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* biology/bcftools: Update to 1.15Jason W. Bacon2022-02-262-5/+4
| | | | | | | Several small enhancements Changes: https://github.com/samtools/bcftools/releases Reported by: portscout
* math/gsl: bump portrevision of consumers after update to 2.7.1Tobias C. Berner2022-01-121-0/+1
| | | | PR: 260201
* biology/bcftools: Update to 1.14Jason W. Bacon2021-12-182-4/+4
| | | | | | A few minor enhancements and bug fixes Changes: https://github.com/samtools/bcftools/tags
* 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
* math/gsl: update to 2.7Tobias C. Berner2021-06-161-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/htslib: Update to 1.12Jason W. Bacon2021-03-206-53/+9
| | | | | | | | | | | | | | biology/samtools: Update to 1.12 biology/bcftools: Update to 1.12 Numerous enhancements, performance improvements, and bug fixes since 1.11 Build-tested all other htslib dependents, no revbumps should be needed Reported by: portscout Notes: svn path=/head/; revision=568874
* biology/bcftools: Upgrade to 1.11Jason W. Bacon2020-11-056-71/+18
| | | | | | | | | | Numerous new features, bug fixes and performance enhancements https://github.com/samtools/bcftools/releases/tag/1.11 Reported by: portscout Notes: svn path=/head/; revision=554157
* biology/bcftools: Upgrade to 1.10.2Jason W. Bacon2020-08-036-78/+69
| | | | | | | | | | | | Numerous bug fixes and enhancements since 1.9: https://github.com/samtools/bcftools/tags Take maintainership per ports/248089. PR: ports/248089 Notes: svn path=/head/; revision=544096
* biology/htslib: Upgrade to 1.10.2Jason W. Bacon2020-08-031-3/+1
| | | | | | | | | | | | Numerous bug fixes and enhancements since 1.9: https://github.com/samtools/htslib/tags Bump PORTREVISION on dependents that don't require additional patching PR: 248089 Notes: svn path=/head/; revision=544090
* math/gsl: update to 2.6Tobias C. Berner2019-10-251-0/+1
| | | | | | | | | | | | | - math/p5-Math-GSL does not seem to have any upstream activity to make it work with this version -> mark it broken - this also breaks the two consumers of this port - biology/gemma: has a conflict with cblas, and is makred broken. PR: 241363 Exp-run by: antoine Notes: svn path=/head/; revision=515671
* Convert to UCL & cleanup pkg-message (categories a-c)Mathieu Arnold2019-08-131-0/+6
| | | | Notes: svn path=/head/; revision=508834
* biology/bcftools: update to 1.9Fernando Apesteguía2018-08-025-24/+41
| | | | | | | | | | | | | | | While here: * Update LICENSE handling * Move all commands to bin/ PR: 230169 Submitted by: ndowens.fbsd@yandex.com Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D16543 Notes: svn path=/head/; revision=476247
* Update math/gsl to 2.5Tobias C. Berner2018-06-231-0/+1
| | | | | | | PR: 229067 Notes: svn path=/head/; revision=473116
* Add a USES=python:env, that will not add a dependency on Python.Mathieu Arnold2017-12-041-2/+1
| | | | | | | | | | It has the same effect than setting PYTHON_NO_DEPENDS, but in a more compact way. Sponsored by: Absolight Notes: svn path=/head/; revision=455518
* biology/htslib biology/bcftools biology/samtools: Update to 1.6Luca Pizzamiglio2017-10-259-68/+101
| | | | | | | | | | | PR: 223094 Submitted by: mzaki@niid.go.jp Approved by: cartwright@asu.edu (maintainer) Approved by: olivier (mentor) Differential Revision: https://reviews.freebsd.org/D12768 Notes: svn path=/head/; revision=452840
* Update math/gsl to 2.4Tobias C. Berner2017-07-031-1/+1
| | | | | | | | Exp-Run by: antoine PR: 220408 Notes: svn path=/head/; revision=444988
* Update math/gsl to 2.3Tobias C. Berner2017-05-021-0/+1
| | | | | | | | | | | | | | | | | | This release introduces some new features and fixes several bugs: http://savannah.gnu.org/forum/forum.php?forum_id=8751 * update to 2.3 and take maintainership * update math/py-gsl to 2.2.0 for gsl2 support * update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support PR: 218952 Exp-run by: antoine Reviewed by: mat, rakuco Approved by: rakuco (mentor) Differential Revision: https://reviews.freebsd.org/D10522 Notes: svn path=/head/; revision=439928
* biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1Kurt Jaeger2016-05-263-4/+8
| | | | | | | | | | | Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer) Notes: svn path=/head/; revision=415914
* - Fix trailing whitespace in pkg-messagesDmitry Marakasov2016-05-191-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415503
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-4/+4
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3Jason Unovitch2015-12-259-78/+108
| | | | | | | | | | | | | | | | - Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require version 1.3 of htslib. - Add CURL option to htslib - Add TEST_TARGET with perl and bash dependencies for testing - Tidy up spacing and pkg-message's PR: 205524 PR: 205525 PR: 205526 Submitted by: cartwright@asu.edu (maintainer) Notes: svn path=/head/; revision=404398
* New port: biology/bcftoolsKurt Jaeger2015-06-059-0/+177
BCFtools is a set of utilities that manipulate variant calls 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. WWW: http://www.htslib.org/ PR: 199747 Submitted by: cartwright@asu.edu Notes: svn path=/head/; revision=388638
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