tservice-plugins
/
quartet-rnaseq-report
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Fix dependencies.

tags/v0.1.2
YJC 3 年之前
父節點
d5bb973165
當前提交
c99aa2cd7a
共有 6 個文件被更改，包括 304 次插入 和 235 次删除
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  1. +1
    -1
      project.clj
  2. 二進制
      resources/quartet-rnaseq-report.tar.gz
  3. +125
    -0
      resources/quartet-rnaseq-report/bin/exp2qcdt.sh
  4. +177
    -233
      resources/renv.lock
  5. +1
    -0
      resources/renv/settings.dcf
  6. +0
    -1
      resources/tservice-plugin.yaml

+ 1
- 1
project.clj 查看文件

@@ -1,4 +1,4 @@
(defproject tservice-plugins/quartet-rnaseq-report "v0.1.1"
(defproject tservice-plugins/quartet-rnaseq-report "v0.1.2"
:description "QC Report for Quartet RNA-Seq."
:url "https://github.com/tservice-plugins/quartet-rnaseq-report"
:license {:name "Eclipse Public License"

二進制
resources/quartet-rnaseq-report.tar.gz 查看文件


+ 125
- 0
resources/quartet-rnaseq-report/bin/exp2qcdt.sh 查看文件

@@ -0,0 +1,125 @@
#!/usr/bin/env bash

# A wrapper for exp2qcdt r package
#
# Author: Jingcheng Yang
# Email: yjcyxky@163.com
#
# License: MIT

# Exit on error. Append "|| true" if you expect an error.
# set -o errexit
# Exit on error inside any functions or subshells.
# set -o errtrace
# Do not allow use of undefined vars. Use ${VAR:-} to use an undefined VAR
set -o nounset
# Catch the error in case mysqldump fails (but gzip succeeds) in `mysqldump |gzip`
set -o pipefail
# Turn on traces, useful while debugging but commented out by default
# set -o xtrace

show_help() {
cat <<EOF
usage: $(echo $0) [-e <FPKM_FILE>] [-c <COUNT_FILE>][-m <META_FILE>] [-o <RESULT_DIR>]
-e FPKM_FILE Fpkm table file.
-c COUNT_FILE Count table file
-m META_FILE Metadata file.
-o RESULT_DIR A directory for result files.
EOF
}

while getopts ":he:c:m:o:" arg; do
case "$arg" in
"e")
FPKM_FILE="$OPTARG"
;;
"c")
COUNT_FILE="$OPTARG"
;;
"m")
META_FILE="$OPTARG"
;;
"o")
RESULT_DIR="$OPTARG"
;;
"?")
echo "Unkown option: $OPTARG"
exit 1
;;
":")
echo "No argument value for option $OPTARG"
;;
h)
show_help
exit 0
;;
*)
echo "Unknown error while processing options"
show_help
exit 1
;;
esac
done

if [ -z "$FPKM_FILE" ]; then
echo "-e argument is not specified."
exit 1
elif [ ! -f "$FPKM_FILE" ]; then
echo "$FPKM_FILE is not a valid file."
exit 1
else
FPKM_FILE=$(realpath $FPKM_FILE)
fi

if [ -z "$COUNT_FILE" ]; then
echo "-c argument is not specified."
exit 1
elif [ ! -f "$COUNT_FILE" ]; then
echo "$COUNT_FILE is not a valid file."
exit 1
else
COUNT_FILE=$(realpath $COUNT_FILE)
fi

if [ -z "$META_FILE" ]; then
echo "-m argument is not specified."
exit 1
elif [ ! -f "$META_FILE" ]; then
echo "$META_FILE is not a valid file."
exit 1
else
META_FILE=$(realpath $META_FILE)
fi

if [ -z "$RESULT_DIR" ]; then
echo "-o argument is not specified."
exit 1
elif [ ! -d "$RESULT_DIR" ]; then
echo "$RESULT_DIR is not a valid directory."
exit 1
else
RESULT_DIR=$(realpath $RESULT_DIR)
fi

TEMP=$(mktemp)

echo "Run script: $TEMP"
cat <<EOF >"$TEMP"
#!/usr/bin/env Rscript

run <- function() {
# Print traceback message
on.exit(traceback())
library(exp2qcdt)
print("Running...")
exp2qcdt("$FPKM_FILE", "$COUNT_FILE", "$META_FILE", "$RESULT_DIR")
}

run()
EOF

printf "\n---------------------\n"
cat "$TEMP"
echo "---------------------"

Rscript $TEMP

+ 177
- 233
resources/renv.lock 查看文件

@@ -12,19 +12,12 @@
"Version": "3.10"
},
"Packages": {
"BH": {
"Package": "BH",
"Version": "1.72.0-3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "8f9ce74c6417d61f0782cbae5fd2b7b0"
},
"BiocManager": {
"Package": "BiocManager",
"Version": "1.30.12",
"Version": "1.30.16",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "462dbb15753eb52fb62e28507f382d2d"
"Hash": "2fdca0877debdd4668190832cdee4c31"
},
"BiocVersion": {
"Package": "BiocVersion",
@@ -32,13 +25,6 @@
"Source": "Bioconductor",
"Hash": "b69e4e634db423b8e6c58103d579ec95"
},
"DT": {
"Package": "DT",
"Version": "0.15",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "85738c69035e67ec4b484a5e02640ef6"
},
"KernSmooth": {
"Package": "KernSmooth",
"Version": "2.23-16",
@@ -48,10 +34,10 @@
},
"MASS": {
"Package": "MASS",
"Version": "7.3-52",
"Version": "7.3-51.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "095c8b0dd20f5d9c2a75cf72fdd74dab"
"Hash": "9efe80472b21189ebab1b74169808c26"
},
"Matrix": {
"Package": "Matrix",
@@ -62,10 +48,10 @@
},
"R6": {
"Package": "R6",
"Version": "2.4.1",
"Version": "2.5.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "292b54f8f4b94669b08f94e5acce6be2"
"Hash": "470851b6d5d0ac559e9d01bb352b4021"
},
"RColorBrewer": {
"Package": "RColorBrewer",
@@ -76,10 +62,10 @@
},
"Rcpp": {
"Package": "Rcpp",
"Version": "0.12.18",
"Version": "1.0.7",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "75ffd49f2ce7309ffd72ca94b491ccf4"
"Hash": "dab19adae4440ae55aa8a9d238b246bb"
},
"askpass": {
"Package": "askpass",
@@ -88,33 +74,12 @@
"Repository": "CRAN",
"Hash": "e8a22846fff485f0be3770c2da758713"
},
"assertthat": {
"Package": "assertthat",
"Version": "0.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7b2aa2be4bd0497000a5a399f07da3f1"
},
"backports": {
"Package": "backports",
"Version": "1.1.9",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b29e2d989dfb2e71ca3fd7d5bb1c0d58"
},
"base64enc": {
"Package": "base64enc",
"Version": "0.1-3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "543776ae6848fde2f48ff3816d0628bc"
},
"boot": {
"Package": "boot",
"Version": "1.3-24",
"Version": "1.3-25",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "72557d88b5f42f01221dfa436de99301"
"Hash": "bd51734a754b6c2baf28b2d1ebc11e91"
},
"brew": {
"Package": "brew",
@@ -123,12 +88,26 @@
"Repository": "CRAN",
"Hash": "92a5f887f9ae3035ac7afde22ba73ee9"
},
"brio": {
"Package": "brio",
"Version": "1.1.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2f01e16ff9571fe70381c7b9ae560dc4"
},
"cachem": {
"Package": "cachem",
"Version": "1.0.6",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "648c5b3d71e6a37e3043617489a0a0e9"
},
"callr": {
"Package": "callr",
"Version": "3.4.3",
"Version": "3.7.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "643163a00cb536454c624883a10ae0bc"
"Hash": "461aa75a11ce2400245190ef5d3995df"
},
"class": {
"Package": "class",
@@ -139,17 +118,17 @@
},
"cli": {
"Package": "cli",
"Version": "2.0.2",
"Version": "3.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ff0becff7bfdfe3f75d29aff8f3172dd"
"Hash": "e3ae5d68dea0c55a12ea12a9fda02e61"
},
"clipr": {
"Package": "clipr",
"Version": "0.7.0",
"Version": "0.7.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "08cf4045c149a0f0eaf405324c7495bd"
"Hash": "ebaa97ac99cc2daf04e77eecc7b781d7"
},
"cluster": {
"Package": "cluster",
@@ -167,10 +146,10 @@
},
"colorspace": {
"Package": "colorspace",
"Version": "1.4-1",
"Version": "2.0-2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6b436e95723d1f0e861224dd9b094dfb"
"Hash": "6baccb763ee83c0bd313460fdb8b8a84"
},
"commonmark": {
"Package": "commonmark",
@@ -179,75 +158,75 @@
"Repository": "CRAN",
"Hash": "0f22be39ec1d141fd03683c06f3a6e67"
},
"covr": {
"Package": "covr",
"Version": "3.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "cbc6df1ef6ee576f844f973c1fc04ab4"
},
"cowplot": {
"Package": "cowplot",
"Version": "1.0.0",
"Version": "1.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "82bae0172ae9d4c4f88a440ad01f73bb"
"Hash": "b418e8423699d11c7f2087c2bfd07da2"
},
"crayon": {
"Package": "crayon",
"Version": "1.3.4",
"Version": "1.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0d57bc8e27b7ba9e45dba825ebc0de6b"
"Hash": "e75525c55c70e5f4f78c9960a4b402e9"
},
"crosstalk": {
"Package": "crosstalk",
"Version": "1.1.0.1",
"credentials": {
"Package": "credentials",
"Version": "1.3.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "ae55f5d7c02f0ab43c58dd050694f2b4"
"Hash": "db9463f8f96444ac790bef2076048699"
},
"curl": {
"Package": "curl",
"Version": "4.3",
"Version": "4.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2b7d10581cc730804e9ed178c8374bd6"
"Hash": "022c42d49c28e95d69ca60446dbabf88"
},
"data.table": {
"Package": "data.table",
"Version": "1.13.0",
"Version": "1.13.6",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "06d5863292e2e8ffbb063ce34e77bb2a"
"Hash": "813fa8857aaa949b243e2e0b4abb8592"
},
"desc": {
"Package": "desc",
"Version": "1.2.0",
"Version": "1.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6c8fe8fa26a23b79949375d372c7b395"
"Hash": "b6963166f7f10b970af1006c462ce6cd"
},
"devtools": {
"Package": "devtools",
"Version": "2.3.1",
"Version": "2.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "271df6a328617c64149283e98b1cd8da"
"Hash": "048d0b914d2cea61f440d35dd3cbddac"
},
"diffobj": {
"Package": "diffobj",
"Version": "0.3.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "feb5b7455eba422a2c110bb89852e6a3"
},
"digest": {
"Package": "digest",
"Version": "0.6.15",
"Version": "0.6.27",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "706759233d88683f590d78ab6c82360a"
"Hash": "a0cbe758a531d054b537d16dff4d58a1"
},
"dplyr": {
"Package": "dplyr",
"Version": "1.0.2",
"Version": "1.0.7",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d0509913b27ea898189ee664b6030dc2"
"Hash": "36f1ae62f026c8ba9f9b5c9a08c03297"
},
"edgeR": {
"Package": "edgeR",
@@ -257,10 +236,10 @@
},
"ellipsis": {
"Package": "ellipsis",
"Version": "0.3.1",
"Version": "0.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a"
"Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
},
"evaluate": {
"Package": "evaluate",
@@ -271,29 +250,36 @@
},
"exp2qcdt": {
"Package": "exp2qcdt",
"Version": "0.2.2",
"Version": "0.2.4",
"Source": "GitHub",
"RemoteType": "github",
"RemoteHost": "api.github.com",
"RemoteRepo": "exp2qcdt",
"RemoteUsername": "clinico-omics",
"RemoteRef": "HEAD",
"RemoteSha": "319a5eba8f9b5b5e3355ac8045f573a400627583",
"Hash": "31f1244a56a68cfb8184738fd9210523"
"RemoteSha": "e2e75426e193ad0dd918ed01817de6ef94624acc",
"Hash": "0efa00adb40481ceec08fc4585681237"
},
"fansi": {
"Package": "fansi",
"Version": "0.4.1",
"Version": "0.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7fce217eaaf8016e72065e85c73027b5"
"Hash": "d447b40982c576a72b779f0a3b3da227"
},
"farver": {
"Package": "farver",
"Version": "2.0.3",
"Version": "2.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "c98eb5133d9cb9e1622b8691487f11bb"
},
"fastmap": {
"Package": "fastmap",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "dad6793a5a1f73c8e91f1a1e3e834b05"
"Hash": "77bd60a6157420d4ffa93b27cf6a58b8"
},
"foreign": {
"Package": "foreign",
@@ -309,61 +295,54 @@
"Repository": "CRAN",
"Hash": "44594a07a42e5f91fac9f93fda6d0109"
},
"gdata": {
"Package": "gdata",
"Version": "2.18.0",
"generics": {
"Package": "generics",
"Version": "0.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "465ccb84427f5fe2c54f8620666db131"
"Hash": "4d243a9c10b00589889fe32314ffd902"
},
"generics": {
"Package": "generics",
"Version": "0.0.2",
"gert": {
"Package": "gert",
"Version": "1.3.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b8cff1d1391fd1ad8b65877f4c7f2e53"
"Hash": "72b34cde959b806e86cb99fc12d1ba58"
},
"ggplot2": {
"Package": "ggplot2",
"Version": "3.3.2",
"Version": "3.3.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4ded8b439797f7b1693bd3d238d0106b"
"Hash": "d7566c471c7b17e095dd023b9ef155ad"
},
"ggthemes": {
"Package": "ggthemes",
"Version": "4.2.0",
"Version": "4.2.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "dfa67ccc3fb199f102a34d557ec1ff45"
"Hash": "617fb2c300f68e8b1ba21043fba88fd7"
},
"gh": {
"Package": "gh",
"Version": "1.1.0",
"Version": "1.3.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "89ea5998938d1ad55f035c8a86f96b74"
"Hash": "38c2580abbda249bd6afeec00d14f531"
},
"git2r": {
"Package": "git2r",
"Version": "0.27.1",
"gitcreds": {
"Package": "gitcreds",
"Version": "0.1.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "531a82d1beed1f545beb25f4f5945bf7"
"Hash": "f3aefccc1cc50de6338146b62f115de8"
},
"glue": {
"Package": "glue",
"Version": "1.4.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f43e0d5e85ccb0a4045670c0607ee504"
},
"gmodels": {
"Package": "gmodels",
"Version": "2.18.1",
"Version": "1.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "beb8ca96406a2828f25e49ab17001c39"
"Hash": "6efd734b14c6471cfe443345f3e35e29"
},
"gtable": {
"Package": "gtable",
@@ -372,33 +351,12 @@
"Repository": "CRAN",
"Hash": "ac5c6baf7822ce8732b343f14c072c4d"
},
"gtools": {
"Package": "gtools",
"Version": "3.8.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "0a749b4458d19a54acae93c64e3e7c85"
},
"highr": {
"Package": "highr",
"Version": "0.8",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "4dc5bb88961e347a0f4d8aad597cbfac"
},
"htmltools": {
"Package": "htmltools",
"Version": "0.5.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "7d651b7131794fe007b1ad6f21aaa401"
},
"htmlwidgets": {
"Package": "htmlwidgets",
"Version": "1.5.1",
"Version": "0.9",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "41bace23583fbc25089edae324de2dc3"
"Hash": "8eb36c8125038e648e5d111c0d7b2ed4"
},
"httr": {
"Package": "httr",
@@ -416,38 +374,31 @@
},
"isoband": {
"Package": "isoband",
"Version": "0.2.2",
"Version": "0.2.5",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "6e58bd3d6b3dd82a944cd6f05ade228f"
"Hash": "7ab57a6de7f48a8dc84910d1eca42883"
},
"jsonlite": {
"Package": "jsonlite",
"Version": "1.7.0",
"Version": "1.7.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "2657f20b9a74c996c602e74ebe540b06"
"Hash": "98138e0994d41508c7a6b84a0600cfcb"
},
"knitr": {
"Package": "knitr",
"Version": "1.29",
"Version": "1.33",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e5f4c41c17df8cdf7b0df12117c0d99a"
"Hash": "0bc1b5da1b0eb07cd4b727e95e9ff0b8"
},
"labeling": {
"Package": "labeling",
"Version": "0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "73832978c1de350df58108c745ed0e3e"
},
"later": {
"Package": "later",
"Version": "1.1.0.1",
"Version": "0.4.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d0a62b247165aabf397fded504660d8a"
"Hash": "3d5108641f47470611a32d0bdf357a72"
},
"lattice": {
"Package": "lattice",
@@ -456,19 +407,12 @@
"Repository": "CRAN",
"Hash": "848f8c593fd1050371042d18d152e3d7"
},
"lazyeval": {
"Package": "lazyeval",
"Version": "0.2.2",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "d908914ae53b04d4c0c0fd72ecc35370"
},
"lifecycle": {
"Package": "lifecycle",
"Version": "0.2.0",
"Version": "1.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "361811f31f71f8a617a9a68bf63f1f42"
"Hash": "3471fb65971f1a7b2d4ae7848cf2db8d"
},
"limma": {
"Package": "limma",
@@ -485,10 +429,10 @@
},
"magrittr": {
"Package": "magrittr",
"Version": "1.5",
"Version": "2.0.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "1bb58822a20301cee84a41678e25d9b7"
"Hash": "41287f1ac7d28a92f0a286ed507928d3"
},
"markdown": {
"Package": "markdown",
@@ -499,10 +443,10 @@
},
"memoise": {
"Package": "memoise",
"Version": "1.1.0",
"Version": "2.0.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "58baa74e4603fcfb9a94401c58c8f9b1"
"Hash": "a0bc51650201a56d00a4798523cc91b3"
},
"mgcv": {
"Package": "mgcv",
@@ -513,10 +457,10 @@
},
"mime": {
"Package": "mime",
"Version": "0.9",
"Version": "0.11",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "e87a35ec73b157552814869f45a63aa3"
"Hash": "8974a907200fc9948d636fe7d85ca9fb"
},
"munsell": {
"Package": "munsell",
@@ -541,38 +485,38 @@
},
"openssl": {
"Package": "openssl",
"Version": "1.4.2",
"Version": "1.4.4",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b3209c62052922b6c629544d94c8fa8a"
"Hash": "f4dbc5a47fd93d3415249884d31d6791"
},
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"Repository": "CRAN",
"Hash": "bdf26e55ccb7df3e49a490150277f002"
"Hash": "43f228eb4b49093d1c8a5c93cae9efe9"
},
"pkgbuild": {
"Package": "pkgbuild",
"Version": "1.1.0",
"Version": "1.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "404684bc4e3685007f9720adf13b06c1"
"Hash": "725fcc30222d4d11ec68efb8ff11a9af"
},
"pkgconfig": {
"Package": "pkgconfig",
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"Version": "2.0.3",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b8a063ca3694e651ac46f71b4bf0e090"
"Hash": "01f28d4278f15c76cddbea05899c5d6f"
},
"pkgload": {
"Package": "pkgload",
"Version": "1.1.0",
"Version": "1.2.1",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "b6b150cd4709e0c0c9b5d51ac4376282"
"Hash": "463642747f81879e6752485aefb831cf"
},
"plyr": {
"Package": "plyr",
@@ -597,24 +541,17 @@
},
"processx": {
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"Source": "Repository",
"Repository": "CRAN",
"Hash": "03446ed0b8129916f73676726cb3c48f"
},
"promises": {
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"Hash": "a8730dcbdd19f9047774909f0ec214a4"
"Hash": "0cbca2bc4d16525d009c4dbba156b37c"
},
"ps": {
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"Repository": "CRAN",
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"Hash": "32620e2001c1dce1af49c49dccbb9420"
},
"purrr": {
"Package": "purrr",
@@ -623,6 +560,13 @@
"Repository": "CRAN",
"Hash": "97def703420c8ab10d8f0e6c72101e02"
},
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"Hash": "5e3c5dc0b071b21fa128676560dbe94d"
},
"rcmdcheck": {
"Package": "rcmdcheck",
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@@ -639,10 +583,10 @@
},
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"Hash": "a85ebb35721573b196317b49ddd2dfe4"
},
"renv": {
"Package": "renv",
@@ -658,19 +602,12 @@
"Repository": "CRAN",
"Hash": "bb5996d0bd962d214a11140d77589917"
},
"rex": {
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},
"rlang": {
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"Repository": "CRAN",
"Hash": "c06d2a6887f4b414f8e927afd9ee976a"
"Hash": "515f341d3affe0de9e4a7f762efb0456"
},
"roxygen2": {
"Package": "roxygen2",
@@ -688,24 +625,24 @@
},
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"Source": "Repository",
"Repository": "CRAN",
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"Hash": "249d8cd1e74a8f6a26194a91b47f21d1"
},
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},
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"Repository": "CRAN",
"Hash": "0ec41191f744d0f5afad8c6f35cc36e4"
"Hash": "f88fab00907b312f8b23ec13e2d437cb"
},
"scales": {
"Package": "scales",
@@ -730,10 +667,10 @@
},
"stringi": {
"Package": "stringi",
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"Version": "1.7.3",
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"Hash": "7943cfae120c77a255025e5f63856532"
},
"stringr": {
"Package": "stringr",
@@ -758,59 +695,59 @@
},
"testthat": {
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"Repository": "CRAN",
"Hash": "0829b987b8961fb07f3b1b64a2fbc495"
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},
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"Package": "tibble",
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},
"tidyr": {
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},
"tidyselect": {
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"Version": "1.1.1",
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"Hash": "6ea435c354e8448819627cf686f66e0a"
"Hash": "7243004a708d06d4716717fa1ff5b2fe"
},
"usethis": {
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"Hash": "360e904f9e623286e1a0c6ca0a98c5f6"
},
"utf8": {
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"Repository": "CRAN",
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"Hash": "c9c462b759a5cc844ae25b5942654d13"
},
"vctrs": {
"Package": "vctrs",
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"Repository": "CRAN",
"Hash": "5ba3006888ac62fd5e97b208d00d3317"
"Hash": "ecf749a1b39ea72bd9b51b76292261f1"
},
"viridisLite": {
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},
"waldo": {
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"Hash": "312b264fae22fdba83b7a74187a24da8"
},
"whisker": {
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@@ -821,17 +758,17 @@
},
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},
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"Hash": "853d45ffff0a9af1e0af017cd359f75e"
},
"xml2": {
"Package": "xml2",
@@ -853,6 +790,13 @@
"Source": "Repository",
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},
"zip": {
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}
}
}

+ 1
- 0
resources/renv/settings.dcf 查看文件

@@ -1,6 +1,7 @@
external.libraries:
ignored.packages:
package.dependency.fields: Imports, Depends, LinkingTo
r.version:
snapshot.type: all
use.cache: TRUE
vcs.ignore.library: TRUE

+ 0
- 1
resources/tservice-plugin.yaml 查看文件

@@ -19,7 +19,6 @@ init:
# Unpack environment file to the directory, repository/envs/quartet-rnaseq-report
- step: unpack-env
envname: quartet-rnaseq-report
postunpack: clone-env /opt/local/quartet-rnaseq-report {{ ENV_DEST_DIR }}
- step: load-namespace
namespace: tservice.plugins.quartet-rnaseq-report
- step: register-plugin

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