git: d17e67375da9 - main - biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 07 Aug 2022 20:30:53 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=d17e67375da9982575cd787209be8775c6f1b491

commit d17e67375da9982575cd787209be8775c6f1b491
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-08-07 20:29:58 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-08-07 20:30:47 +0000

    biology/kmcp: New port:  Accurate metagenomic profiling & fast large-scale genome searching
---
 biology/Makefile       |  1 +
 biology/kmcp/Makefile  | 59 +++++++++++++++++++++++++++++++++++++++
 biology/kmcp/distinfo  | 75 ++++++++++++++++++++++++++++++++++++++++++++++++++
 biology/kmcp/pkg-descr |  5 ++++
 4 files changed, 140 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 422c8fdd52b4..6d4c981769d2 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -77,6 +77,7 @@
     SUBDIR += jalview
     SUBDIR += jellyfish
     SUBDIR += kallisto
+    SUBDIR += kmcp
     SUBDIR += lamarc
     SUBDIR += libbigwig
     SUBDIR += libgff
diff --git a/biology/kmcp/Makefile b/biology/kmcp/Makefile
new file mode 100644
index 000000000000..959cdf4e4732
--- /dev/null
+++ b/biology/kmcp/Makefile
@@ -0,0 +1,59 @@
+PORTNAME=	kmcp
+DISTVERSIONPREFIX=	v
+DISTVERSION=	0.8.2
+CATEGORIES=	biology
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Accurate metagenomic profiling & fast large-scale genome searching
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+USES=		go:modules
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	shenwei356
+GH_TUPLE=	\
+		VividCortex:ewma:v1.1.1:vividcortex_ewma/vendor/github.com/VividCortex/ewma \
+		acarl005:stripansi:5a71ef0e047d:acarl005_stripansi/vendor/github.com/acarl005/stripansi \
+		clausecker:pospop:677120eb417c:clausecker_pospop/vendor/github.com/clausecker/pospop \
+		dustin:go-humanize:v1.0.0:dustin_go_humanize/vendor/github.com/dustin/go-humanize \
+		edsrzf:mmap-go:v1.1.0:edsrzf_mmap_go/vendor/github.com/edsrzf/mmap-go \
+		go-yaml:yaml:v2.4.0:go_yaml_yaml/vendor/gopkg.in/yaml.v2 \
+		golang:sys:1d35b9e2eb4e:golang_sys/vendor/golang.org/x/sys \
+		grailbio:base:v0.0.10:grailbio_base/vendor/github.com/grailbio/base \
+		iafan:cwalk:586a8832a711:iafan_cwalk/vendor/github.com/iafan/cwalk \
+		inconshreveable:mousetrap:v1.0.0:inconshreveable_mousetrap/vendor/github.com/inconshreveable/mousetrap \
+		klauspost:compress:v1.15.0:klauspost_compress/vendor/github.com/klauspost/compress \
+		klauspost:pgzip:v1.2.5:klauspost_pgzip/vendor/github.com/klauspost/pgzip \
+		mattn:go-colorable:v0.1.12:mattn_go_colorable/vendor/github.com/mattn/go-colorable \
+		mattn:go-isatty:v0.0.14:mattn_go_isatty/vendor/github.com/mattn/go-isatty \
+		mattn:go-runewidth:v0.0.13:mattn_go_runewidth/vendor/github.com/mattn/go-runewidth \
+		mitchellh:go-homedir:v1.1.0:mitchellh_go_homedir/vendor/github.com/mitchellh/go-homedir \
+		pkg:errors:v0.9.1:pkg_errors/vendor/github.com/pkg/errors \
+		rivo:uniseg:v0.2.0:rivo_uniseg/vendor/github.com/rivo/uniseg \
+		shenwei356:bio:v0.7.0:shenwei356_bio/vendor/github.com/shenwei356/bio \
+		shenwei356:breader:v0.3.1:shenwei356_breader/vendor/github.com/shenwei356/breader \
+		shenwei356:go-logging:c6b9702d88ba:shenwei356_go_logging/vendor/github.com/shenwei356/go-logging \
+		shenwei356:kmers:v0.1.0:shenwei356_kmers/vendor/github.com/shenwei356/kmers \
+		shenwei356:natsort:600d539c017d:shenwei356_natsort/vendor/github.com/shenwei356/natsort \
+		shenwei356:pand:v0.0.5:shenwei356_pand/vendor/github.com/shenwei356/pand \
+		shenwei356:unik:v5.0.1:shenwei356_unik_v5/vendor/github.com/shenwei356/unik/v5 \
+		shenwei356:util:v0.5.0:shenwei356_util/vendor/github.com/shenwei356/util \
+		shenwei356:xopen:v0.2.1:shenwei356_xopen/vendor/github.com/shenwei356/xopen \
+		spf13:cobra:v1.4.0:spf13_cobra/vendor/github.com/spf13/cobra \
+		spf13:pflag:v1.0.5:spf13_pflag/vendor/github.com/spf13/pflag \
+		tatsushid:go-prettytable:ed2d14c29939:tatsushid_go_prettytable/vendor/github.com/tatsushid/go-prettytable \
+		twotwotwo:sorts:bf5c1f2b8553:twotwotwo_sorts/vendor/github.com/twotwotwo/sorts \
+		ulikunitz:xz:v0.5.10:ulikunitz_xz/vendor/github.com/ulikunitz/xz \
+		vbauerster:mpb:v5.4.0:vbauerster_mpb_v5/vendor/github.com/vbauerster/mpb/v5 \
+		will-rowe:nthash:v0.4.0:will_rowe_nthash/vendor/github.com/will-rowe/nthash \
+		zeebo:wyhash:v0.0.1:zeebo_wyhash/vendor/github.com/zeebo/wyhash \
+		zeebo:xxh3:v0.13.0:zeebo_xxh3/vendor/github.com/zeebo/xxh3
+
+GO_PKGNAME=	github.com/${GH_ACCOUNT}/${GH_PROJECT}
+GO_TARGET=	./kmcp
+
+PLIST_FILES=	bin/${PORTNAME}
+
+.include <bsd.port.mk>
diff --git a/biology/kmcp/distinfo b/biology/kmcp/distinfo
new file mode 100644
index 000000000000..99cbe8df98ad
--- /dev/null
+++ b/biology/kmcp/distinfo
@@ -0,0 +1,75 @@
+TIMESTAMP = 1659902903
+SHA256 (shenwei356-kmcp-v0.8.2_GH0.tar.gz) = ae7abc5f7e1e3547a4bf95ac6233215b24d92a0117e7cab30b4cc9cb9dc31ca4
+SIZE (shenwei356-kmcp-v0.8.2_GH0.tar.gz) = 17000789
+SHA256 (VividCortex-ewma-v1.1.1_GH0.tar.gz) = 3b2d62412b7ba2726a379cc0ae557595c027dc8206d0ef98f13831281b8f2b85
+SIZE (VividCortex-ewma-v1.1.1_GH0.tar.gz) = 6042
+SHA256 (acarl005-stripansi-5a71ef0e047d_GH0.tar.gz) = 832ad7232c573cec3eece91af4cdf40d2d06bca94e026dd7d5add0f44f802f0f
+SIZE (acarl005-stripansi-5a71ef0e047d_GH0.tar.gz) = 1477
+SHA256 (clausecker-pospop-677120eb417c_GH0.tar.gz) = 276deb9bde64a63b5d3b9efe3273372b1b979f7093d22c09def77f9351072617
+SIZE (clausecker-pospop-677120eb417c_GH0.tar.gz) = 9038
+SHA256 (dustin-go-humanize-v1.0.0_GH0.tar.gz) = e4540bd50ac855143b4f2e509313079c50cf5d8774f09cc10dbca5ae9803d8ba
+SIZE (dustin-go-humanize-v1.0.0_GH0.tar.gz) = 17260
+SHA256 (edsrzf-mmap-go-v1.1.0_GH0.tar.gz) = f5b3fe0c6b243706cffeb3f37207dda409bb73d3abb248cb3f82d21b4b29bcd4
+SIZE (edsrzf-mmap-go-v1.1.0_GH0.tar.gz) = 6888
+SHA256 (go-yaml-yaml-v2.4.0_GH0.tar.gz) = d8e94679e5fff6bd1a35e10241543929a5f3da44f701755babf99b3daf0faac0
+SIZE (go-yaml-yaml-v2.4.0_GH0.tar.gz) = 73209
+SHA256 (golang-sys-1d35b9e2eb4e_GH0.tar.gz) = cb599b1befb8f0b8550a528272ac5ebdba968676702bc4adbc8f5122243ede5f
+SIZE (golang-sys-1d35b9e2eb4e_GH0.tar.gz) = 1255687
+SHA256 (grailbio-base-v0.0.10_GH0.tar.gz) = 35be080e77a67816270cca9975143650b050d3c57b3f2a4faa4c58175e42cb0b
+SIZE (grailbio-base-v0.0.10_GH0.tar.gz) = 607018
+SHA256 (iafan-cwalk-586a8832a711_GH0.tar.gz) = 6c02330d1e2e25d19f40477962ebdd07f5e4455c0e336cda91a99af24e7babb6
+SIZE (iafan-cwalk-586a8832a711_GH0.tar.gz) = 5497
+SHA256 (inconshreveable-mousetrap-v1.0.0_GH0.tar.gz) = 5edc7731c819c305623568e317aa253d342be3447def97f1fa9e10eb5ad819f6
+SIZE (inconshreveable-mousetrap-v1.0.0_GH0.tar.gz) = 2290
+SHA256 (klauspost-compress-v1.15.0_GH0.tar.gz) = f4d06e703c1f47d5d39d8aa15d93123c53895b8d904f703992a011c88b43e798
+SIZE (klauspost-compress-v1.15.0_GH0.tar.gz) = 15631358
+SHA256 (klauspost-pgzip-v1.2.5_GH0.tar.gz) = a64bad5981a232f6b5a40e488708b19a0551e83465f6792b7925f90829d7a830
+SIZE (klauspost-pgzip-v1.2.5_GH0.tar.gz) = 125923
+SHA256 (mattn-go-colorable-v0.1.12_GH0.tar.gz) = 32493594aee411896ffe13aaed14df4a23c3006866c46c1a908af79eacd102b2
+SIZE (mattn-go-colorable-v0.1.12_GH0.tar.gz) = 9801
+SHA256 (mattn-go-isatty-v0.0.14_GH0.tar.gz) = e6460325edf600297cf2ef68834938fb1c5b8d5f234b3b24ec7c0a29a2d70b39
+SIZE (mattn-go-isatty-v0.0.14_GH0.tar.gz) = 4710
+SHA256 (mattn-go-runewidth-v0.0.13_GH0.tar.gz) = 9b2aeafa5d95a40b32067ba22accdf42cc83414ec5b433ea7de330791beaa196
+SIZE (mattn-go-runewidth-v0.0.13_GH0.tar.gz) = 17353
+SHA256 (mitchellh-go-homedir-v1.1.0_GH0.tar.gz) = 646671c73a84a8dfb4a5a76b80c7b63549ffefa906524d45077301bc7da76600
+SIZE (mitchellh-go-homedir-v1.1.0_GH0.tar.gz) = 3362
+SHA256 (pkg-errors-v0.9.1_GH0.tar.gz) = 56bfd893023daa498508bfe161de1be83299fcf15376035e7df79cbd7d6fa608
+SIZE (pkg-errors-v0.9.1_GH0.tar.gz) = 13415
+SHA256 (rivo-uniseg-v0.2.0_GH0.tar.gz) = 3ad738b5c9162ede110d75b23564b6e40e52dd9150ebbced402f4f70be106197
+SIZE (rivo-uniseg-v0.2.0_GH0.tar.gz) = 44036
+SHA256 (shenwei356-bio-v0.7.0_GH0.tar.gz) = 7b4b8a06a98a8ee5dc57954153e9e0a183370f898a0f597e9ad260718b1f05de
+SIZE (shenwei356-bio-v0.7.0_GH0.tar.gz) = 230715
+SHA256 (shenwei356-breader-v0.3.1_GH0.tar.gz) = 1c14bf7fa06d3a28b81772d253957dd8f34f22970ef3311feaf0361ef9bf4f47
+SIZE (shenwei356-breader-v0.3.1_GH0.tar.gz) = 5347
+SHA256 (shenwei356-go-logging-c6b9702d88ba_GH0.tar.gz) = a5d895a2d8e359101cde7d58cfa7c7accd695d9b958bbfb7ff79cf49f53e84a7
+SIZE (shenwei356-go-logging-c6b9702d88ba_GH0.tar.gz) = 36401
+SHA256 (shenwei356-kmers-v0.1.0_GH0.tar.gz) = afd5b9b08e11e3ff7d6e50990446bffa03a086d9f6fab407ee4fc44fc6f36426
+SIZE (shenwei356-kmers-v0.1.0_GH0.tar.gz) = 5777
+SHA256 (shenwei356-natsort-600d539c017d_GH0.tar.gz) = db3963ef47bcc204a52967ac63e050049e295829101d7541062a20064b0ae3a0
+SIZE (shenwei356-natsort-600d539c017d_GH0.tar.gz) = 2870
+SHA256 (shenwei356-pand-v0.0.5_GH0.tar.gz) = 4fdf66bc4943ac3c5019fd99b262f685b14869539b45a44974c230c20210f74a
+SIZE (shenwei356-pand-v0.0.5_GH0.tar.gz) = 7440
+SHA256 (shenwei356-unik-v5.0.1_GH0.tar.gz) = 2f4bab300f1fafe5213cf06caae33f754a8287513d68b6d960f76504d78cbd4b
+SIZE (shenwei356-unik-v5.0.1_GH0.tar.gz) = 187973
+SHA256 (shenwei356-util-v0.5.0_GH0.tar.gz) = 7c2c6365b6c3b7bf46f192f8c10cdf554104b299203c99cf5d5f43d6e3fc8710
+SIZE (shenwei356-util-v0.5.0_GH0.tar.gz) = 38070
+SHA256 (shenwei356-xopen-v0.2.1_GH0.tar.gz) = c751bb678235097f6b82e1060cb2451930619abfcc07c212afff9791a2ff19ff
+SIZE (shenwei356-xopen-v0.2.1_GH0.tar.gz) = 4803
+SHA256 (spf13-cobra-v1.4.0_GH0.tar.gz) = de32a9d3f94c55ddc433aa4eefe05fc85ae621d182114b6e628258753fc03148
+SIZE (spf13-cobra-v1.4.0_GH0.tar.gz) = 94547
+SHA256 (spf13-pflag-v1.0.5_GH0.tar.gz) = 9a2cae1f8e8ab0d2cc8ebe468e871af28d9ac0962cf0520999e3ba85f0c7b808
+SIZE (spf13-pflag-v1.0.5_GH0.tar.gz) = 50796
+SHA256 (tatsushid-go-prettytable-ed2d14c29939_GH0.tar.gz) = d92668d863d5e176d10ac3b34059e92d18204654ac42ffa622fca501f1ad546b
+SIZE (tatsushid-go-prettytable-ed2d14c29939_GH0.tar.gz) = 4765
+SHA256 (twotwotwo-sorts-bf5c1f2b8553_GH0.tar.gz) = 09d981203b6e3184b715d5f0924a8e036edd33ff1a3a9f6c7b4fa398de8f3bc1
+SIZE (twotwotwo-sorts-bf5c1f2b8553_GH0.tar.gz) = 20284
+SHA256 (ulikunitz-xz-v0.5.10_GH0.tar.gz) = 515f83921cf3e80b9196156cb4a0c1328243d5e09eca7c5ac7ce7e31b218c35b
+SIZE (ulikunitz-xz-v0.5.10_GH0.tar.gz) = 479622
+SHA256 (vbauerster-mpb-v5.4.0_GH0.tar.gz) = bd733ebe8fe71a4744330526ce369c561582ececc531bfc414210e578949fefc
+SIZE (vbauerster-mpb-v5.4.0_GH0.tar.gz) = 59031
+SHA256 (will-rowe-nthash-v0.4.0_GH0.tar.gz) = c8858c58d83da029aa9dffe99a27cff2cb478b884fe04665ffb8f8ee11316ccf
+SIZE (will-rowe-nthash-v0.4.0_GH0.tar.gz) = 5406
+SHA256 (zeebo-wyhash-v0.0.1_GH0.tar.gz) = 10a7a9bea1e87e571de6397ed573993a768905a5bbf184c81af2a52766833d40
+SIZE (zeebo-wyhash-v0.0.1_GH0.tar.gz) = 25785
+SHA256 (zeebo-xxh3-v0.13.0_GH0.tar.gz) = 59798e8e348e5d06f8fc6b05da74d950600f273ea6834e9cfd48fac223b3fbac
+SIZE (zeebo-xxh3-v0.13.0_GH0.tar.gz) = 149631
diff --git a/biology/kmcp/pkg-descr b/biology/kmcp/pkg-descr
new file mode 100644
index 000000000000..11fa668c8755
--- /dev/null
+++ b/biology/kmcp/pkg-descr
@@ -0,0 +1,5 @@
+KMCP: accurate metagenomic profiling of both prokaryotic and viral populations
+by pseudo-mapping.
+
+WWW: https://bioinf.shenwei.me/kmcp/
+WWW: https://github.com/shenwei356/kmcp