git: acb3a0de6468 - main - biology/megahit: Ultra-fast single-node metagenomics assembly

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=acb3a0de6468b1fe930e53af1894505e9b8d64c7

commit acb3a0de6468b1fe930e53af1894505e9b8d64c7
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-11-22 16:38:31 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-11-22 16:39:22 +0000

    biology/megahit: Ultra-fast single-node metagenomics assembly
    
    MEGAHIT is a single node assembler for large and complex metagenomics
    NGS reads, such as soil. It makes use of succinct de Bruijn graph
    (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize
    a CUDA-enabled GPU to accelerate its SdBG contstruction.
---
 biology/Makefile          |  1 +
 biology/megahit/Makefile  | 23 +++++++++++++++++++++++
 biology/megahit/distinfo  |  3 +++
 biology/megahit/pkg-descr |  4 ++++
 biology/megahit/pkg-plist | 14 ++++++++++++++
 5 files changed, 45 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 25ed50f54925..2ba55e0738ae 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -90,6 +90,7 @@
     SUBDIR += linux-foldingathome
     SUBDIR += mafft
     SUBDIR += mapm3
+    SUBDIR += megahit
     SUBDIR += migrate
     SUBDIR += minimap2
     SUBDIR += mmseqs2
diff --git a/biology/megahit/Makefile b/biology/megahit/Makefile
new file mode 100644
index 000000000000..30080e9d2564
--- /dev/null
+++ b/biology/megahit/Makefile
@@ -0,0 +1,23 @@
+PORTNAME=		megahit
+DISTVERSIONPREFIX=	v
+DISTVERSION=		1.2.9
+CATEGORIES=		biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Ultra-fast single-node large and complex metagenomics assembly
+WWW=		https://github.com/voutcn/megahit
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+ONLY_FOR_ARCHS=	amd64 powerpc64 powerpc64le riscv64
+ONLY_FOR_ARCHS_REASON=	"Uses specific 64-bit CPU features"
+
+USES=		cmake python shebangfix
+SHEBANG_FILES=	src/megahit
+USE_GITHUB=	yes
+GH_ACCOUNT=	voutcn
+
+CFLAGS+=	-pthread
+
+.include <bsd.port.mk>
diff --git a/biology/megahit/distinfo b/biology/megahit/distinfo
new file mode 100644
index 000000000000..a70a74294d7a
--- /dev/null
+++ b/biology/megahit/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1669058254
+SHA256 (voutcn-megahit-v1.2.9_GH0.tar.gz) = 09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852
+SIZE (voutcn-megahit-v1.2.9_GH0.tar.gz) = 268591
diff --git a/biology/megahit/pkg-descr b/biology/megahit/pkg-descr
new file mode 100644
index 000000000000..8bf2914062fd
--- /dev/null
+++ b/biology/megahit/pkg-descr
@@ -0,0 +1,4 @@
+MEGAHIT is a single node assembler for large and complex metagenomics NGS
+reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve
+low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to
+accelerate its SdBG contstruction.
diff --git a/biology/megahit/pkg-plist b/biology/megahit/pkg-plist
new file mode 100644
index 000000000000..cda27e5d670d
--- /dev/null
+++ b/biology/megahit/pkg-plist
@@ -0,0 +1,14 @@
+bin/megahit
+bin/megahit_core
+bin/megahit_core_no_hw_accel
+bin/megahit_core_popcnt
+bin/megahit_toolkit
+%%DATADIR%%/test_data/empty.fa
+%%DATADIR%%/test_data/generate_random_fasta.py
+%%DATADIR%%/test_data/loop.fa
+%%DATADIR%%/test_data/r1.il.fa.gz
+%%DATADIR%%/test_data/r2.il.fa.bz2
+%%DATADIR%%/test_data/r3_1.fa
+%%DATADIR%%/test_data/r3_2.fa
+%%DATADIR%%/test_data/r4.fa
+%%DATADIR%%/test_data/ref.fa