summaryrefslogtreecommitdiff
path: root/biology
AgeCommit message (Collapse)AuthorFilesLines
2020-03-26Fix portabilityjoerg2-1/+15
2020-03-20*: Convert broken sourceforge HOMEPAGEs back to httpnia1-2/+2
2020-03-10librsvg: update bl3.mk to remove libcroco in rust casewiz4-8/+8
recursive bump for the dependency change
2020-03-08*: recursive bump for libffiwiz8-16/+16
2020-01-26all: migrate homepages from http to httpsrillig6-12/+12
pkglint -r --network --only "migrate" As a side-effect of migrating the homepages, pkglint also fixed a few indentations in unrelated lines. These and the new homepages have been checked manually.
2020-01-26all: migrate some SourceForge homepage URLs back from https to httprillig5-10/+10
https://mail-index.netbsd.org/pkgsrc-changes/2020/01/18/msg205146.html In the above commit, the homepage URLs were migrated from http to https, assuming that SourceForge would use the same host names for both http and https connections. This assumption was wrong. Their documentation at https://sourceforge.net/p/forge/documentation/Custom%20VHOSTs/ states that the https URLs use the domain sourceforge.io instead. To make the homepages from the above commit reachable again, pkglint has been extended to check for reachable homepages. This check is only enabled when the --network command line option is given. Each of the homepages that referred to https://$project.sourceforge.net before was migrated to https://$project.sourceforge.io (27), and if that was not reachable, to the fallback URL http://$project.sourceforge.net (163).
2020-01-18all: migrate several HOMEPAGEs to httpsrillig8-16/+16
pkglint --only "https instead of http" -r -F With manual adjustments afterwards since pkglint 19.4.4 fixed a few indentations in unrelated lines. This mainly affects projects hosted at SourceForce, as well as freedesktop.org, CTAN and GNU.
2020-01-18*: Recursive revision bump for openssl 1.1.1.jperkin1-2/+2
2020-01-12*: Recursive revbump from devel/boost-libsryoon2-4/+4
2020-01-11chemtool: Mark as PaX mprotect unsafe to prevent segfaultryoon1-2/+5
Bump PKGREVISION.
2019-12-21Don't hardcode libgomp, but use -fopenmp for linking. Fixes clang withjoerg2-1/+15
libomp.
2019-11-20gnome-chemistry-utils: Revbump for openbabel 3.0.0nb1kamil1-2/+2
2019-11-20openbabel: Fix pkg-config .pc filekamil4-4/+21
Point to the proper includedir. Bump PKGREVISION
2019-11-20openbabel: Upgrade to 3.0.0kamil12-198/+199
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
2019-11-02biology: align variable assignmentsrillig10-33/+33
pkglint -Wall -F --only aligned --only indent -r
2019-10-01py-pydicom: Update to 1.3.0nia3-138/+150
From Eric A. Borisch in pull request NetBSD/pkgsrc#52.
2019-09-02Changed PYTHON_VERSIONS_INCOMPATIBLE to PYTHON_VERSIONS_ACCEPTED; needed for ↵adam1-2/+2
future Python 3.8
2019-08-30Switch packages using GLUT to FreeGLUT.nia2-6/+6
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.
2019-08-22Recursive revbump from boost-1.71.0ryoon2-4/+4
2019-08-14Add the biopython license to DEFAULT_ACCEPTABLE_LICENSES.brook1-2/+2
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.
2019-08-11Bump PKGREVISIONs for perl 5.30.0wiz16-32/+32
2019-08-09py-biopython: initial commitbrook5-1/+1301
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.
2019-07-21*: recursive bump for gdk-pixbuf2-2.38.1wiz4-8/+8
2019-07-20*: recursive bump for nettle 3.5.1wiz2-4/+4
2019-07-01Recursive revbump from boost-1.70.0ryoon2-3/+4
2019-06-30Update packages using a search.cpan.org HOMEPAGE to metacpan.org.nia1-2/+2
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.
2019-06-28biology/ncbi-blast+: Unbreak configurebacon1-3/+4
Configure script does not support --enable-option-checking Also add perl to USE_TOOLS
2019-06-24More http -> https.nia1-2/+2
Reviewed by hand.
2019-05-29Revbump after updating graphics/glewadam1-2/+2
2019-05-11biology/vsearch: Upgrade to 2.13.4bacon7-99/+10
pkgsrc patches incorporated into upstream release
2019-05-10Add vsearchbacon1-1/+2
2019-05-10biology/vsearch: import vsearch-2.13.3bacon8-0/+173
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).
2019-05-04Add fastpbacon1-1/+2
2019-05-04biology/fastp: import fastp-0.20.0bacon5-0/+83
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.
2019-05-01biology/kallisto: Switch from archivers/szip to archivers/libaecbacon1-2/+3
libaec is a BSD-licensed drop-in replacement for the non-redistributable szip
2019-04-26fix some whitespace, mostly introduced in the previousmaya1-2/+2
python 3.4 / 3.5 removal commit.
2019-04-26Omit mentions of python 34 and 35, after those were removed.maya1-2/+2
- Includes some whitespace changes, to be handled in a separate commit.
2019-04-25PKGREVISION bump for anything using python without a PYPKGPREFIX.maya5-6/+10
This is a semi-manual PKGREVISION bump.
2019-04-06biology/chemtool: Fix build on CentOS and NetBSDbacon1-2/+6
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.
2019-04-03Recursive revbump from textproc/icuryoon1-1/+2
2019-03-27biology/samtools: Add zlib dependency for Linuxbacon1-1/+2
Fixes build on CentOS 7 minimal.
2019-03-27biology/bcftools: Add zlib dependency for Linuxbacon1-2/+3
Resolves build failures on CentOS
2019-01-15Add hisat2bacon1-1/+2
2019-01-15biology/hisat2: import hisat2-2.1.0.23bacon6-0/+579
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).
2019-01-13Multiple packages: Replace obsolete maintainer emailbacon3-6/+6
jwbacon@tds.net ==> bacon@NetBSD.org
2019-01-07ncbi-blast+: Upgrade to 2.8.1bacon6-38/+157
Support for new BLAST database format Increased makeblastdb output file size limit to 4GB Other minor bug fixes and enhancements OK wiz@
2019-01-07Add canubacon1-1/+2
2019-01-07biology/canu: import canu-1.8bacon8-0/+356
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
2018-12-22Add stacksbacon1-1/+2
2018-12-22biology/stacks: import stacks-2.2bacon4-0/+102
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.
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-06 17:49:51 +0000