used. This makes configuration failures more obvious.
The default SAM version has been changed to 1.6. This is in line with the latest version specification and indicates that HTSlib supports the CG tag used to store long CIGAR data in BAM format.
bgzip integrity check option '--test'
Faidx can now index fastq files as well as fasta. The fastq index adds an extra column to the .fai index which gives the offset to the quality values. New interfaces have been added to htslib/faidx.h to read the fastq index and retrieve the quality values. It is possible to open a fastq index as if fasta (only sequences will be returned), but not the other way round.
New API interfaces to add or update integer, float and array aux tags.
Add level=<number> option to hts_set_opt() to allow the compression level to be set. Setting level=0 enables uncompressed output.
Improved bgzip error reporting.
Better error reporting when CRAM reference files can't be opened.
Fixes to make tests work properly on Windows/MinGW - mainly to handle line ending differences.
Efficiency improvements:
Small speed-up for CRAM indexing.
Reduce the number of unnecessary wake-ups in the thread pool.
Avoid some memory copies when writing data, notably for uncompressed BGZF output.
Bug fixes:
Fix multi-region iterator bugs on CRAM files.
Fixed multi-region iterator bug that caused some reads to be skipped incorrectly when reading BAM files.
Fixed synced_bcf_reader() bug when reading contigs multiple times.
Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when removing samples.
Fixed bug where the VCF record ref length was calculated incorrectly if an INFO END tag was present. (71b00a)
Fixed warnings found when compiling with gcc 8.1.0.
sam_hdr_read() and sam_hdr_write() will now return an error code if passed a NULL file pointer, instead of crashing.
Fixed possible negative array look-up in sam_parse1() that somehow escaped previous fuzz testing.
Fixed bug where cram range queries could incorrectly report an error when using multiple threads.
Fixed very rare rANS normalisation bug that could cause an assertion failure when writing CRAM files.
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