dfam: initial commit of dfam 3.5

[Brook Milligan <34843815+brook-milligan%users.noreply.github.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <34843815+brook-milligan%users.noreply.github.com@localhost>
Pushed By:	brook
Date:		Wed Jan 19 12:28:16 2022 -0700
Changeset:	fcd73b5c8ffc2c7b93422448597109515929695e

Added Files:
	dfam/DESCR
	dfam/Makefile
	dfam/PLIST
	dfam/distinfo

Log Message:
dfam: initial commit of dfam 3.5

The Dfam database is a open collection of Transposable Element DNA
sequence alignments, hidden Markov Models (HMMs), consensus sequences,
and genome annotations.

Transposable elements (or interspersed repeats) account for a
substantial portion of eukaryotic genomes. Accurate annotation of TEs
enables research into their biology and can shed light on the
evolutionary processes that shape genomes. Dfam represents a
collection of multiple sequence alignments, each containing a set of
representative members of a specific transposable element
family. These alignments (seed alignments) are used to generate HMMs
and consensus sequences for each family. The Dfam website gives
information about each family, and provides genome annotations for a
collection of core genomes. The HMM models, and consensus sequences
may also be downloaded from the ftp site, for example to mask repeats
in new genomes.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=fcd73b5c8ffc2c7b93422448597109515929695e

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

diffstat:
 dfam/DESCR    | 16 ++++++++++++++++
 dfam/Makefile | 24 ++++++++++++++++++++++++
 dfam/PLIST    |  2 ++
 dfam/distinfo |  5 +++++
 4 files changed, 47 insertions(+)

diffs:
diff --git a/dfam/DESCR b/dfam/DESCR
new file mode 100644
index 0000000000..921f965e86
--- /dev/null
+++ b/dfam/DESCR
@@ -0,0 +1,16 @@
+The Dfam database is a open collection of Transposable Element DNA
+sequence alignments, hidden Markov Models (HMMs), consensus sequences,
+and genome annotations.
+
+Transposable elements (or interspersed repeats) account for a
+substantial portion of eukaryotic genomes. Accurate annotation of TEs
+enables research into their biology and can shed light on the
+evolutionary processes that shape genomes. Dfam represents a
+collection of multiple sequence alignments, each containing a set of
+representative members of a specific transposable element
+family. These alignments (seed alignments) are used to generate HMMs
+and consensus sequences for each family. The Dfam website gives
+information about each family, and provides genome annotations for a
+collection of core genomes. The HMM models, and consensus sequences
+may also be downloaded from the ftp site, for example to mask repeats
+in new genomes.
diff --git a/dfam/Makefile b/dfam/Makefile
new file mode 100644
index 0000000000..e062fe471c
--- /dev/null
+++ b/dfam/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD$
+
+DISTNAME=	Dfam.h5
+PKGNAME=	dfam-3.5
+CATEGORIES=	biology
+MASTER_SITES=	https://www.dfam.org/releases/Dfam_3.5/families/
+DIST_SUBDIR=	${PKGNAME_NOREV}
+EXTRACT_SUFX=	.gz
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://www.dfam.org/home
+COMMENT=	Collection of genome annotation data
+LICENSE=	cc0-1.0-universal
+
+WRKSRC=		${WRKDIR}
+USE_LANGUAGES=	# none
+NO_BUILD=	yes
+
+INSTALLATION_DIRS+=	share/${PKGNAME_NOREV}
+
+do-install:
+	${INSTALL_DATA} ${WRKSRC}/Dfam.h5 ${DESTDIR}${PREFIX}/share/${PKGNAME_NOREV}
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/dfam/PLIST b/dfam/PLIST
new file mode 100644
index 0000000000..71ead23b2d
--- /dev/null
+++ b/dfam/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+share/dfam-3.5/Dfam.h5
diff --git a/dfam/distinfo b/dfam/distinfo
new file mode 100644
index 0000000000..0989a26709
--- /dev/null
+++ b/dfam/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (dfam-3.5/Dfam.h5.gz) = a61d4719bc0f7fab6511bc4f8e92a60dc54960b1d4fd80289baa07f22af5bb8d
+SHA512 (dfam-3.5/Dfam.h5.gz) = bf5c7c34442c7f20ea3f84b1aaa85e6c29701a4320f881ea25659c07bfe6d8a3070eaf9d96820155d17b578814186def06e84c369118586cef36e5dae8d61343
+Size (dfam-3.5/Dfam.h5.gz) = 16391211951 bytes