biology/bedtools: Update to 2.31.1

Code updates for modern compilers

Changes: https://github.com/arq5x/bedtools2/releases

biology/bedtools: Update to 2.31.0

New summary tool
Numerous minor fixes and enhancements
Changes: https://github.com/arq5x/bedtools2/releases

Reported by:    portscout

Remove WWW entries moved into port Makefiles

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

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.

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/bedtools: Upgrade to 2.30.0

Several bug fixes and performance enhancements

Reported by:    portscout

biology/bedtools: License changed upstream

biology/bedtools: Upgrade to 2.29.2

Fixed a bug that mistakenly removed a BAM/CRAM header line

Reported by:    portscout

biology/bedtools: Upgrade to 2.29.1

Several important bug fixes.

Reported by:    portscout

biology/bedtools: Upgrade to 2.29.0

Add test target to run test scripts in dist

Reported by:    portscout

Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330

biology/bedtools: unbreak with libc++ 8

In file included from FileReader.cpp:1:
In file included from /usr/include/c++/v1/iostream:38:
In file included from /usr/include/c++/v1/ios:216:
In file included from /usr/include/c++/v1/__locale:15:
In file included from /usr/include/c++/v1/string:505:
In file included from /usr/include/c++/v1/string_view:176:
In file included from /usr/include/c++/v1/__string:57:
In file included from /usr/include/c++/v1/algorithm:640:
In file included from /usr/include/c++/v1/initializer_list:47:
In file included from /usr/include/c++/v1/cstddef:38:
../../../utils//gzstream/version:1:1: error: expected unqualified-id
1.5 (08 Jan 2003)
^

PR:		236192
Approved by:	portmgr blanket

Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590

Fix build on gcc-based archs by updating USES.

Tested on powerpc64 and amd64 (for no regression).

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

biology/bedtools: Fix Makefile to respect PREFIX

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15851

biology/bedtools: Upgrade to 2.27.1

PR:             227272
Submitted by:   jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15137

- Fix build on 11+

Approved by:	portmgr blanket

Mark more recently failing ports broken on aarch64.

While here, pet portlint and reformat some other BROKEN statements.

Approved by:	portmgr (tier-2 blanket)

For ports that are marked BROKEN on armv6, and also fail to build on
armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run

Mark some ports failing on armv6, for errors classified as "clang".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

biology/bedtools is not jobs safe

The version.o target tries to use version_git.h before that header is
created.

The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.

WWW: http://bedtools.readthedocs.org/

PR:		204536
Submitted by:	scottcheloha@gmail.com