Bug 199747
| Summary: | [NEW PORT] biology/bcftools: Tools for manipulating next-generation sequencing data | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Product: | Ports & Packages | Reporter: | cartwright | ||||||
| Component: | Individual Port(s) | Assignee: | Kurt Jaeger <pi> | ||||||
| Status: | Closed FIXED | ||||||||
| Severity: | Affects Only Me | CC: | koobs, pi, portmgr, wen | ||||||
| Priority: | --- | Keywords: | feature, patch, patch-ready | ||||||
| Version: | Latest | ||||||||
| Hardware: | Any | ||||||||
| OS: | Any | ||||||||
| URL: | https://lists.freebsd.org/pipermail/freebsd-ports/2015-May/099262.html | ||||||||
| Attachments: |
|
||||||||
Created attachment 156060 [details]
poudriere testport log for 10.1
I had to do one weird thing and change the LICENSE depending on what options are selected. I'm not sure if that is okay. I would set the LICENSE as : LICENSE= MIT GPLv2 LICENSE_COMB= dual wen From: https://github.com/samtools/bcftools/blob/develop/LICENSE """ This software is available to you under a choice of one of two licenses. You may chose to be licensed under the terms of the MIT/Expat license or the GNU General Public License (GPL), both included below. If compiled with the GNU Scientific Library (which is optional and disabled by default as explained in the INSTALL document), the use of this software is governed by the GPL license. """ So I guess by default it is dual licensed, but if the USE_GPL option is enabled (which it is by default), only the GPL license is valid. So should I make it GPL by default and set it to dual if the option is not selected? CC portmgr@, requesting advice/review on conditional LICENSE use: See reporters question on freebsd-ports: https://lists.freebsd.org/pipermail/freebsd-ports/2015-May/099262.html build-tested on 10.1a, 9.3a, 8.4i. Looks fine. No one seems to have any better way of doing it. Can we just commit this as is? Yes. I'll commit it. A commit references this bug: Author: pi Date: Fri Jun 5 21:01:16 UTC 2015 New revision: 388638 URL: https://svnweb.freebsd.org/changeset/ports/388638 Log: New port: biology/bcftools 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 Changes: head/biology/Makefile head/biology/bcftools/ head/biology/bcftools/Makefile head/biology/bcftools/distinfo head/biology/bcftools/files/ head/biology/bcftools/files/patch-Makefile head/biology/bcftools/files/patch-plugins_fixploidy.mk head/biology/bcftools/files/patch-plugins_vcf2sex.mk head/biology/bcftools/files/patch-prob1.c head/biology/bcftools/files/pkg-message.in head/biology/bcftools/pkg-descr head/biology/bcftools/pkg-plist Committed, thanks. |
Created attachment 156059 [details] patch to add biology/bcftools 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. It is the companion to the biology/samtools and biology/htslib ports that I already maintain.