From 4244d9353ceaa9d186c892b28a3eb369c56b1658 Mon Sep 17 00:00:00 2001
From: Pariksheet Nanda <pariksheet.nanda@uconn.edu>
Date: Mon, 15 Aug 2016 14:45:42 -0400
Subject: [PATCH] ENH: Initial commit

---
 README.md              | 74 ++++++++++++++++++++++++++++++++++++++++++
 cgi-updater-payload.sh | 56 ++++++++++++++++++++++++++++++++
 2 files changed, 130 insertions(+)
 create mode 100644 README.md
 create mode 100755 cgi-updater-payload.sh

diff --git a/README.md b/README.md
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--- /dev/null
+++ b/README.md
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+## Update CGI computers remotely
+
+Updates Ubuntu 14.04 computers with latest version of R, RStudio, R
+libraries, Python and BioPython, for bioinformatics training.
+
+
+### Remote computer requirements:
+
+- ClusterShell
+- ssh key authentication for all 10 laptops
+- Wired connection (wireless in the building is flaky)
+
+### Usage
+
+Setup your `/etc/hosts` and map the target laptops as e.g. cgi01,
+cgi02, etc.  The Ubuntu machines don't have openssh-server installed
+on them, so install it, copy the keys, and then disable password
+authentication.
+
+``sh
+# On the laptops
+local$ sudo apt-get update && sudo apt-get -y install openssh-server
+local$ sudo sed -i 's/#Pass.*/PasswordAuthentication no/' /etc/ssh/sshd_config
+
+Then create an ssh keys and copy it over:
+
+```sh
+remote$ idf=~/.ssh/id_rsa-cgi-202
+remote$ ssh-keygen -f $idf -N ""
+remote$ for host in cgi{01..10}; do ssh-copy-id -i $idf cgi_user@$host; done
+```
+
+Add the identity file to your `~/.ssh/config`
+
+```
+Host cgi*
+     IdentityFile ~/.ssh/id_rsa-cgi-202
+     User cgi_user	  
+```
+
+Test that the keys work with:
+
+```sh
+remote$ alias clush="clush -B -w cgi[01-10]"
+remote$ type clush # verify alias
+remote$ clush id -u
+1000
+```
+
+On each computer, locally restart SSH server for the disabled password
+authentication to take effect.
+
+```sh
+local$ sudo service ssh restart
+```
+
+Running sudo remotely is a pain, so use the same key for remote root
+access.
+
+```sh
+local$ sudo mkdir -p /root/.ssh
+local$ sudo sh -c "echo $(tail -1 ~/.ssh/authorized_keys) >> /root/.ssh/authorized_keys"
+local$ sudo cat /root/.ssh/authorized_keys
+```
+
+In the present configuration, commands are normally executed as
+cgi_user.  To execute as root, use the `-l root` option of `clush`:
+
+```sh
+remote$ clush -l root id -u
+0
+remote$ clush -l root --copy cgi-updater-payload.sh --dest /root/
+remote$ clush -l root ./cgi-updater-payload.sh
+```
diff --git a/cgi-updater-payload.sh b/cgi-updater-payload.sh
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+++ b/cgi-updater-payload.sh
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+#!/bin/bash
+
+r_pkgs=( DESeq2 grDevices genefilter biomaRt ggplot2 gplots RColorBrewer )
+pip_pkgs=( biopython )
+
+if [[ $(id -u) -ne 0 ]]; then
+    echo "Error: run this script as the root user, not EUID $(id -u)."
+    exit 1
+fi
+
+set -e				# Make most errors fatal.
+
+ubuntu_update () {
+    apt-get update
+    apt-get -y upgrade
+}
+
+ubuntu_install_r_cran () {
+    cat <<EOF > /etc/apt/sources.list.d/cgi-r-cran.list
+# Newest R version from CRAN per
+# https://cran.r-project.org/bin/linux/ubuntu/
+deb https://cran.fhcrc.org/bin/linux/ubuntu $(lsb_release -cs)/
+EOF
+    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
+    apt-get update
+    apt-get -y install r-base-dev
+}
+
+python_install_packages() {
+    pip install --upgrade ${pip_pkgs[@]}
+}
+
+r_install_packages() {
+    local pkgs=\"$(sprintf "\",%s\"" "${r_pkgs[@]}")\"
+    R --quiet -vanilla -e <<EOF
+source("https://bioconductor.org/biocLite.R")
+biocLite(c(${pkgs:3})
+EOF
+}
+
+main () {
+    ubuntu_update
+    ubuntu_install_r_cran
+
+    python_install_packages
+    
+    # Install R libraries in the user home directory so that updating
+    # the libraries later on does not triggering the "unwritable
+    # directory" warning.
+    export r_pkgs
+    export -f r_install packages
+    su cgi_user -c "bash -c r_install_packages"
+    unset r_pkgs r_install_packages
+}
+
+main