20210320

Contents

1. Working directories

Working directories

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R/CRAN update

# update indices
sudo apt update -qq
# install two helper packages we need
sudo apt install --no-install-recommends software-properties-common dirmngr
# import the signing key (by Michael Rutter) for these repo
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -sc)-cran40/"

1	sudo apt install --no-install-recommends r-base

The Comprehensive R Archive Network

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install.packages("knitr", dependencies=TRUE)
#
install.packages(c("BH", "jquerylib", "ps", "sys", "httpuv", "xtable", "sourcetools", "later", "promises", "crayon", "fastmap", "commonmark", "bslib", "cachem", "lazyeval", "miniUI", "processx", "askpass", "utf8", "cpp11", "assertthat", "R.methodsS3", "R.oo", "R.utils", "stringi", "shiny", "crosstalk", "manipulateWidget", "callr", "filehash", "rappdirs", "Rcpp", "curl", "openssl", "R6", "sysfonts", "showtextdb", "ellipsis", "fansi", "lifecycle", "pillar", "pkgconfig", "vctrs", "fs", "systemfonts", "textshaping", "backports", "cli", "purrr", "R.cache", "rematch2", "rprojroot", "withr", "stringr", "formatR", "testit", "rgl", "rmarkdown", "htmlwidgets", "webshot", "tikzDevice", "reticulate", "JuliaCall", "magick", "png", "jpeg", "gifski", "xml2", "httr", "DBI", "showtext", "tibble", "sass", "ragg", "styler"))

1	install.packages(c("mime", "highr", "markdown", "digest", "base64enc"), dependencies=TRUE)

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install.packages(c("mime", "highr", "markdown", "digest", "base64enc", "rlang", "glue", "magrittr", "stringi", "knitr", "yaml", "htmltools", "evaluate", "jsonlite", "tinytex", "xfun", "stringr"))
install.packages(c("ape", "assertthat", "backports", "BH", "cli", "colorspace", "crayon", "crosstalk", "digest", "dplyr", "DT", "evaluate", "fansi", "ggplot2", "glue", "gtable", "highr", "htmltools", "htmlwidgets", "httpuv", "jsonlite", "knitr", "labeling", "later", "lazyeval", "magrittr", "markdown", "mime", "pander", "pillar", "pkgconfig", "plyr", "promises", "purrr", "R6", "Rcpp", "readxl", "reshape2", "rlang", "rmarkdown", "rprojroot", "rvcheck", "scales", "shiny", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "tidytree", "tinytex", "utf8", "withr", "xfun", "xtable", "yaml"))

1	install.packages(c("stringi", "Rcpp", "stringr", "httpuv", "later", "promises", "miniUI", "knitr", "shiny", "manipulateWidget"))

1	install.packages(c("stringi", "Rcpp", "stringr", "httpuv", "later", "promises", "miniUI", "knitr", "shiny", "manipulateWidget"))

RStudio download

Download the RStudio IDE - RStudio

cd /media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/CRAN/RStudio/Installers/Desktop
cat 20210321.list | ag ']: '
cat 20210321.list | ag ']: ' | ag -v "/\n" | sed "s/]: /\t/" | awk ' { print $2 } ' > 2.list
#
cd /media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/CRAN/RStudio/Installers/Desktop
sh /media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/CRAN/RStudio/Installers/Desktop/DL_20210321.sh

Download in remote computer (Vision)

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/media/ht/ht_5T/Database/Virus/Bacteriophage/PhagesDB/Figures/Cluster/DL.sh # download scripts
# Remote computer
mkdir ~/Downloads/20210320

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https://phagesdb.org/plaques/download/A/
https://phagesdb.org/empics/download/A/
https://phagesdb.org/vdigests/download/A/

Latest BLASTn database files for local BLAST (.nhr, .nin, .nsq), Actino_DB.tar.gz

Expand/Collapse

/hosts/genera/9/
/hosts/genera/3/
/hosts/genera/7/
/hosts/genera/6/
/hosts/genera/12/
/hosts/genera/1/
/hosts/genera/8/
/hosts/genera/2/
/hosts/genera/4/
/hosts/genera/10/
/hosts/genera/11/
http://bacillus.phagesdb.org/
/addphage/
/modphage/
/data/
/annotation/
/thumbnails/
/blast/
/blastp/
/publications/
/pubgroups/all/
/pubgroups/SEA-PHAGES/
/api/schema/
/documents/
/phagehunters/
/glossary/
/institutions/
/links/
/workflow/
/DNAMaster/
/DNAMaster/faq/
/Phamerator/faq/
/AceUtil/
/blog/
http://facebook.com/phages/
http://twitter.com/phagesdb/
/miab/
/blog/taglist/
/about/
/contact/
/people/
/terms/
/phages/BedellType/
/phages/Obiageli/
/phages/Battleship/
/phages/Horcrux/
/phages/Hauge/
/phages/VWB/
/phages/Indra/
/phages/Sedona/
/phages/TuertoX/
/phages/DrSeegs/
/phages/I3/
/phages/BrazzalePHS/
/phages/JalFarm20/
/phages/Warda/
/phages/Berka/
/accounts/login/
/accounts/signup/
/media/Actinobacteriophages-All.fasta
/data/unphameratedfastas/
/data/accessions/?names=True
/data/accessions/
/data/submissionfiles/
/data/clusterpending/
/media/BLAST_DBs/Actino_DB.tar.gz
/plaques/download/A/
/empics/download/A/
/vdigests/download/A/
/plaques/download/AA/
/empics/download/AA/
/vdigests/download/AA/
/plaques/download/AB/
/empics/download/AB/
/vdigests/download/AB/
/plaques/download/AC/
/empics/download/AC/
/vdigests/download/AC/
/plaques/download/AK/
/empics/download/AK/
/vdigests/download/AK/
/plaques/download/AL/
/empics/download/AL/
/vdigests/download/AL/
/plaques/download/AM/
/empics/download/AM/
/vdigests/download/AM/
/plaques/download/AN/
/empics/download/AN/
/vdigests/download/AN/
/plaques/download/AO/
/empics/download/AO/
/vdigests/download/AO/
/plaques/download/AP/
/empics/download/AP/
/vdigests/download/AP/
/plaques/download/AQ/
/empics/download/AQ/
/vdigests/download/AQ/
/plaques/download/AR/
/empics/download/AR/
/vdigests/download/AR/
/plaques/download/AS/
/empics/download/AS/
/vdigests/download/AS/
/plaques/download/AT/
/empics/download/AT/
/vdigests/download/AT/
/plaques/download/AU/
/empics/download/AU/
/vdigests/download/AU/
/plaques/download/AV/
/empics/download/AV/
/vdigests/download/AV/
/plaques/download/AW/
/empics/download/AW/
/vdigests/download/AW/
/plaques/download/AX/
/empics/download/AX/
/vdigests/download/AX/
/plaques/download/AY/
/empics/download/AY/
/vdigests/download/AY/
/plaques/download/AZ/
/empics/download/AZ/
/vdigests/download/AZ/
/plaques/download/B/
/empics/download/B/
/vdigests/download/B/
/plaques/download/BA/
/empics/download/BA/
/vdigests/download/BA/
/plaques/download/BB/
/empics/download/BB/
/vdigests/download/BB/
/plaques/download/BC/
/empics/download/BC/
/vdigests/download/BC/
/plaques/download/BD/
/empics/download/BD/
/vdigests/download/BD/
/plaques/download/BE/
/empics/download/BE/
/vdigests/download/BE/
/plaques/download/BF/
/empics/download/BF/
/vdigests/download/BF/
/plaques/download/BG/
/empics/download/BG/
/vdigests/download/BG/
/plaques/download/BH/
/empics/download/BH/
/vdigests/download/BH/
/plaques/download/BI/
/empics/download/BI/
/vdigests/download/BI/
/plaques/download/BJ/
/empics/download/BJ/
/vdigests/download/BJ/
/plaques/download/BK/
/empics/download/BK/
/vdigests/download/BK/
/plaques/download/BL/
/empics/download/BL/
/vdigests/download/BL/
/plaques/download/BM/
/empics/download/BM/
/vdigests/download/BM/
/plaques/download/BN/
/empics/download/BN/
/vdigests/download/BN/
/plaques/download/BO/
/empics/download/BO/
/vdigests/download/BO/
/plaques/download/BP/
/empics/download/BP/
/vdigests/download/BP/
/plaques/download/BQ/
/empics/download/BQ/
/vdigests/download/BQ/
/plaques/download/BR/
/empics/download/BR/
/vdigests/download/BR/
/plaques/download/BU/
/empics/download/BU/
/vdigests/download/BU/
/plaques/download/BV/
/empics/download/BV/
/vdigests/download/BV/
/plaques/download/BW/
/empics/download/BW/
/vdigests/download/BW/
/plaques/download/BX/
/empics/download/BX/
/vdigests/download/BX/
/plaques/download/C/
/empics/download/C/
/vdigests/download/C/
/plaques/download/CA/
/empics/download/CA/
/vdigests/download/CA/
/plaques/download/CB/
/empics/download/CB/
/vdigests/download/CB/
/plaques/download/CC/
/empics/download/CC/
/vdigests/download/CC/
/plaques/download/CD/
/empics/download/CD/
/vdigests/download/CD/
/plaques/download/CE/
/empics/download/CE/
/vdigests/download/CE/
/plaques/download/CQ/
/empics/download/CQ/
/vdigests/download/CQ/
/plaques/download/CR/
/empics/download/CR/
/vdigests/download/CR/
/plaques/download/CS/
/empics/download/CS/
/vdigests/download/CS/
/plaques/download/CT/
/empics/download/CT/
/vdigests/download/CT/
/plaques/download/CU/
/empics/download/CU/
/vdigests/download/CU/
/plaques/download/CV/
/empics/download/CV/
/vdigests/download/CV/
/plaques/download/CW/
/empics/download/CW/
/vdigests/download/CW/
/plaques/download/CX/
/empics/download/CX/
/vdigests/download/CX/
/plaques/download/CY/
/empics/download/CY/
/vdigests/download/CY/
/plaques/download/CZ/
/empics/download/CZ/
/vdigests/download/CZ/
/plaques/download/D/
/empics/download/D/
/vdigests/download/D/
/plaques/download/DA/
/empics/download/DA/
/vdigests/download/DA/
/plaques/download/DB/
/empics/download/DB/
/vdigests/download/DB/
/plaques/download/DC/
/empics/download/DC/
/vdigests/download/DC/
/plaques/download/DE/
/empics/download/DE/
/vdigests/download/DE/
/plaques/download/DF/
/empics/download/DF/
/vdigests/download/DF/
/plaques/download/DG/
/empics/download/DG/
/vdigests/download/DG/
/plaques/download/DH/
/empics/download/DH/
/vdigests/download/DH/
/plaques/download/DI/
/empics/download/DI/
/vdigests/download/DI/
/plaques/download/DJ/
/empics/download/DJ/
/vdigests/download/DJ/
/plaques/download/DK/
/empics/download/DK/
/vdigests/download/DK/
/plaques/download/DL/
/empics/download/DL/
/vdigests/download/DL/
/plaques/download/DM/
/empics/download/DM/
/vdigests/download/DM/
/plaques/download/DN/
/empics/download/DN/
/vdigests/download/DN/
/plaques/download/DO/
/empics/download/DO/
/vdigests/download/DO/
/plaques/download/DP/
/empics/download/DP/
/vdigests/download/DP/
/plaques/download/DQ/
/empics/download/DQ/
/vdigests/download/DQ/
/plaques/download/DR/
/empics/download/DR/
/vdigests/download/DR/
/plaques/download/DS/
/empics/download/DS/
/vdigests/download/DS/
/plaques/download/DT/
/empics/download/DT/
/vdigests/download/DT/
/plaques/download/DU/
/empics/download/DU/
/vdigests/download/DU/
/plaques/download/DV/
/empics/download/DV/
/vdigests/download/DV/
/plaques/download/DW/
/empics/download/DW/
/vdigests/download/DW/
/plaques/download/DX/
/empics/download/DX/
/vdigests/download/DX/
/plaques/download/DY/
/empics/download/DY/
/vdigests/download/DY/
/plaques/download/DZ/
/empics/download/DZ/
/vdigests/download/DZ/
/plaques/download/E/
/empics/download/E/
/vdigests/download/E/
/plaques/download/EA/
/empics/download/EA/
/vdigests/download/EA/
/plaques/download/EB/
/empics/download/EB/
/vdigests/download/EB/
/plaques/download/EC/
/empics/download/EC/
/vdigests/download/EC/
/plaques/download/ED/
/empics/download/ED/
/vdigests/download/ED/
/plaques/download/EE/
/empics/download/EE/
/vdigests/download/EE/
/plaques/download/EF/
/empics/download/EF/
/vdigests/download/EF/
/plaques/download/EG/
/empics/download/EG/
/vdigests/download/EG/
/plaques/download/EH/
/empics/download/EH/
/vdigests/download/EH/
/plaques/download/EI/
/empics/download/EI/
/vdigests/download/EI/
/plaques/download/EJ/
/empics/download/EJ/
/vdigests/download/EJ/
/plaques/download/EK/
/empics/download/EK/
/vdigests/download/EK/
/plaques/download/EL/
/empics/download/EL/
/vdigests/download/EL/
/plaques/download/EM/
/empics/download/EM/
/vdigests/download/EM/
/plaques/download/EN/
/empics/download/EN/
/vdigests/download/EN/
/plaques/download/EO/
/empics/download/EO/
/vdigests/download/EO/
/plaques/download/EP/
/empics/download/EP/
/vdigests/download/EP/
/plaques/download/F/
/empics/download/F/
/vdigests/download/F/
/plaques/download/FA/
/empics/download/FA/
/vdigests/download/FA/
/plaques/download/FB/
/empics/download/FB/
/vdigests/download/FB/
/plaques/download/FC/
/empics/download/FC/
/vdigests/download/FC/
/plaques/download/FD/
/empics/download/FD/
/vdigests/download/FD/
/plaques/download/FE/
/empics/download/FE/
/vdigests/download/FE/
/plaques/download/FF/
/empics/download/FF/
/vdigests/download/FF/
/plaques/download/FG/
/empics/download/FG/
/vdigests/download/FG/
/plaques/download/FH/
/empics/download/FH/
/vdigests/download/FH/
/plaques/download/FK/
/empics/download/FK/
/vdigests/download/FK/
/plaques/download/FL/
/empics/download/FL/
/vdigests/download/FL/
/plaques/download/G/
/empics/download/G/
/vdigests/download/G/
/plaques/download/GA/
/empics/download/GA/
/vdigests/download/GA/
/plaques/download/GB/
/empics/download/GB/
/vdigests/download/GB/
/plaques/download/GC/
/empics/download/GC/
/vdigests/download/GC/
/plaques/download/GD/
/empics/download/GD/
/vdigests/download/GD/
/plaques/download/GE/
/empics/download/GE/
/vdigests/download/GE/
/plaques/download/H/
/empics/download/H/
/vdigests/download/H/
/plaques/download/I/
/empics/download/I/
/vdigests/download/I/
/plaques/download/J/
/empics/download/J/
/vdigests/download/J/
/plaques/download/K/
/empics/download/K/
/vdigests/download/K/
/plaques/download/L/
/empics/download/L/
/vdigests/download/L/
/plaques/download/M/
/empics/download/M/
/vdigests/download/M/
/plaques/download/N/
/empics/download/N/
/vdigests/download/N/
/plaques/download/O/
/empics/download/O/
/vdigests/download/O/
/plaques/download/P/
/empics/download/P/
/vdigests/download/P/
/plaques/download/Q/
/empics/download/Q/
/vdigests/download/Q/
/plaques/download/R/
/empics/download/R/
/vdigests/download/R/
/plaques/download/S/
/empics/download/S/
/vdigests/download/S/
/plaques/download/Singleton/
/empics/download/Singleton/
/vdigests/download/Singleton/
/plaques/download/T/
/empics/download/T/
/vdigests/download/T/
/plaques/download/U/
/empics/download/U/
/vdigests/download/U/
/plaques/download/V/
/empics/download/V/
/vdigests/download/V/
/plaques/download/W/
/empics/download/W/
/vdigests/download/W/
/plaques/download/X/
/empics/download/X/
/vdigests/download/X/
/plaques/download/Y/
/empics/download/Y/
/vdigests/download/Y/
/plaques/download/Z/
/empics/download/Z/
/vdigests/download/Z/