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* biology/unikmer: Update 0.18.1 -> 0.18.3Yuri Victorovich2021-07-282-6/+6
| | | | Reported by: portscout
* biology/bcftools: Update to 1.13Jason W. Bacon2021-07-122-5/+4
| | | | | | | Numerous enhancements and bug fixes Changes: https://github.com/samtools/bcftools/releases/tag/1.13 Reported by: portscout
* biology/samtools: Update to 1.13Jason W. Bacon2021-07-123-4/+5
| | | | | | Numerous enhancements and bug fixes Changes: https://github.com/samtools/samtools/releases/tag/1.13
* htslib: Update to 1.13Jason W. Bacon2021-07-123-14/+4
| | | | | | Numerous enhancements and bug fixes Changes: https://github.com/samtools/htslib/releases/tag/1.13
* biology/biostar-tools: Add erminej run depend to metaportJason W. Bacon2021-07-092-3/+4
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* biology/erminej: Analyses of gene sets, e.g. gene expression profilingJason W. Bacon2021-07-097-0/+107
| | | | | | | | | | ErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing something interesting" in an experiment that generates long lists of candidates. The software is designed to be used by biologists with little or no informatics background (but if you do, you might be interested in the CLI or the R support).
* biology/hhsuite: fix build on powerpc64*Piotr Kubaj2021-07-081-10/+4
| | | | hhsuite now supports VSX.
* biology/bamtools: Update to 2.5.2Jason W. Bacon2021-07-065-17/+11
| | | | | | | Code clean up Changes: https://github.com/pezmaster31/bamtools/releases/tag/v2.5.2 Reported by: portscout
* biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7Po-Chuan Hsieh2021-07-062-4/+4
| | | | Changes: https://metacpan.org/dist/Bio-DB-NCBIHelper/changes
* biology/diamond: Update to 2.0.11-1Joseph Mingrone2021-07-062-4/+5
| | | | | | Includes a build fix for 2.0.11 on FreeBSD https://github.com/bbuchfink/diamond/releases/tag/v2.0.11
* biology/diamond: Update to 2.0.10Joseph Mingrone2021-07-032-4/+4
| | | | https://github.com/bbuchfink/diamond/releases/tag/v2.0.10
* biology/biostar-tools: Add biology/py-goatools to metaport dependsJason W. Bacon2021-07-022-3/+4
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* biology/py-goatools: Tools for processing and visualizing Gene Ontology termsJason W. Bacon2021-07-024-0/+37
| | | | | Goatools is a python library for processing Gene Ontology (GO) terms. It includes routines for processing, filtering, and visualizing GO data.
* biology/ncbi-blast+: Update to 2.12.0Jason W. Bacon2021-07-023-14/+182
| | | | | Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/ Reported by: portscout
* biology/rubygem-bio: Update to 2.0.2Po-Chuan Hsieh2021-06-302-4/+4
| | | | Changes: https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
* biology/mmseqs2: Fix runtime error when built with clangJason W. Bacon2021-06-291-6/+2
| | | | | Disable IPS4O to avoid deadlocks (upstream developer fix) Removing USE_GCC should fix pkg build errors caused by
* biology/biostar-tools: Remove falsehood in pkg-messageJason W. Bacon2021-06-281-7/+0
| | | | We now use native sra-tools, not linux-sra-tools
* biology/igv: Fix buildGuangyuan Yang2021-06-271-2/+2
| | | | | | | | | When switching the build dependency from devel/gradle to devel/gradle6, the build is accidentally broken. This attempts to revert part of the change and fix build. Fixes: 55044a2200a4c42b6b653349f0a65dfca3f96f36 Approved by: lwhsu (mentor, implicit), portmgr (fix build)
* biology/jalview: Fix buildGuangyuan Yang2021-06-271-2/+2
| | | | | | | | | When switching the build dependency from devel/gradle to devel/gradle6, the build is accidentally broken. This attempts to revert part of the change and fix build. Fixes: 55044a2200a4c42b6b653349f0a65dfca3f96f36 Approved by: lwhsu (mentor, implicit), portmgr (fix build)
* devel/gradle6: New portGuangyuan Yang2021-06-272-4/+4
| | | | | | | | | | | | | devel/gradle needs to be updated to 7.x, while some ports build failed under the newer version, including: - biology/jalview - biology/igv Updated them to use this devel/gradle6 until they officially support 7.x. No functional changes for these ports. Approved by: lwhsu (mentor)
* biology/mmseqs2: Enable at least SSE2 by defaultJason W. Bacon2021-06-266-4/+90
| | | | | Hangs when built with clang and minimal optimizations, so build with GCC temporarily. Upstream is investigating.
* biology/ugene: update Unipro UGENE to version 39.0.Alexey Dokuchaev2021-06-253-6/+10
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* biology/linux-foldingathome: Update to 7.6.21Mateusz Piotrowski2021-06-253-19/+15
| | | | | | | | | | | | | Unfortunately, this version of FAHClient is not able to daemonize successfully anymore. Even though the --daemon flag is passed, FAHClient does not detach from the controlling terminal. In addition to that it does not go into background. The --log seems to be broken as well as since all the logs are printed to the terminal instead of the log file. In order to alleviate those problems, use daemon(8). PR: 250463 Changes: https://foldingforum.org/viewtopic.php?t=36307
* biology/unikmer: Update 0.18.0 -> 0.18.1Yuri Victorovich2021-06-242-6/+6
| | | | Reported by: portscout
* biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suiteJason W. Bacon2021-06-245-0/+94
| | | | | | | | | | | MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for FreeBSD, Linux, MacOS, and (via via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.
* graphics/mesa-libs: Bump reverse deps for libglvndKevin Bowling2021-06-222-1/+2
| | | | | | | | | | Per discussion with bapt on helping pkg handle the changing of these deps and avoiding impossible upgrade senarios. PR: 246767 Reviewed by: manu, bapt Approved by: x11 Differential Revision: https://reviews.freebsd.org/D30824
* biostar-tools: Add sra-tools dependency to metaportJason W. Bacon2021-06-222-1/+2
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* biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read ↵Jason W. Bacon2021-06-2245-0/+2350
| | | | | | | | | | | | | | Archives SRA tools is a toolkit for using data in the INSDC Sequence Read Archives. SRAs operated by International Nucleotide Sequence Database Collaboration houses sequence reads and alignments generated by "next-gen" sequencers. This port is a bit convoluted due to the fact that the sra-tools build requires access to the ncbi-vdb source tree. Hence, ncbi-vdb is treated as a submodule here rather than a separate library port. We are working with upstream with hope for long-term improvements.
* biology/seqan-apps: fix packaging on armv7Piotr Kubaj2021-06-211-1/+1
| | | | Same issue as on i386.
* biology/seqan-apps: fix packaging on powerpcPiotr Kubaj2021-06-201-1/+1
| | | | Same issue as on i386.
* biology/vsearch: Update to 2.17.1Jason W. Bacon2021-06-192-6/+5
| | | | | | Changes: https://github.com/torognes/vsearch/releases Also enabled powerpc64le
* biology/biostar-tools: Meta-port for Biostar Handbook toolsJason W. Bacon2021-06-186-0/+126
| | | | | | | | Biostar-Tools is a metaport for installing all the tools necessary to work through the Biostar Handbook, except for bedGrapToBigWig, which has license restrictions. If you need bedGraphToBigWig, run cd /usr/ports/biology/ucsc-userapps && make install clean
* math/gsl: update to 2.7Tobias C. Berner2021-06-163-0/+3
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | From [1] * What is new in gsl-2.7: * fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com) * fixed bug #60335 (spmatrix test failure, J. Lamb) * fixed bug #36577 * clarified documentation on interpolation accelerators (V. Krishnan) * fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M. Sitte) * fixed doc bug #59758 * fixed bug #58202 (rstat median for n=5) * added support for native C complex number types in gsl_complex when using a C11 compiler * upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6 * updated exponential fitting example for nonlinear least squares * added banded LU decomposition and solver (gsl_linalg_LU_band) * New functions added to the library: - gsl_matrix_norm1 - gsl_spmatrix_norm1 - gsl_matrix_complex_conjtrans_memcpy - gsl_linalg_QL: decomp, unpack - gsl_linalg_complex_QR_* (thanks to Christian Krueger) - gsl_vector_sum - gsl_matrix_scale_rows - gsl_matrix_scale_columns - gsl_multilarge_linear_matrix_ptr - gsl_multilarge_linear_rhs_ptr - gsl_spmatrix_dense_add (renamed from gsl_spmatrix_add_to_dense) - gsl_spmatrix_dense_sub - gsl_linalg_cholesky_band: solvem, svxm, scale, scale_apply - gsl_linalg_QR_UD: decomp, lssolve - gsl_linalg_QR_UU: decomp, lssolve, QTvec - gsl_linalg_QR_UZ: decomp - gsl_multifit_linear_lcurvature - gsl_spline2d_eval_extrap * bug fix in checking vector lengths in gsl_vector_memcpy (dieggsy@pm.me) * made gsl_sf_legendre_array_index() inline and documented - gsl_sf_legendre_nlm() [1] http://git.savannah.gnu.org/cgit/gsl.git/tree/NEWS PR: 256423 Exp-run by: antoine
* biology/fasttree: fix build on armv7Piotr Kubaj2021-06-151-2/+1
| | | | Same issue as with powerpc.
* biology/peak-classifier: Classify peaks based on GFF featuresJason W. Bacon2021-06-145-0/+45
| | | | | | | | | | Classify ChIP/ATAC-Seq peaks based on features provided in a GFF Peaks are provided in a BED file sorted by chromosome and position. The GFF must be sorted by chromosome and position, with gene-level features separated by ### tags and each gene organized into subfeatures such as transcripts and exons. This is the default for common data sources.
* math/lapack: +math/blas et al., upgrade to 3.9.1Thierry Thomas2021-06-132-1/+13
| | | | | | | | | | | | | | | | | - Upgrade math/blas, math/cblas, math/lapack, math/lapacke and math/xlapack to 3.9.1; Latest release notes at <http://www.netlib.org/lapack/lapack-3.9.1.html> - Chase this upgrade in biology/treekin; - Add a test target; - Remove a conflict with math/openblas (PR 244296); - Fix the build with Gcc10 (PR 247485). PR: 247542 Approved by: expr-run by antoine@
* biology/vcf2hap: Remove comment used to silence portlintJason W. Bacon2021-06-111-2/+0
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* biology/ad2vcf: Remove comment used to silence portlintJason W. Bacon2021-06-111-2/+0
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* biology/biolibc: Remove comment used to silence portlintJason W. Bacon2021-06-111-2/+0
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* biology/vcf-split: Update to 0.1.2Jason W. Bacon2021-06-112-5/+5
| | | | | | Updates for new biolibc API Changes: https://github.com/auerlab/vcf-split/releases
* biology/vcf2hap: Update to 0.1.3Jason W. Bacon2021-06-113-7/+11
| | | | | | Updates for new biolibc API Changes: https://github.com/auerlab/vcf2hap/releases
* biology/ad2vcf: Update to 0.1.3Jason W. Bacon2021-06-113-9/+9
| | | | | | Updates for new biolibc API Changes: https://github.com/auerlab/ad2vcf/releases
* biology/biolibc: Update to 0.1.3Jason W. Bacon2021-06-113-9/+42
| | | | Changes: https://github.com/auerlab/biolibc/releases
* biology/fasttree: fix build on powerpcPiotr Kubaj2021-06-101-0/+6
| | | | | LLVM on powerpc doesn't have libomp. Same issue happens on armv6 and armv7 but someone has to test whether doing the same for those architectures is enough.
* biology/cd-hit: fix build on powerpcPiotr Kubaj2021-06-101-0/+6
| | | | | LLVM on powerpc doesn't have libomp: cdhit-common.c++:36:9: fatal error: 'omp.h' file not found
* biology/hyphy: Update to 2.5.31Joseph Mingrone2021-06-053-4/+31
| | | | https://github.com/veg/hyphy/releases/tag/2.5.31
* biology/jalview: Broken on 11Yuri Victorovich2021-06-052-4/+3
| | | | | | Also fix number of lines in pkg-descr, and replace space with tab. Reported by: fallout
* biology/seqan3: Update 3.0.2-1195 -> 3.0.3Yuri Victorovich2021-05-303-7/+16
| | | | Reported by: portscout
* biology/minimap2: Update to 2.20Jason W. Bacon2021-05-293-14/+30
| | | | | | Add "extra" binaries to install Changes: https://github.com/lh3/minimap2/releases/tag/v2.20
* biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkitYuri Victorovich2021-05-264-0/+35
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