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(8.16.1/8.16.1) with ESMTP id 277KUric058742; Sun, 7 Aug 2022 20:30:53 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 277KUrfN058741; Sun, 7 Aug 2022 20:30:53 GMT (envelope-from git) Date: Sun, 7 Aug 2022 20:30:53 GMT Message-Id: <202208072030.277KUrfN058741@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: d17e67375da9 - main - biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: dev-commits-ports-main@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: d17e67375da9982575cd787209be8775c6f1b491 Auto-Submitted: auto-generated ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1659904253; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=LcC8FoeMb/n2Z7rqoMYsV2Uz6oFn0XEDRbfd/qUIDAk=; b=QfL1CUfCB+5+5uWG6IHpDa4cAgyNV1HLHQWSs0YBQvhDx9ny1d0jtz1qgrBqXuqe4x+0xn kB/ksZWyn24NXCHOguTOL1XZxmmawLPIFm6GEGJC5GVYV8OVh5qgFAwtBRhaCLY2VHWLR0 ZZHFg1GurSo5IVpdxbwhJy+GkzvTvDSIwHq/cEYgCBn6kWlvygtjw3D1arfGvmvUvAGdEY UgbZ0j0Lj3Rdm6j6Gz0XFmz7g3/HHEEziTo9dkF+67TmvNFcmJbhknkWLvo9UH/wN9Vgrs cloHDqJvTLqdbdMINvM+BO1VelKhd7a7vzb1CFAG7f8CUSgVo13aopWGiHgEOA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1659904253; a=rsa-sha256; cv=none; b=TDaIWwQsQRvz/NceDcE5DNCMpMqnb1YjsAzCq0NZPsG5CeevvigJZW3drwl07FTX/VlMGm hxb2N2cLEKg4QzeRgp3WzCUzlLnkt2BnRx1x1EJ3ue2m0RRA6JvqGzAOWHNYcgLaGUCpiu 8JXRmECYrL7SYlR6D8eCGsqK0Q4+wJvHHW6sV7o5HFqdGK9BaCMQ5whjcXeOR9IJbr8ZXV LkAlVhfUz8MUXqGBVhCC6+iVvc+HP+7e1qKUnsJ/WkWfEVTT84fWlYwP/7yJP0ProimLC/ j6rf4020BWce52DTazfq5K5Gf/tSeo7ymsXN24hAhxLj18SEVNdb+D9XV7/PCA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=d17e67375da9982575cd787209be8775c6f1b491 commit d17e67375da9982575cd787209be8775c6f1b491 Author: Yuri Victorovich AuthorDate: 2022-08-07 20:29:58 +0000 Commit: Yuri Victorovich 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 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