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* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0
| | | | Reported by: lwhsu
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* Drop python 2.7 support from a few portsAntoine Brodin2020-12-281-1/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=559531
* biology/py-pysam: Update 0.16.0 -> 0.16.0.1Yuri Victorovich2020-11-152-4/+4
| | | | Notes: svn path=/head/; revision=555425
* biology/py-pysam: Update 0.15.4 -> 0.16.0Yuri Victorovich2020-06-092-4/+4
| | | | | | | Reported by: potscout Notes: svn path=/head/; revision=538275
* biology/py-pysam: Update 0.15.3 -> 0.15.4Yuri Victorovich2020-01-232-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=523862
* biology/py-pysam: Update 0.15.2 -> 0.15.3Yuri Victorovich2019-08-312-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=510398
* biology/py-pysam: Update 0.15.1 -> 0.15.2Yuri Victorovich2019-01-262-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=491232
* biology/py-pysam: Update 0.15.0 -> 0.15.1Yuri Victorovich2018-09-172-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=479938
* biology/py-pysam: Update 0.14.1 -> 0.15.0Yuri Victorovich2018-07-303-8/+5
| | | | | | | | | | | Port changes: * Remove stripping: done by the project now * Update WWW Reported by: portscout Notes: svn path=/head/; revision=475906
* Switch all pypi.python.org WWWs to a new PyPi home pypi.org whereDmitry Marakasov2018-04-251-1/+1
| | | | | | | | | | they now redirect to anyway. All new urls checked to return 200, I've fixed a couple of them in the process. Approved by: portmgr blanket, mat Notes: svn path=/head/; revision=468282
* biology/py-pysam: Update to 0.14.1Yuri Victorovich2018-03-212-5/+5
| | | | | | | | | Also silenced STRIP_CMD. Reported by: portscout Notes: svn path=/head/; revision=465157
* biology/py-pysam: Update to 0.14Yuri Victorovich2018-02-102-4/+4
| | | | | | | | | | | Changelog: https://github.com/pysam-developers/pysam/releases/tag/v0.14 Reported by: portscout Approved by: tcberner (mentor, implicit) Notes: svn path=/head/; revision=461449
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-301-4/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Ports using USE_PYTHON=distutils are now flavored. They will automatically get flavors (py27, py34, py35, py36) depending on what versions they support. There is also a USE_PYTHON=flavors for ports that do not use distutils but need FLAVORS to be set. A USE_PYTHON=noflavors can be set if using distutils but flavors are not wanted. A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been added to cope with Python ports that did not have the Python PKGNAMEPREFIX but are flavored. USES=python now also exports a PY_FLAVOR variable that contains the current python flavor. It can be used in dependency lines when the port itself is not python flavored. For example, deskutils/calibre. By default, all the flavors are generated. To only generate flavors for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf. In all the ports with Python dependencies, the *_DEPENDS entries MUST end with the flavor so that the framework knows which to build/use. This is done by appending '@${PY_FLAVOR}' after the origin (or @${FLAVOR} if in a Python module with Python flavors, as the content will be the same). For example: RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} PR: 223071 Reviewed by: portmgr, python Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D12464 Notes: svn path=/head/; revision=455210
* biology/py-pysam: Update to 0.13Yuri Victorovich2017-11-052-6/+8
| | | | | | | | Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D12967 Notes: svn path=/head/; revision=453556
* Update biology/py-pysam to 0.12.0.1Tobias C. Berner2017-10-262-4/+4
| | | | | | | | PR: 223254 Submitted by: Yuri Victorovich <yuri@rawbw.com> (maintainer) Notes: svn path=/head/; revision=452904
* - Update to 0.11.2.2Wen Heping2017-06-102-4/+4
| | | | | | | | PR: 219892 Submitted by: yuri@rawbw.com(maintainer) Notes: svn path=/head/; revision=443056
* - Update to 0.11.2.1Jochen Neumeister2017-05-232-5/+5
| | | | | | | | | | PR: 219396 Submitted by: Yuri Victorovich (Maintainer) <yuri@rawbw.com> Approved by: rene (mentor) Differential Revision: https://reviews.freebsd.org/D10856 Notes: svn path=/head/; revision=441555
* - Update to 0.11.1Martin Wilke2017-05-072-4/+4
| | | | | | | | PR: 219122 Submitted by: maintainer Notes: svn path=/head/; revision=440347
* pysam is a lightweight wrapper of the htslib C-API and provides facilities toMartin Wilke2017-05-064-0/+46
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com> Notes: svn path=/head/; revision=440231
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