git: af7a74db0001 - main - biology/preseq: Predict yield of distinct reads from a genomic library

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=af7a74db0001a2996b12a6e45c3ac235b92647b7

commit af7a74db0001a2996b12a6e45c3ac235b92647b7
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2024-11-22 20:35:51 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2024-11-22 20:35:51 +0000

    biology/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.
---
 biology/Makefile         |  1 +
 biology/preseq/Makefile  | 21 +++++++++++++++++++++
 biology/preseq/distinfo  |  3 +++
 biology/preseq/pkg-descr |  5 +++++
 biology/preseq/pkg-plist | 17 +++++++++++++++++
 5 files changed, 47 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 3f12e044804a..35727e12139c 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -156,6 +156,7 @@
     SUBDIR += picard-tools
     SUBDIR += plink
     SUBDIR += pooler
+    SUBDIR += preseq
     SUBDIR += primer3
     SUBDIR += prodigal
     SUBDIR += prodigy-lig
diff --git a/biology/preseq/Makefile b/biology/preseq/Makefile
new file mode 100644
index 000000000000..f25bd80cbe9d
--- /dev/null
+++ b/biology/preseq/Makefile
@@ -0,0 +1,21 @@
+PORTNAME=		preseq
+DISTVERSION=		3.2.0
+CATEGORIES=		biology
+# Github-generated distfiles are incomplete
+MASTER_SITES=		https://github.com/smithlabcode/preseq/releases/download/v${DISTVERSION}/
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Predict yield of distinct reads from a genomic library
+WWW=		https://github.com/smithlabcode/preseq
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+LIB_DEPENDS=	libhts.so:biology/htslib
+
+USES=		localbase
+
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--enable-hts
+
+.include <bsd.port.mk>
diff --git a/biology/preseq/distinfo b/biology/preseq/distinfo
new file mode 100644
index 000000000000..6a9390f4dbc5
--- /dev/null
+++ b/biology/preseq/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1732301093
+SHA256 (preseq-3.2.0.tar.gz) = 95b81c9054e0d651de398585c7e96b807ad98f0bdc541b3e46665febbe2134d9
+SIZE (preseq-3.2.0.tar.gz) = 6488708
diff --git a/biology/preseq/pkg-descr b/biology/preseq/pkg-descr
new file mode 100644
index 000000000000..3e9357056178
--- /dev/null
+++ b/biology/preseq/pkg-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/biology/preseq/pkg-plist b/biology/preseq/pkg-plist
new file mode 100644
index 000000000000..b876eadc3daf
--- /dev/null
+++ b/biology/preseq/pkg-plist
@@ -0,0 +1,17 @@
+bin/preseq
+bin/to-mr
+include/GenomicRegion.hpp
+include/MappedRead.hpp
+include/OptionParser.hpp
+include/QualityScore.hpp
+include/bisulfite_utils.hpp
+include/chromosome_utils.hpp
+include/cigar_utils.hpp
+include/dna_four_bit.hpp
+include/htslib_wrapper_deprecated.hpp
+include/sam_record.hpp
+include/sim_utils.hpp
+include/smithlab_os.hpp
+include/smithlab_utils.hpp
+include/zlib_wrapper.hpp
+lib/libsmithlab_cpp.a