trf: Import trf-4.09.1 as wip/trf.

[Brook Milligan <brook%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Mon Sep 13 13:24:02 2021 -0600
Changeset:	ef8ba5aff1bf6d963d7363ed1f4ede2ca3136fe8

Modified Files:
	Makefile
Added Files:
	trf/DESCR
	trf/Makefile
	trf/PLIST
	trf/distinfo

Log Message:
trf: Import trf-4.09.1 as wip/trf.

A tandem repeat in DNA is two or more adjacent, approximate copies of
a pattern of nucleotides. Tandem Repeats Finder is a program to locate
and display tandem repeats in DNA sequences. In order to use the
program, the user submits a sequence in FASTA format. There is no need
to specify the pattern, the size of the pattern or any other
parameter. The output consists of two files: a repeat table file and
an alignment file. The repeat table, viewable in a web browser,
contains information about each repeat, including its location, size,
number of copies and nucleotide content. Clicking on the location
indices for one of the table entries opens a second browser page that
shows an alignment of the copies against a consensus pattern. The
program is very fast, analyzing sequences on the order of .5Mb in just
a few seconds. Submitted sequences may be of arbitrary length. Repeats
with pattern size in the range from 1 to 2000 bases are detected.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ef8ba5aff1bf6d963d7363ed1f4ede2ca3136fe8

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile     |  1 +
 trf/DESCR    | 14 ++++++++++++++
 trf/Makefile | 42 ++++++++++++++++++++++++++++++++++++++++++
 trf/PLIST    |  4 ++++
 trf/distinfo |  6 ++++++
 5 files changed, 67 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index c1321ebe63..168a61c305 100644
--- a/Makefile
+++ b/Makefile
@@ -5632,6 +5632,7 @@ SUBDIR+=	tree-sitter
 SUBDIR+=	treetool
 SUBDIR+=	treeviewx
 SUBDIR+=	trelby
+SUBDIR+=	trf
 SUBDIR+=	triangle
 SUBDIR+=	triforceafl
 SUBDIR+=	triforcenetbsdsyscallfuzzer
diff --git a/trf/DESCR b/trf/DESCR
new file mode 100644
index 0000000000..abc1570bdc
--- /dev/null
+++ b/trf/DESCR
@@ -0,0 +1,14 @@
+A tandem repeat in DNA is two or more adjacent, approximate copies of
+a pattern of nucleotides. Tandem Repeats Finder is a program to locate
+and display tandem repeats in DNA sequences. In order to use the
+program, the user submits a sequence in FASTA format. There is no need
+to specify the pattern, the size of the pattern or any other
+parameter. The output consists of two files: a repeat table file and
+an alignment file. The repeat table, viewable in a web browser,
+contains information about each repeat, including its location, size,
+number of copies and nucleotide content. Clicking on the location
+indices for one of the table entries opens a second browser page that
+shows an alignment of the copies against a consensus pattern. The
+program is very fast, analyzing sequences on the order of .5Mb in just
+a few seconds. Submitted sequences may be of arbitrary length. Repeats
+with pattern size in the range from 1 to 2000 bases are detected.
diff --git a/trf/Makefile b/trf/Makefile
new file mode 100644
index 0000000000..753eb5b663
--- /dev/null
+++ b/trf/Makefile
@@ -0,0 +1,42 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	TRF
+GITHUB_TAG=	refs/tags/v4.09.1
+DISTNAME=	v4.09.1
+# PKGNAME=	${GITHUB_PROJECT}-${DISTNAME:S,^v,,}
+PKGNAME=	${GITHUB_PROJECT:tl}-4.09.1.20210623
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=Benson-Genomics-Lab/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://tandem.bu.edu/trf/trf.html
+COMMENT=	Genome tandom repeats finder
+LICENSE=	gnu-agpl-v3
+
+WRKSRC=		${WRKDIR}/TRF-4.09.1
+GNU_CONFIGURE=	yes
+USE_LANGUAGES+=	c
+
+# XXX - this package installs version-specific links to the main
+# executable.  However, despite the DISTNAME and the links on github,
+# the code itself has a different version (i.e., 4.10.0-rc.2 not
+# 4.09.1), which makes handling this awkward.  Besides, this distfile
+# appears to be a release candidate not a release, again despite the
+# information upstream.  For the time being, just ignore this file
+# altogether, but leave most of the infrastructure in place for the
+# future, just in case.
+#
+.include "../../mk/bsd.prefs.mk"
+
+# TODO - handle other OSes
+PLIST_VARS+=	Darwin
+.if ${OPSYS} == "Darwin"
+# PLIST.Darwin=	yes	# TODO - uncomment when versions are fixed upstream
+.endif
+
+# TODO - remove this when the versions get sorted out upstream
+post-install:
+	${RM} -f ${DESTDIR}${PREFIX}/bin/trf*.exe
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/trf/PLIST b/trf/PLIST
new file mode 100644
index 0000000000..2c993a115f
--- /dev/null
+++ b/trf/PLIST
@@ -0,0 +1,4 @@
+@comment $NetBSD$
+bin/trf
+${PLIST.Darwin}bin/trf${PKGVERSION}.mac.exe
+share/doc/trf/README.md
diff --git a/trf/distinfo b/trf/distinfo
new file mode 100644
index 0000000000..0c31c7e0c1
--- /dev/null
+++ b/trf/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (TRF/v4.09.1.tar.gz) = d9edd62b0b916cc539534fbe22eabffdea8139ac
+RMD160 (TRF/v4.09.1.tar.gz) = 94756b79c3e8b327209f863a20f820e7924f9c6b
+SHA512 (TRF/v4.09.1.tar.gz) = d1e8caf8358c1155d6343b33d20191e2a1c5f0378262bec0cfadbce31194d3da2b8084efade205c3465c4477255ba9f5e772d3995b443e14a6f2aae02a969ff2
+Size (TRF/v4.09.1.tar.gz) = 274103 bytes