rctl is a set of R command line tools to wrapper useful R functions.
rctl
Now, there are several difficulties for next-generation sequencing (NGS) data analysis projects that needs to be solved:
- Standardized project management, directory structured，recording and checking of raw data and analysis result, standardized logging for input, output and commands
- Construction and redeployment of computing environment including all required tools, databases and other files.
- Lack of integration and unify of massive data analysis workflows.
- Lack of the unified distribution platform for various data analysis workflows (e.g. snakemake, nextflow, Galaxy, etc.).
- Reuse of workflows language codes (e.g. commands, input and output information) on other programming platform are still complicated.
- The readability and reusable will also be decreased when massive Python and R codes mixed with the workflows language codes.
This project is part of openanno, and aim to integrate and develop command line tools based on R and JavaScript ecosystem.
We proposed that using node to distribute the bioinformatics data analysis required workflows (e.g Common workflow language (CWL)) or the command line scripts that created by users. The creation, update and upload of a node package are very simple. Well-tested and high-performance distribution tools of node packages, such as npm and yarn, are providing the service for more than 1,264,413 packages.
Command line scripts supported now:
| tool | function |
|---|---|
| rdeps | Getting all rctl required R packages |
| rsession | sessionInfo() and sessioninfo::session\_info() |
| rinstall | Install R packages and BioInstaller resources using install.packages() and R packages devtools, BiocManager and BioInstaller |
| rconfig | Parsing and generating json, ini, yaml, and toml format configuration files |
| rbashful | run bashful |
| rclrs | Generating colors for visulization using a theme key |
| rmv | Formating the file names. |
| ranystr | Generating any counts and any length random strings (e.g. Ies1y7fpgMVjsAyBAtTT) |
| rtime_stamp | Generating time stamp (e.g. 2018_11_15_22_43_25_, 2018/11/15/, 2018/11/15/22/). |
| rdownload | Parallel download URLs with logs |
| rbin | Collecting R packages inst/bin files to a directory, e.g. PATH |
R packages
- optparse
- configr
- stringi
- futile.logger
- glue
- ngstk
- BioInstaller
- devtools
- pacman
- BiocManager
- sessioninfo
- future
Installation
# Use conda to manage the envconda install go nodejs \echo 'export NODE_PATH="/path/miniconda2/lib/node_modules/"\n' >> ~/.bashrc \&& npm install -g yarn \&& echo 'export PATH=$PATH:~/.yarn/bin/\n' >> ~/.bashrc# Other see https://nodejs.org/en/download/package-manager/# For: Ubuntuapt updateapt install -y npm# For MacOSbrew install node
npm install -g rctl# oryarn global add rctl# If you not to globaly install rctl# You need to set the PATHecho "export rctl_ROOT=/path/node_modules/nodejs" >> ~/.bashrcecho "export PATH=$PATH:${rctl_ROOT}/bin" >> ~/.bashrc# Current dir is /pathnpm install rctl# oryarn add rctl
Usage
Before try your rctl command line tools, you need run the rdeps
getting all the extra R packages required by rctl.
# install the extra R packages used in `rctl` scriptsrdeps
Then you can use the rctl to run all sub-commands.
rctl -h#> Description:#> Main interface of rctl package tools. View the rctl homepage https://github.com/openanno/rctl for more detail.#> Now, total 11 subcmds are supported: rbashful rconfig rdeps rinstall rsession rclrs rmv rtime_stamp ranystr rdownload rbin.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rctl [subcmds] [options]#> /Users/apple/.config/yarn/global/node_modules/.bin/rctl rconfig -h#>#> Options:#> -l, --list-all-subcmds#> Print all supported subcmds of rctl.#> -h, --help#> Show this help message and exit#>#> Commands:#> rbashful An R-based tool to extend GO bashful tool for style bash commands#> rconfig An R-based tool to parse and generate configuration file#> rdeps An R-based tool to install rctl command line tools required R packages.#> rinstall An R-based tool to install or download R packages and other resources supported by R package BioInstaller.#> rsession An R-based tool to show R environment using sessionInfo() and sessioninfo::session_info()#> rclrs An R-based tool to generate colors for visulization using a theme key#> rmv An R-based tool to format file names#> rtime_stamp An R-based tool to generate time stamp#> ranystr An R-based tool to generate any counts and any urls random strings#> rdownload An R-based tool to concurrently download urls with logging.#> rbin An R-based tool to collect R packages bin files.
rbashful
bashful is a GO program and used
by rbashful, so you need to install it before use the rbashful.
Ubuntu/Debian
wget https://github.com/wagoodman/bashful/releases/download/v0.0.10/bashful_0.0.10_linux_amd64.debsudo apt install ./bashful_0.0.10_linux_amd64.deb
RHEL/Centos
wget https://github.com/wagoodman/bashful/releases/download/v0.0.10/bashful_0.0.10_linux_amd64.rpmrpm -i bashful_0.0.10_linux_amd64.rpm
Mac
brew tap wagoodman/bashfulbrew install bashful
or download a Darwin build from the releases page.
Go tools
go get github.com/wagoodman/bashful
View a rbashful demo
here.
source_dir <- "/Users/apple/Documents/repositories/rctl/examples/rbashful/rnaseq_splicing/02_leafcutter_majiq"# View the cli.yamlcat(paste0(readLines(sprintf("%s/cli.yaml", source_dir)),collapse = "\n"), sep = "\n")#> config:#> log-path: "{{submit_log}}"#> tasks:#> - name: "RNA-seq splicing analysis step 01: parse the task YAML and link bams"#> parallel-tasks:#> - cmd: ./scripts/01_link_bams.R --env-parsed-yaml "{{env_parsed_yaml}}" --task-name "majiq_splicing_01_link_bams"# View the env.tomlcat(paste0(readLines(sprintf("%s/env.toml", source_dir)),collapse = "\n"), sep = "\n")#> title = "Environment variables for running splicing analysis (from bam start)"#>#> global_vars = ["project_dir", "workdir", "submit_yaml", "log_dir",#> "env_parsed_yaml", "env_toml", "rbashful", "submit_log"]#>#> # Global var (Replace all '{{var}}' in cli.yaml).#> project_dir = "/home/ljf/projects/eqtf"#> workdir = "!!glue {config$project_dir}/analysis/rnaseq_splicing"#> submit_yaml = "!!glue {config$workdir}/cli.yaml"#> log_dir = "!!glue {config$workdir}/logs"#> env_toml = "!!glue {config$workdir}/env.toml"#> env_parsed_yaml = "!!glue {config$workdir}/env.parsed.yaml"#> rbashful = "rbashful"#>#> # Sample specific var#> id = "{{id}}"#> [input]#> samples_info_fn = "{{workdir}}/samples"#> leafcutter_root = "/opt/bin/caller/leafcutter"#> bam2_junc_script = "!!glue {config$input$leafcutter_root}/scripts/bam2junc.sh"#> rawbamdir = "{{project_dir}}/analysis/rnaseq/output/bam/merge"#> rawbamfile = "!!glue {config$input$rawbamdir}/{config$id}{config$input$bam_suffix}"#> bamdir = "{{project_dir}}/analysis/rnaseq_splicing/bam_tmp"#> bam_suffix = ".bam_AddGroup.bam_MarkDup.bam_SplitNtrim.bam_IndelRealigner.bam_PrintReads.bam"#> bamfile = "!!glue {config$input$bamdir}/{config$id}{config$input$bam_suffix}"#> genome = "hg19"#> genome_path = "/u4/jhuangdata/reference/ucsc/hg19"#> hg19_gtf = "!!glue {config$input$genome_path}/Homo_sapiens.GRCh37.75.gtf"#> hg19_gff = "!!glue {config$input$genome_path}/Homo_sapiens.GRCh37.75.gff"#>#> [output]#> leafcutter_out_dir = "!!glue {config$project_dir}}/analysis/rnaseq_splicing/leafcutter/bamfile_juncs/"#> majiq_build_out_dir = "!!glue {config$project_dir}/analysis/rnaseq_splicing/output/majiq_build"#> leafcutter_bamfile_junc = "!!glue {config$output$leafcutter_out_dir}/{config$id}.junc"#>#> [cmds]#> bam2junc = "!!glue sh {config$input$bam2_junc_script} {config$input$bamfile} {config$output$leafcutter_bamfile_junc}"#> generate_majiq_conf = """#> !!glue rconfig majiq.ini -e {{dqm}}extra.list=list(bamdir='{config$input$bamdir}', \#> genome = '{config$input$genome}', genome_path='{config$input$genome_path}'){{dqm}} \#> -r {{dqm}}write.config(x, 'majiq.parsed.ini'){{dqm}}\#> """#> majiq_splicing_01_link_bams = """#> !!glue rawbam={config$input$rawbamdir}/{config$id}{config$input$bam_suffix}; \#> if [ -f $rawbam ]#> then#> ln -s $rawbam {config$input$bamdir}#> fi#> """#>#> majiq_builder_step = """#> !!glue majiq build {config$input$hg19_gff} -conf majiq.parsed.ini --nthreads 10 --output {config$output$majiq_build_out_dir}#> """# View the submit.shcat(paste0(readLines(sprintf("%s/submit", source_dir)),collapse = "\n"), sep = "\n")#> #! /usr/bin/env Rscript#>#> # yarn global add rctl#> # system("rdeps")#> pkgs <- c("stringi", "configr")#> pacman::p_load(pkgs, character.only = TRUE)#>#> env_toml = "/u7/home/ljf/projects/eqtf/analysis/rnaseq_splicing/env.toml"#>#> config <- read.config(env_toml, extra.list = list('dqm'='"'),#> global.vars.field = NULL, rcmd.parse = TRUE)#> rm(env_toml)#> for (i in 1:1) config <- parse.extra(config, glue.parse = TRUE,#> global.vars.field = NULL)#> for (i in 1:1) config <- parse.extra(config, glue.parse = TRUE)#> config$submit_log <- paste0(file.path(config[["workdir"]], "logs", format(Sys.time(), "%Y_%m_%d_%H_%M_%S_")),#> stri_rand_strings(1, 20), ".log")#> attach(config)#> x <- write.config(config, env_parsed_yaml, write.type = "yaml", indent = 4)#> if (!x) {stop(sprintf("Generating %s failed.", env_parsed_yaml))}#>#> extra_list <- paste0(global_vars, "='", unname(sapply(config[global_vars],#> function(x){return(x)[1]})), "'", collapse = ", ")#> print(extra_list)#> cmd <- sprintf('./rbashful -c %s -e "%s" -p >> %s', submit_yaml, extra_list, submit_log)#> if (!dir.exists(dirname(submit_log))) dir.create(dirname(submit_log))#> cat(cmd, file = submit_log, append = TRUE)#> message(cmd, sep = "\n")#> system(cmd)#>#> cmd <- "bashful run cli.parsed.yaml"#> message(cmd, sep = "\n")#> system(cmd)
rbashful -h#> Description:#> rbashful is an extend bashful tool for style bash commands.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rbashful [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rbashful -c ${workdir}/cli.yaml --env-toml ${workdir}/env.toml --cmd-name default -v#>#> Options:#> -v, --verbose#> Print extra output [FALSE]#> -c CLI-YAML, --cli-yaml=CLI-YAML#> bashful used YAML file [cli.yaml]#> -t ENV-TOML, --env-toml=ENV-TOML#> TOML file stores environment variables [env.toml]#> -e EXTRA-LIST, --extra-list=EXTRA-LIST#> Need to replaced environment variables#> -p, --parse-cli-yaml#> Replace cli config keys [FALSE]#> -o OUTPUT-CLI-YAML, --output-cli-yaml=OUTPUT-CLI-YAML#> Output file of parsed cli YAML file [*.parsed.yaml]#> -n CMD-NAME, --cmd-name=CMD-NAME#> Run CMDs section using name [NULL]#> --auto-create-dir#> Auto create dir in env.toml output section [FALSE]#> -h, --help#> Show this help message and exit
rsession
# Print commandline help of rsessionrsession -h# Print rsession R document (Just like ?sessionInfo in R client)rsession -d# Print R sessionInfo()# The followed three lines are equivalent.rsessionrsession -f 1rsession -f sessionInfo# The followed two lines are equivalent.rsession -f 2 -e 'include_base=TRUE'rsession -f sessioninfo::session_info -e 'include_base=TRUE'
rsession -f 2 -e 'include_base=TRUE'rsession -h#> ─ Session info ───────────────────────────────────────────────────────────────#> setting value#> version R version 3.6.3 (2020-02-29)#> os macOS Catalina 10.15.4#> system x86_64, darwin15.6.0#> ui X11#> language (EN)#> collate en_US.UTF-8#> ctype en_US.UTF-8#> tz Asia/Shanghai#> date 2020-04-21#>#> ─ Packages ───────────────────────────────────────────────────────────────────#> ! package * version date lib source#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0)#> R base * 3.6.3 <NA> [?] <NA>#> cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.3)#> R codetools 0.2-16 <NA> [2] <NA>#> R compiler 3.6.3 <NA> [2] <NA>#> configr 0.3.4.1 2019-11-12 [1] Github (Miachol/configr@0df7b68)#> crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0)#> data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.0)#> R datasets * 3.6.3 <NA> [2] <NA>#> digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.3)#> fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.0)#> future 1.16.0 2020-01-16 [1] CRAN (R 3.6.3)#> getopt 1.20.3 2019-03-22 [1] CRAN (R 3.6.0)#> globals 0.12.5 2019-12-07 [1] CRAN (R 3.6.0)#> glue 1.3.2 2020-03-12 [1] CRAN (R 3.6.3)#> R graphics * 3.6.3 <NA> [2] <NA>#> R grDevices * 3.6.3 <NA> [2] <NA>#> ini 0.3.1 2018-05-20 [1] CRAN (R 3.6.0)#> jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.3)#> listenv 0.8.0 2019-12-05 [1] CRAN (R 3.6.0)#> magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0)#> R methods * 3.6.3 <NA> [2] <NA>#> ngstk * 0.2.3 2019-11-12 [1] Github (JhuangLab/ngstk@e5953e3)#> optparse 1.6.4 2019-09-16 [1] CRAN (R 3.6.0)#> pacman * 0.5.1 2019-03-11 [1] CRAN (R 3.6.0)#> R parallel 3.6.3 <NA> [2] <NA>#> Rcpp 1.0.4 2020-03-17 [1] CRAN (R 3.6.3)#> RcppTOML 0.1.6 2019-06-25 [1] CRAN (R 3.6.0)#> rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.3)#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0)#> R stats * 3.6.3 <NA> [2] <NA>#> stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.3)#> stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0)#> R tools 3.6.3 <NA> [2] <NA>#> R utils * 3.6.3 <NA> [2] <NA>#> withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0)#> yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.3)#>#> [1] /Users/apple/.R/library/3.6#> [2] /Library/Frameworks/R.framework/Versions/3.6/Resources/library#>#> R ── Package was removed from disk.#> Description:#> rsession is an R-based tool to show R environment using sessionInfo() and sessioninfo::session_info().#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rsession [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rsession#> /Users/apple/.config/yarn/global/node_modules/.bin/rsession -f 1#> /Users/apple/.config/yarn/global/node_modules/.bin/rsession -f 2 -e 'include_base=TRUE'#> /Users/apple/.config/yarn/global/node_modules/.bin/rsession -d#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Function name [e.g. sessionInfo (1), sessioninfo::session_info (2)]#> -e EXTRA, --extra=EXTRA#> Extra parameters [e.g. include_base=TRUE]#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
rinstall
# Print commandline help of rinstallrinstall -h# Print rinstall R document (Just like ?sessionInfo in R client)rinstall -d# Install CRAN R package yaml (install.package)rinstall yamlrinstall -f 1 yaml# Install R package ngstk from GitHub rctl/ngstk (devtools::install_github)rinstall -f 2 rctl/ngstk# Install R package ngstk from GitHub rctl/ngstk (install.package)# devtools::install_github with force = TRUE, ref = 'develop'rinstall -f 2 -e "force = TRUE, ref = 'develop'" rctl/ngstk# Install Bioconductor package ggtree (BiocManager)# BiocManager::install('ggtree')rinstall -f 3 ggtree# Install R packages (pacman)# pacman::p_load(ggtree)rinstall -f 4 ggtree# Install and download BioInstaller resources# Show all BioInstaller default resources namerinstall -f BioInstaller::install.bioinfo -e "show.all.names=T"rinstall -f 5 -e "show.all.names=T"# Show ANNOVAR refgene and avsnp versionsrinstall -f BioInstaller::install.bioinfo -e "show.all.versions=T" db_annovar_refgenerinstall -f 5 -e "show.all.versions=T" db_annovar_avsnp# Show ANNOVAR hg19 refgene and avsnprinstall -f 5 -e "download.dir='/tmp/refgene', extra.list=list(buildver='hg19')" db_annovar_refgenerinstall -f 5 -e "download.dir='/tmp/avsnp', extra.list=list(buildver='hg19')" db_annovar_avsnp
rinstall -h#> Description:#> rinstall is an R-based tool to install or download R packages and other resources supported by R package BioInstaller.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall [options] [params]#> Examples:#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall -p ini#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall ini,yaml#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall -f 2 JhuangLab/ngstk#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall -f 2 -e "force = TRUE, ref = 'develop'" JhuangLab/ngstk#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall -f 3 ggtree; /Users/apple/.config/yarn/global/node_modules/.bin/rinstall rinstall -f 4 ggtree#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall -f 5 -e "show.all.names=T"#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall -f 5 -e "show.all.versions=T" db_annovar_avsnp#> /Users/apple/.config/yarn/global/node_modules/.bin/rinstall -f 5 -e "download.dir='/tmp/avsnp', extra.list=list(buildver='hg19')" db_annovar_avsnp#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. install.packages (1), devtools::install_github (2), BiocManager::install (3), pacman::p_load (4), BioInstaller::install.bioinfo (5)].#> -p PKGS, --pkgs=PKGS#> Package or item names [e.g. ggplot2,stringr or JhuangLab/BioInstaller (mode is devtools::install_github)].#> -e EXTRA, --extra=EXTRA#> Extra parameters [e.g. ref='develop'].#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
rdownload
rdownload "https://img.shields.io/npm/dm/rctl.svg,https://img.shields.io/npm/v/rctl.svg,https://img.shields.io/npm/l/rctl.svg"rdownload "https://img.shields.io/npm/dm/rctl.svg,https://img.shields.io/npm/v/rctl.svg,https://img.shields.io/npm/l/rctl.svg" --destfiles "/tmp/rctl1.svg,rctl2.svg,rctl3.svg"rdownload --urls "https://img.shields.io/npm/dm/rctl.svg , https://img.shields.io/npm/v/rctl.svg,https://img.shields.io/npm/l/rctl.svg" \--destfiles "rctl1.svg,rctl2.svg,rctl3.svg" --max-cores 1
rdownload -h#> Description:#> rdownload is an R-based tool to concurrently download urls with logging.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rdownload [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rdownload "https://img.shields.io/npm/dm/rctl.svg,https://img.shields.io/npm/l/rctl.svg"#> /Users/apple/.config/yarn/global/node_modules/.bin/rdownload "https://img.shields.io/npm/dm/rctl.svg,https://img.shields.io/npm/l/rctl.svg" \#> --destfiles "rctl1.svg,rctl2.svg"#> /Users/apple/.config/yarn/global/node_modules/.bin/rdownload --urls "https://img.shields.io/npm/dm/rctl.svg,https://img.shields.io/npm/l/rctl.svg" \#> --destfiles "rctl1.svg,rctl2.svg"#> /Users/apple/.config/yarn/global/node_modules/.bin/rdownload --urls "https://img.shields.io/npm/dm/rctl.svg,https://img.shields.io/npm/l/rctl.svg" \#> --destfiles "rctl1.svg,rctl2.svg" --max-cores 1#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. ngstk::par_download (1).#> -u URLS, --urls=URLS#> URLs of of a resource to be downloaded (multiple files split by ',' or ';'#> --destfiles=DESTFILES#> Filenames of downloaded files, default use the basename(urls)#> --max-cores=MAX-CORES#> Define the maxium used cores [future::availableCores()]#> -r RFUNC, --rfunc=RFUNC#> R function (input param 'x') to process the returned colors or urls [e.g. function(x){return(x[[2]])} or x[[2]]]#> -e EXTRA, --extra=EXTRA#> Extra parameters [...]#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
rconfig
# Use configr::read.config parsing json format file# Reture the list object outputrconfig package.jsonrconfig -c package.json# Use configr::read.config parsing json format file with the custom R functionrconfig -c test.json -r 'function(x){x[["a"]] + x[["b"]]}'rconfig -c test.json -r 'function(x){x[["a"]]}'rconfig -c test.json -r 'function(x){x[["b"]]}'rconfig -c test.json -r 'x[["b"]]'# Use configr::write.config parsing json format filerconfig -f "configr::write.config" test.json -e "config.dat=list(a=1, b=2), write.type='json'"rconfig -f 2 test.json -e "config.dat=list(a=1, b=2), write.type='json'"
rconfig -f "configr::fetch.config" "https://raw.githubusercontent.com/Miachol/configr/master/inst/extdata/config.global.toml"rconfig -h#> trying URL 'https://raw.githubusercontent.com/Miachol/configr/master/inst/extdata/config.global.toml'#> Error in download.file(link, config.download.tmp) :#> cannot open URL 'https://raw.githubusercontent.com/Miachol/configr/master/inst/extdata/config.global.toml'#> Calls: eval -> eval -> do.call -> <Anonymous> -> download.file#> In addition: Warning message:#> In download.file(link, config.download.tmp) :#> URL 'https://raw.githubusercontent.com/Miachol/configr/master/inst/extdata/config.global.toml': status was 'Couldn't connect to server'#> Execution halted#> Description:#> rconfig is an R-based tool to parse and generate configuration file.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig package.json#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig -c package.json#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig -f 2 test.json -e "config.dat=list(a=1, b=2), write.type='json'"#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig -f "configr::write.config" test.json -e "config.dat=list(a=1, b=2), write.type='json'"#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig -i test.json -r 'function(x){x[["a"]] + x[["b"]]}'#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig -i test.json -r 'function(x){x[["a"]]}'#> /Users/apple/.config/yarn/global/node_modules/.bin/rconfig -i test.json -r 'function(x){x[["b"]]}'#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. configr::read.config (1), configr::fetch.config (2), configr::write.config (3), configr::get.config.type (4)].#> -c CFG, --cfg=CFG#> Input or output configuationo file.#> -e EXTRA, --extra=EXTRA#> Extra parameters [e.g. extra.list=list(key='value')].#> -r RFUNC, --rfunc=RFUNC#> R function (input param 'x') to process the parsed configuation file [e.g. function(x){return(x[[1]])} or x[[1]] ].#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
rclrs
# Show default and red/blue theme colorsrclrs defaultrclrs -t defaultrclrs -t red_blue# Show default theme colors (extract the first element)rclrs -t default -r 'x[1]'# Show all supported themerclrs --show-all-themes#> #0073c3#> #efc000#> #696969#> #ce534c#> #7ba6db#> #035892#> #052135#> #666633#> #660000#> #990000#> #0073c3#> #efc000#> #696969#> #ce534c#> #7ba6db#> #035892#> #052135#> #666633#> #660000#> #990000#> #c20b01#> #196abd#> #0073c3#> List of 35#> $ Title : chr "ngstk theme configuration file (colors)"#> $ adobe_color_cc_1 :List of 1#> ..$ colors: chr [1:10] "#FFE350" "#E8740C" "#FF0000" "#9C0CE8" ...#> $ ball_subtype_colors :List of 4#> ..$ colors : chr [1:10] "#0071bc" "#82a6d7" "#003b64" "#e8c122" ...#> ..$ doi : chr "10.1200/JCO.2016.70.7836"#> ..$ figure : chr "figure1"#> ..$ journal: chr "Journal of Clinical Oncology"#> $ default :List of 1#> ..$ colors: chr [1:10] "#0073c3" "#efc000" "#696969" "#ce534c" ...#> $ ggsci_aaas_default :List of 1#> ..$ colors: chr [1:10] "#3B4992" "#EE0000" "#008B45" "#631879" ...#> $ ggsci_d3_category10 :List of 1#> ..$ colors: chr [1:10] "#1F77B4" "#FF7F0E" "#2CA02C" "#D62728" ...#> $ ggsci_d3_category20 :List of 1#> ..$ colors: chr [1:20] "#1F77B4" "#FF7F0E" "#2CA02C" "#D62728" ...#> $ ggsci_d3_category20b :List of 1#> ..$ colors: chr [1:20] "#393B79" "#637939" "#8C6D31" "#843C39" ...#> $ ggsci_d3_category20c :List of 1#> ..$ colors: chr [1:20] "#3182BD" "#E6550D" "#31A354" "#756BB1" ...#> $ ggsci_futurama_planetexpress:List of 1#> ..$ colors: chr [1:12] "#FF6F00" "#C71000" "#008EA0" "#8A4198" ...#> $ ggsci_gsea_default :List of 1#> ..$ colors: chr [1:12] "#4500AD" "#2700D1" "#6B58EF" "#8888FF" ...#> $ ggsci_igv_alternating :List of 1#> ..$ colors: chr [1:2] "#5773CC" "#FFB900"#> $ ggsci_igv_default :List of 1#> ..$ colors: chr [1:51] "#5050FF" "#CE3D32" "#749B58" "#F0E685" ...#> $ ggsci_jama_defalut :List of 1#> ..$ colors: chr [1:7] "#374E55" "#DF8F44" "#00A1D5" "#B24745" ...#> $ ggsci_jco_default :List of 1#> ..$ colors: chr [1:10] "#0073C2" "#EFC000" "#868686" "#CD534C" ...#> $ ggsci_lancet_lanonc :List of 1#> ..$ colors: chr [1:9] "#00468B" "#ED0000" "#42B540" "#0099B4" ...#> $ ggsci_locuszoom :List of 1#> ..$ colors: chr [1:7] "#D43F3A" "#EEA236" "#5CB85C" "#46B8DA" ...#> $ ggsci_nejm_default :List of 1#> ..$ colors: chr [1:8] "#BC3C29" "#0072B5" "#E18727" "#20854E" ...#> $ ggsci_npg_nrc :List of 1#> ..$ colors: chr [1:10] "#E64B35" "#4DBBD5" "#00A087" "#3C5488" ...#> $ ggsci_rickandmorty_schwifty :List of 1#> ..$ colors: chr [1:12] "#FAFD7C" "#82491E" "#24325F" "#B7E4F9" ...#> $ ggsci_simpsons_springfield :List of 1#> ..$ colors: chr [1:16] "#FED439" "#709AE1" "#8A9197" "#D2AF81" ...#> $ ggsci_startrek_uniform :List of 1#> ..$ colors: chr [1:7] "#CC0C00" "#5C88DA" "#84BD00" "#FFCD00" ...#> $ ggsci_tron_legacy :List of 1#> ..$ colors: chr [1:7] "#FF410D" "#6EE2FF" "#F7C530" "#95CC5E" ...#> $ ggsci_uchicago_dark :List of 1#> ..$ colors: chr [1:9] "#800000" "#767676" "#CC8214" "#616530" ...#> $ ggsci_uchicago_default :List of 1#> ..$ colors: chr [1:9] "#800000" "#767676" "#FFA319" "#8A9045" ...#> $ ggsci_uchicago_light :List of 1#> ..$ colors: chr [1:9] "#800000" "#D6D6CE" "#FFB547" "#ADB17D" ...#> $ ggsci_ucscgb_default :List of 1#> ..$ colors: chr [1:26] "#FF0000" "#FF9900" "#FFCC00" "#00FF00" ...#> $ nature_brest_signatures :List of 4#> ..$ colors : chr [1:12] "#3d1572" "#7d4594" "#e84286" "#f7c0ba" ...#> ..$ doi : chr "10.1038/nature17676"#> ..$ figure : chr "figure3b"#> ..$ hournal: chr "Nature"#> $ ng_mutations :List of 4#> ..$ colors : chr [1:9] "#609ec2" "#b56248" "#d0cb6c" "#9cb46f" ...#> ..$ doi : chr "10.1038/ng.3900"#> ..$ figure : chr "figure4a"#> ..$ journal: chr "Nature Gentics"#> $ nm_lines :List of 4#> ..$ colors : chr [1:6] "#3b7ab5" "#e7211c" "#ff831d" "#2ee0d1" ...#> ..$ doi : chr "10.1038/nmeth.4083"#> ..$ figure : chr "figure2"#> ..$ journal: chr "Nature Methods"#> $ proteinpaint_chromHMM_state :List of 2#> ..$ colors : chr [1:16] "#c0222c" "#f12424" "#ff00c7" "#d192fb" ...#> ..$ journal: chr "Nature Gentics"#> $ proteinpaint_domains :List of 2#> ..$ colors : chr [1:8] "#a6d854" "#8dd3c7" "#fb8072" "#80b1d3" ...#> ..$ journal: chr "Nature Gentics"#> $ proteinpaint_mutations :List of 2#> ..$ colors : chr [1:10] "#3987cc" "#ff7f0e" "#db3d3d" "#6633ff" ...#> ..$ journal: chr "Nature Gentics"#> $ proteinpaint_significance :List of 2#> ..$ colors : chr [1:7] "#aaaaaa" "#e99002" "#5bc0de" "#f04124" ...#> ..$ journal: chr "Nature Gentics"#> $ red_blue :List of 1#> ..$ colors: chr [1:2] "#c20b01" "#196abd"
rclrs -h#> Description:#> rclrs is an R-based tool to generate colors for visulization using a theme key.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rclrs [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rclrs default#> /Users/apple/.config/yarn/global/node_modules/.bin/rclrs -t default#> /Users/apple/.config/yarn/global/node_modules/.bin/rclrs -t default -r 'x[1]'#> /Users/apple/.config/yarn/global/node_modules/.bin/rclrs -t red_blue#> /Users/apple/.config/yarn/global/node_modules/.bin/rclrs --show-all-themes#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. ngstk::set_colors (1).#> -t THEME, --theme=THEME#> Input the theme name and return the colors.#> -s, --show-all-themes#> Show all included themes.#> -r RFUNC, --rfunc=RFUNC#> R function (input param 'x') to process the returned colors or theme [e.g. function(x){return(x[[2]])} or x[[2]]].#> -e EXTRA, --extra=EXTRA#> Extra parameters [e.g. theme_config_file = 'your_color_cfg.toml'].#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
rmv
# do.rename is used to preview the new filenames#rmv "`ls`" -e "do.rename = F, prefix = 'prefix', suffix = 'suffix'"rmv "`ls`" -e "do.rename = F, replace = list(old =c('-', '__'), new = c('_', '_'))"rmv "`ls`" -e "do.rename = F, toupper = TRUE"rmv "`ls`" -e "do.rename = F, tolower = TRUE"rmv "`ls`" -e "do.rename=T, replace=list(old='new', new='old')"
rmv -h#> Description:#> rmv is an R-based tool to format file names.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rmv [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rmv "`ls`" -e "do.rename = FALSE, prefix = 'prefix', suffix = 'suffix'"#> /Users/apple/.config/yarn/global/node_modules/.bin/rmv "`ls`" -e "do.rename = FALSE, replace = list(old =c('-', '__'), new = c('_', '_'))"#> /Users/apple/.config/yarn/global/node_modules/.bin/rmv "`ls`" -e "do.rename = FALSE, toupper = TRUE"#> /Users/apple/.config/yarn/global/node_modules/.bin/rmv "`ls`" -e "do.rename = FALSE, tolower = TRUE"#> /Users/apple/.config/yarn/global/node_modules/.bin/rmv -e "files_dir = '.', pattern = '.*.txt', do.rename=F, replace=list(old='old', new='new')"#> /Users/apple/.config/yarn/global/node_modules/.bin/rmv "`ls`" -e "do.rename=T, replace=list(old='old', new='new')"#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. ngstk::format_filenames (1).#> -l OLD-FILES, --old-files=OLD-FILES#> Input the files need to be renamed (string will be split by '\n', ',' and ';').#> -r RFUNC, --rfunc=RFUNC#> R function (input param 'x') to process the returned colors or old-files [e.g. function(x){return(x[[2]])} or x[[2]]].#> -e EXTRA, --extra=EXTRA#> Extra parameters [e.g. toupper = TRUE)].#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
rtime_stamp
rtime_stamprtime_stamp -r 'x[[1]]'rtime_stamp -r 'x[[1]][1]'rtime_stamp -t '%Y_%d'rtime_stamp -e "extra_flag=c('*')"rtime_stamp -h#> [[1]]#> [1] "2020_04_21_19_55_46_" "2020_04_21_19_55_" "2020_04_21_19_"#> [4] "2020_04_21_" "2020_04_" "2020_"#>#> [[2]]#> [1] "2020-04-21-19-55-47-" "2020-04-21-19-55-" "2020-04-21-19-"#> [4] "2020-04-21-" "2020-04-" "2020-"#>#> [[3]]#> [1] "2020/04/21/19/55/47/" "2020/04/21/19/55/" "2020/04/21/19/"#> [4] "2020/04/21/" "2020/04/" "2020/"#>#> [[4]]#> [1] "2020@04@21@19@55@47@" "2020@04@21@19@55@" "2020@04@21@19@"#> [4] "2020@04@21@" "2020@04@" "2020@"#>#> 2020_04_21_19_55_48_#> 2020_04_21_19_55_#> 2020_04_21_19_#> 2020_04_21_#> 2020_04_#> 2020_#> 2020_04_21_19_55_49_#> [[1]]#> [1] "2020_21"#>#> [[2]]#> [1] "2020-21"#>#> [[3]]#> [1] "2020/21"#>#> [[4]]#> [1] "2020@21"#>#> [[1]]#> [1] "2020_04_21_19_55_51_" "2020_04_21_19_55_" "2020_04_21_19_"#> [4] "2020_04_21_" "2020_04_" "2020_"#>#> [[2]]#> [1] "2020*04*21*19*55*51*" "2020*04*21*19*55*" "2020*04*21*19*"#> [4] "2020*04*21*" "2020*04*" "2020*"#>#> Description:#> rtime_stamp is an R-based tool to generate time stamp.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rtime_stamp [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rtime_stamp#> /Users/apple/.config/yarn/global/node_modules/.bin/rtime_stamp -r 'x[[1]]'#> /Users/apple/.config/yarn/global/node_modules/.bin/rtime_stamp -r 'x[[1]][1]'#> /Users/apple/.config/yarn/global/node_modules/.bin/rtime_stamp -t '%Y_%d'#> /Users/apple/.config/yarn/global/node_modules/.bin/rtime_stamp -e "extra_flat=c('-')"#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. ngstk::time_stamp (1).#> -t TEMPLATE, --template=TEMPLATE#> Input the template and return the time stamps.#> -r RFUNC, --rfunc=RFUNC#> R function (input param 'x') to process the returned colors or template [e.g. function(x){return(x[[2]])} or x[[2]]].#> -e EXTRA, --extra=EXTRA#> Extra parameters [e.g. extra_flag = c('-', '/')].#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
ranystr
./bin/ranystr./bin/ranystr -l 30./bin/ranystr -l 20 -n 3#> KVaFz2XPrPx37RZDFyEA#> yDkKv9wiuGdBJf9QltxY4IC2023sDu#> TeLz128LQmRkRTjGe0C2#> 5cXtaQjXLGGLCgEWGCya#> OfuQDalqrWA0fRfvWgZf
ranystr -h#> Description:#> ranystr is an R-based tool to generate any counts and any length random strings.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/ranystr [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/ranystr#> /Users/apple/.config/yarn/global/node_modules/.bin/ranystr -l 30#> /Users/apple/.config/yarn/global/node_modules/.bin/ranystr -l 20 -n 3#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. stringi::stri_rand_strings (1).#> -n NUM, --num=NUM#> Counts of random strings [1].#> -l LENGTH, --length=LENGTH#> Length of one of random string [20].#> -p PATTERN, --pattern=PATTERN#> Character vector specifying character classes to draw elements ['[A-Za-z0-9]'].#> -r RFUNC, --rfunc=RFUNC#> R function (input param 'x') to process the returned colors or length [e.g. function(x){return(x[[2]])} or x[[2]]].#> -e EXTRA, --extra=EXTRA#> Extra parameters [...].#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
# Collect system.files("extdata", "bin", package = "ngstk")# multiple packages (i.e. ngstk,configr)rbin ngstkrbin --destdir /tmp/path ngstkrbin -h#> Copying ngstk bin/ demo_bin.sh to /Users/apple/.ngstk/bin#> Please set /Users/apple/.ngstk/bin in your PATH to use the bin files.#> Linux/Mac OS X: echo 'export PATH=$PATH:/Users/apple/.ngstk/bin\n' >> ~/.bashrc#> R users: echo 'Sys.setenv(PATH="/usr/local/Cellar/spack/bin:/Users/apple/miniconda3/bin:/Users/apple/.yarn/bin:/Users/apple/.config/yarn/global/node_modules/.bin:/Users/apple/Documents/gopath/bin:/usr/local/Cellar/gnu-sed/4.7/bin:/usr/local/opt/gnu-sed/libexec/gnubin:/Users/apple/.go/bin:/usr/local/bin:/usr/local/opt/coreutils/libexec/gnubin:/usr/local/Cellar/spack/bin:/usr/local/Cellar/modules/4.3.0/bin:/Users/apple/miniconda3/bin:/Users/apple/.yarn/bin:/Users/apple/.config/yarn/global/node_modules/.bin:/Users/apple/repositories/local/mac/go/bin:/usr/local/Cellar/gnu-sed/4.7/bin:/usr/local/opt/gnu-sed/libexec/gnubin:/Users/apple/.go/bin:/usr/local/bin:/usr/local/opt/coreutils/libexec/gnubin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/go/bin:/opt/X11/bin:/Users/apple/.ngstk/bin")\n' >> ~/.Rprofile#> ngstk.demo_bin.sh#> TRUE#> Copying ngstk bin/ demo_bin.sh to /private/tmp/path#> Please set /private/tmp/path in your PATH to use the bin files.#> Linux/Mac OS X: echo 'export PATH=$PATH:/private/tmp/path\n' >> ~/.bashrc#> R users: echo 'Sys.setenv(PATH="/usr/local/Cellar/spack/bin:/Users/apple/miniconda3/bin:/Users/apple/.yarn/bin:/Users/apple/.config/yarn/global/node_modules/.bin:/Users/apple/Documents/gopath/bin:/usr/local/Cellar/gnu-sed/4.7/bin:/usr/local/opt/gnu-sed/libexec/gnubin:/Users/apple/.go/bin:/usr/local/bin:/usr/local/opt/coreutils/libexec/gnubin:/usr/local/Cellar/spack/bin:/usr/local/Cellar/modules/4.3.0/bin:/Users/apple/miniconda3/bin:/Users/apple/.yarn/bin:/Users/apple/.config/yarn/global/node_modules/.bin:/Users/apple/repositories/local/mac/go/bin:/usr/local/Cellar/gnu-sed/4.7/bin:/usr/local/opt/gnu-sed/libexec/gnubin:/Users/apple/.go/bin:/usr/local/bin:/usr/local/opt/coreutils/libexec/gnubin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/go/bin:/opt/X11/bin:/private/tmp/path")\n' >> ~/.Rprofile#> ngstk.demo_bin.sh#> TRUE#> Description:#> rbin is an R-based tool to collect R packages bin files.#>#> Usage:#> /Users/apple/.config/yarn/global/node_modules/.bin/rbin [options] [params]#> /Users/apple/.config/yarn/global/node_modules/.bin/rbin ngstk#> /Users/apple/.config/yarn/global/node_modules/.bin/rbin --destdir /usr/local/bin/ ngstk#>#> Options:#> -v, --verbose#> Print extra output [default FALSE]#> -f FUNC, --func=FUNC#> Index or name of used function [e.g. ngstk::bin (1)].#> -c PKGS, --pkgs=PKGS#> Package names used to copy inst/bin directory files to PATH.#> -o DESTDIR, --destdir=DESTDIR#> Destination directory to store the inst/bin files [~/.ngstk/bin].#> -e EXTRA, --extra=EXTRA#> Extra parameters [e.g. extra.list=list(key='value')].#> -r RFUNC, --rfunc=RFUNC#> R function (input param 'x') to process the parsed configuation file [e.g. function(x){return(x[[1]])} or x[[1]] ].#> -d, --doc#> Print functions document#> -h, --help#> Show this help message and exit
How to contribute?
Please fork the GitHub rctl repository, modify it, and submit a pull request to us.
Maintainer
License
MIT