biology/peak-classifier 0.1.4.13_2

all: bump PORTREVISION after updating graphics/libyuv

Using the Tools/scripts/bump_revision.pl script

biology/peak-classifier: Clean up USES=python

- Fix d6b521a455883ea2b387fb9cf61637ea879b746c
- Reapply 1d86601d3200c531e7fcd174cdd1feaf6d616518

USES=python means USES=python:3.8+ now.

Approved by:	portmgr (blanket)
With hat:	python

biology/peak-classifier: Move man pages to share/man

Approved by:	portmgr (blanket)

biology/peak-classifier: Update to 0.1.4.13

Updates for new libxtend API

biology/peak-classifier: Clean up USES=python

Approved by:	portmgr (blanket)
With hat:	python

biology/peak-classifier: Update to 0.1.4.11

Updates for biolibc GFF3 API changes

all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++ -DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable -Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi -Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings -Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x -MT _quickfix_la-QuickfixPython.lo -MD -MP -MF .deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o .libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean '-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>

biology/peak-classifier: Update to 0.1.4.8

Updates for libxtend API
Minor fixes

*: Bump PORTREVISIONs for math/mpc update to 1.3.1

biology/peak-classifier: Update to 0.1.4-5

Update for biolibc API changes

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.

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/peak-classifier: Update to 0.1.4

Update for bl_gff_t API streamlining

Changes:        https://github.com/auerlab/peak-classifier/tags

biology/peak-classifier: Update to 0.1.3

Minor update for biolibc 0.2.2 API changes

biology/peak-classifier: Update to 0.1.2

Mainly updates for evolving libxtend and biolibc APIs
A few minor fixes and enhancements

biology/peak-classifier: Update to 0.1.1.21

Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks

biology/peak-classifier: Update to 0.1.1.20

Updates for libxtend and biolibc API changes

biology/peak-classifier: Classify peaks based on GFF features

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF

Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons.  This is the default for
common data sources.