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This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -24,6 +24,110 @@ $ source beRi_setup.sh $ source beRi_setup.sh ``` Install R from source using rinse if it's not already installed on the system ```bash # should already be in the ~/demo directory $ cd ~/demo # install the latest version of R from source # This will take a while $ rinse # Add the folder where R is located to PATH (may not be the same as below) # You can also add this line to your .bashrc and then source .bashrc $ export PATH="$PATH:~/src/bin/" $ which R ``` Create a virtual environment with renv ```bash # If R is in your PATH $ renv -d ~/hackseq2018 $ source hackseq2018/bin/activate # The environment should be activated. # If you call R it will be the R in the environment. The default .Rprofile will ask some questions. # For a quick demo select yes for bioconductor and no for the rest $ R R version 3.5.1 (2018-07-02) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Attaching package: ‘utils’ The following object is masked _by_ ‘.GlobalEnv’: askYesNo ..................Attempting to Load Bioconductor................... Warning: Prompting for Bioconductor Installation... Do you want to install Bioconductor??? [Y/N] Y ..................Attempting to Load Devtools................... Warning: Prompting for Devtools Installation... Do you want to install Devtools??? [Y/N] N ..................Attempting to Load Tidyverse................... Warning: Prompting for Tidyverse Installation... Do you want to install Tidyverse??? [Y/N] N Warning: Installing Bioconductor from /home/demo/.Rprofile. into /home/demo/hackseq2018/lib/R/library trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/BiocInstaller_1.30.0.tar.gz' Content type 'application/x-gzip' length 19149 bytes (18 KB) ================================================== downloaded 18 KB WARNING: ignoring environment value of R_HOME * installing *source* package ‘BiocInstaller’ ... ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded WARNING: ignoring environment value of R_HOME Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help * DONE (BiocInstaller) The downloaded source packages are in ‘/tmp/Rtmp89KFhA/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help ..............Bioconductor was successfully installed............... ..............Bioconductor was successfully installed!!............... # Now install something from bioconductor > biocLite('edgeR') ``` ## Bash script preview ```bash # Make directories -
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This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -12,6 +12,18 @@ _**rut LICENSING: [rut](https://github.com/datasnakes/rut/blob/add-license-1/LIC _**rinse LICENSING: [rinse](https://github.com/datasnakes/rinse/blob/add-license-1/LICENSE)**_ ## Instructions First download the beRi_setup.sh file into your home directory ```bash $ cd $ curl -O https://gist.github.com/grabear/498b67b89ba1c0d45fe3a7fef6271f29/raw/e47cd735ec5432edf6f4795a45481a7182ab4f14/beRi_setup.sh # Source the file once if pip is already installed. $ source beRi_setup.sh # Source the file twice if pip is not installed. The bash shell needs to be reloaded. $ source beRi_setup.sh ``` ## Bash script preview ```bash # Make directories -
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This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,60 @@ # beRi demo (tested on Ubuntu-16.04) This demo was tested on Ubuntu-16.04 which comes pre-installed with bash, Python 3.6, git, and curl. The beRi package have been built using Python 3.6. Other versions of Python have not been tested. Other operating systems have not been tested. Know bugs include [renv Issue #32](https://github.com/datasnakes/renv/issues/32) _**WARNING: USE THIS AT YOUR OWN RISK. THIS CODE IS UNTESTED.**_ _**beRi LICENSING: [beRi](https://github.com/datasnakes/beRi/blob/master/LICENSE)**_ _**renv LICENSING: [renv](https://github.com/datasnakes/renv/blob/add-license-1/LICENSE)**_ _**rut LICENSING: [rut](https://github.com/datasnakes/rut/blob/add-license-1/LICENSE)**_ _**rinse LICENSING: [rinse](https://github.com/datasnakes/rinse/blob/add-license-1/LICENSE)**_ ## Bash script preview ```bash # Make directories mkdir scripts mkdir GitHub mkdir demo # Download and/or install important dependencies if ! type "pip" > /dev/null; then cd ~/scripts curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py python3.6 get-pip.py --user exec bash --login pip install --user poetry cookiecutter else pip install --user poetry cookiecutter fi # Setup renv cd ~/GitHub git clone https://github.com/datasnakes/renv cd renv git checkout santina/symlink poetry install -vvv poetry build pip install --user dist/renv*.whl # Setup rinse cd ~/GitHub git clone https://github.com/datasnakes/rinse cd rinse poetry install -vvv poetry build pip install --user dist/rinse*.whl # Setup rut cd ~/GitHub git clone https://github.com/datasnakes/rut cd rut git checkout old_remotes poetry install -vvv poetry build pip install --user dist/rut*.whl cd ~/demo ``` This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters. Learn more about bidirectional Unicode charactersOriginal file line number Diff line number Diff line change @@ -0,0 +1,43 @@ # Make directories mkdir scripts mkdir GitHub mkdir demo # Download and/or install important dependencies if ! type "pip" > /dev/null; then cd ~/scripts curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py python3.6 get-pip.py --user exec bash --login pip install --user poetry cookiecutter else pip install --user poetry cookiecutter fi # Setup renv cd ~/GitHub git clone https://github.com/datasnakes/renv cd renv git checkout santina/symlink poetry install -vvv poetry build pip install --user dist/renv*.whl # Setup rinse cd ~/GitHub git clone https://github.com/datasnakes/rinse cd rinse poetry install -vvv poetry build pip install --user dist/rinse*.whl # Setup rut cd ~/GitHub git clone https://github.com/datasnakes/rut cd rut git checkout old_remotes poetry install -vvv poetry build pip install --user dist/rut*.whl cd ~/demo