ports - FreeBSD ports tree

	Commit message (Collapse)	Author	Age	Files	Lines
*	biology/bio-mocha: Update to 1.16	Jason W. Bacon	2023-01-05	3	-13/+9
\| \| \| \| \| \|	New release to sync with bcftools Changes: https://github.com/freeseek/mocha/commits/master
*	Remove WWW entries moved into port Makefiles	Stefan Eßer	2022-09-07	1	-2/+0
\| \| \| \| \| \| \| \| \| \|	Commit b7f05445c00f has added WWW entries to port Makefiles based on WWW: lines in pkg-descr files. This commit removes the WWW: lines of moved-over URLs from these pkg-descr files. Approved by: portmgr (tcberner)
*	Add WWW entries to port Makefiles	Stefan Eßer	2022-09-07	1	-0/+1
\| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \| \|	It has been common practice to have one or more URLs at the end of the ports' pkg-descr files, one per line and prefixed with "WWW:". These URLs should point at a project website or other relevant resources. Access to these URLs required processing of the pkg-descr files, and they have often become stale over time. If more than one such URL was present in a pkg-descr file, only the first one was tarnsfered into the port INDEX, but for many ports only the last line did contain the port specific URL to further information. There have been several proposals to make a project URL available as a macro in the ports' Makefiles, over time. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner)
*	biology/bio-mocha: Update bcftools submodule to 1.15	Jason W. Bacon	2022-02-26	2	-4/+5
\| \| \| \|	Compatibility confirmed with upstream
*	biology/bio-mocha: Update to 1.14-20220112	Jason W. Bacon	2022-01-13	5	-507/+8
\| \| \| \| \| \|	Upstream incorporated my patches to eliminate nested functions, which are not standard C and pose security risks. A few other minor updated.
*	bio-mocha: Build plugin against bcftools 1.14, the current port	Jason W. Bacon	2021-12-21	2	-5/+7
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*	biology/bio-mocha: bcftools plugin for mosaic chromosomal alterations	Jason W. Bacon	2021-12-03	8	-0/+612
	MoChA is a bcftools plugin released under the MIT license for mosaic chromosomal alteration detection and analysis from DNA microarray or whole genome sequence data. It can be used both with Illumina and Affymetrix data. It can also be used for detection of germline copy number variants. Data can be prepared in usable file formats using the gtc2vcf plugin.