preseq/: Predict yield of distinct reads from a genomic library

[Jason W. Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Nov 23 07:39:54 2024 -0600
Changeset:	264a27f1f691a5b7727797833fb4edfdaac149e1

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

Log Message:
preseq/:  Predict yield of distinct reads from a genomic library

The preseq package is aimed at predicting the yield of distinct reads
from a genomic library from an initial sequencing experiment. The
estimates can then be used to examine the utility of further
sequencing, optimize the sequencing depth, or to screen multiple
libraries to avoid low complexity samples.

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=264a27f1f691a5b7727797833fb4edfdaac149e1

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

diffstat:
 Makefile        |  1 +
 preseq/DESCR    |  5 +++++
 preseq/Makefile | 24 ++++++++++++++++++++++++
 preseq/PLIST    |  3 +++
 preseq/distinfo |  5 +++++
 5 files changed, 38 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index a7d4b443d7..275a9c58e6 100644
--- a/Makefile
+++ b/Makefile
@@ -3221,6 +3221,7 @@ SUBDIR+=	praat
 SUBDIR+=	preload
 SUBDIR+=	premake
 SUBDIR+=	premake4
+SUBDIR+=	preseq
 SUBDIR+=	primesieve
 SUBDIR+=	prjtrellis
 SUBDIR+=	probcons
diff --git a/preseq/DESCR b/preseq/DESCR
new file mode 100644
index 0000000000..3e93570561
--- /dev/null
+++ b/preseq/DESCR
@@ -0,0 +1,5 @@
+The preseq package is aimed at predicting the yield of distinct reads
+from a genomic library from an initial sequencing experiment. The
+estimates can then be used to examine the utility of further
+sequencing, optimize the sequencing depth, or to screen multiple
+libraries to avoid low complexity samples.
diff --git a/preseq/Makefile b/preseq/Makefile
new file mode 100644
index 0000000000..26999a83f4
--- /dev/null
+++ b/preseq/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Sat Nov 23 07:27:35 CST 2024               #
+###########################################################
+
+DISTNAME=	preseq-3.2.0
+CATEGORIES=	biology
+MASTER_SITES=	https://github.com/smithlabcode/preseq/releases/download/v\${PKGVERSION_NOREV}/
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/smithlabcode/preseq
+COMMENT=	Predict yield of distinct reads from a genomic library
+LICENSE=	gnu-gpl-v3
+
+USE_LANGUAGES=	c c++
+USE_TOOLS=	gmake
+GNU_CONFIGURE=	yes
+
+CONFIGURE_ARGS=	--enable-hts
+
+.include "../../biology/htslib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/preseq/PLIST b/preseq/PLIST
new file mode 100644
index 0000000000..da790fc033
--- /dev/null
+++ b/preseq/PLIST
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+bin/preseq
+bin/to-mr
diff --git a/preseq/distinfo b/preseq/distinfo
new file mode 100644
index 0000000000..6e543c0040
--- /dev/null
+++ b/preseq/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (preseq-3.2.0.tar.gz) = d6e2e24de766d82114ba1c26b57b970bcba415fc11fb5a5e956ce80bb95acf21
+SHA512 (preseq-3.2.0.tar.gz) = a06c198a6080c2e7a2a88af6211e93745cc18474d9bf44867f6562adecbf210e778df109aa2ff0f81083f0958b01278a7dabeb56399b949fd27bb4783f913cd9
+Size (preseq-3.2.0.tar.gz) = 6488708 bytes