exonerate: Import exonerate-2.2.0 as wip/exonerate.

[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 12:57:00 2021 -0600
Changeset:	86cb395ea8579a7cecc97fb36f62abda2a62b27f

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

Log Message:
exonerate: Import exonerate-2.2.0 as wip/exonerate.

Exonerate is a generic tool for pairwise sequence comparison. It
allows you to align sequences using a many alignment models, either
exhaustive dynamic programming or a variety of heuristics.

It uses the C4 dynamic programming library. It is designed to be both
general and fast. It can produce either gapped or ungapped alignments,
according to a variety of different alignment models. The C4 library
allows sequence alignment using a reduced space full dynamic
programming implementation, but also allows automated generation of
heuristics from the alignment models, using bounded sparse dynamic
programming, so that these alignments may also be rapidly
generated. Alignments generated using these heuristics will represent
a valid path through the alignment model, yet (unlike the exhaustive
alignments), the results are not guaranteed to be optimal.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=86cb395ea8579a7cecc97fb36f62abda2a62b27f

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

diffstat:
 Makefile           |  1 +
 exonerate/DESCR    | 14 ++++++++++++++
 exonerate/Makefile | 17 +++++++++++++++++
 exonerate/PLIST    | 32 ++++++++++++++++++++++++++++++++
 exonerate/distinfo |  6 ++++++
 5 files changed, 70 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 8ee7876b06..c1321ebe63 100644
--- a/Makefile
+++ b/Makefile
@@ -800,6 +800,7 @@ SUBDIR+=	evilvte
 SUBDIR+=	exabgp4
 SUBDIR+=	exact-image
 SUBDIR+=	exhume
+SUBDIR+=	exonerate
 SUBDIR+=	expiretable
 SUBDIR+=	exult-snapshot
 SUBDIR+=	ez-pine-gpg
diff --git a/exonerate/DESCR b/exonerate/DESCR
new file mode 100644
index 0000000000..869caf2045
--- /dev/null
+++ b/exonerate/DESCR
@@ -0,0 +1,14 @@
+Exonerate is a generic tool for pairwise sequence comparison. It
+allows you to align sequences using a many alignment models, either
+exhaustive dynamic programming or a variety of heuristics.
+
+It uses the C4 dynamic programming library. It is designed to be both
+general and fast. It can produce either gapped or ungapped alignments,
+according to a variety of different alignment models. The C4 library
+allows sequence alignment using a reduced space full dynamic
+programming implementation, but also allows automated generation of
+heuristics from the alignment models, using bounded sparse dynamic
+programming, so that these alignments may also be rapidly
+generated. Alignments generated using these heuristics will represent
+a valid path through the alignment model, yet (unlike the exhaustive
+alignments), the results are not guaranteed to be optimal.
diff --git a/exonerate/Makefile b/exonerate/Makefile
new file mode 100644
index 0000000000..80d464c884
--- /dev/null
+++ b/exonerate/Makefile
@@ -0,0 +1,17 @@
+# $NetBSD$
+
+DISTNAME=	exonerate-2.2.0
+CATEGORIES=	biology
+MASTER_SITES=	http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/
+
+MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE=	https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
+COMMENT=	Generic tool for pairwise sequence comparison
+LICENSE=	gnu-gpl-v3
+
+USE_TOOLS+=	gmake
+GNU_CONFIGURE=	yes
+MAKE_JOBS_SAFE=	no
+
+.include "../../devel/glib2/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/exonerate/PLIST b/exonerate/PLIST
new file mode 100644
index 0000000000..e4434a2483
--- /dev/null
+++ b/exonerate/PLIST
@@ -0,0 +1,32 @@
+@comment $NetBSD$
+bin/esd2esi
+bin/exonerate
+bin/exonerate-server
+bin/fasta2esd
+bin/fastaannotatecdna
+bin/fastachecksum
+bin/fastaclean
+bin/fastaclip
+bin/fastacomposition
+bin/fastadiff
+bin/fastaexplode
+bin/fastafetch
+bin/fastahardmask
+bin/fastaindex
+bin/fastalength
+bin/fastanrdb
+bin/fastaoverlap
+bin/fastareformat
+bin/fastaremove
+bin/fastarevcomp
+bin/fastasoftmask
+bin/fastasort
+bin/fastasplit
+bin/fastasubseq
+bin/fastatranslate
+bin/fastavalidcds
+bin/ipcress
+man/man1/exonerate-server.1
+man/man1/exonerate.1
+man/man1/fastautils.1
+man/man1/ipcress.1
diff --git a/exonerate/distinfo b/exonerate/distinfo
new file mode 100644
index 0000000000..9c6354b956
--- /dev/null
+++ b/exonerate/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (exonerate-2.2.0.tar.gz) = ad4de207511e4d421e5cc28dda2261421c515bf0
+RMD160 (exonerate-2.2.0.tar.gz) = 3441a642c75af8b5676253b020f47650360ba320
+SHA512 (exonerate-2.2.0.tar.gz) = c0aec4df83fbf6bcd1b27242397349769211ab88d71e2d081e20cb5453a03acd805807535a69841e991cf543d99fcd458cbd22d60b21f0fc6ce813eac45b838c
+Size (exonerate-2.2.0.tar.gz) = 509870 bytes