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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2022-11-22 16:38:31 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2022-11-22 16:39:22 +0000 |
| commit | acb3a0de6468b1fe930e53af1894505e9b8d64c7 (patch) | |
| tree | 87844081bc183607d091b17a191921e8eafb2be1 | |
| parent | af39b50f6bf7c60f51fa2dcabcd628b7c68d299a (diff) | |
| download | ports-acb3a0de6468b1fe930e53af1894505e9b8d64c7.tar.gz ports-acb3a0de6468b1fe930e53af1894505e9b8d64c7.zip | |
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.
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/megahit/Makefile | 23 | ||||
| -rw-r--r-- | biology/megahit/distinfo | 3 | ||||
| -rw-r--r-- | biology/megahit/pkg-descr | 4 | ||||
| -rw-r--r-- | biology/megahit/pkg-plist | 14 |
5 files changed, 45 insertions, 0 deletions
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 |