Shortcuts for running shinyscreen new and old

README.md

@@ -17,7 +17,7 @@ or as a package from your GNU/Linux distribution.
 
 
 **Before** connecting, you need: 
-	- A X509 certificate file.
+	- A X509 certificate file (`*.pem`).
 	- The IP address of the server.
 	- Your username and password.
 
@@ -35,9 +35,23 @@ or as a package from your GNU/Linux distribution.
    append `:5950` to it. So, the `VNC server` entry should look like
    this `XXX.XXX.XXX.XXX:5950`.
 9. Click `Connect`.
+10. When at the login screen, ensure you are using the `Xfce Session` (settings wheel, bottom right) before entering your password.
+11. Pro-tip: User experience may be better in fullscreen (`F8` and select `fullscreen`)
 
 ## Using Environmental Cheminformatics Programs
 
+### Getting started
+1. Fire up emacs
+2. `Alt-x` and `R` gets you an R session
+3. Enter `library(shinyscreen)`
+4. Enter `options(browser="chromium")`
+5. Enter `launch()` 
+
+### JustInCase - Downloading instructions
+1. Raw files `*.mzML` can be downloaded from [here](https://zenodo.org/record/3666069) 
+2. Input files for Shinyscreen from [here](https://git-r3lab.uni.lu/eci/isb401/-/tree/master/shinyscreen_files)
+
+### The Rest
 TODO
 
 

ansibleit

@@ -2,4 +2,4 @@
 
 ansible-playbook -i hosts.txt main.yml\
  --vault-password-file meta/zubizareta\
- -u root --skip-tags guix -t $1
+ -u root -t $1

files/etc/guix_new_shinyscreen_manifest.scm

+(use-modules (guix packages)
+	     (guix profiles)
+	     (gnu packages)
+	     (srfi srfi-1))
+
+
+
+(specifications->manifest       
+ '( ;; Utilities
+   "recutils"
+   "curl"
+   "git"
+   "git:send-email"
+   "subversion"
+   "bash"
+   "guile"
+   "nano"
+   "nss-certs"
+   "glibc-locales"
+   "gcc-toolchain"
+   "gfortran-toolchain"
+   "python"
+   "perl"
+   "htop"
+   "ansible"
+   "pigz"
+   "libsass"
+
+   ;; Autotools
+   "autoconf"
+   "automake"
+   "autobuild"
+   "m4"
+
+   ;; Emacs
+   "the-silver-searcher"
+   "emacs"
+   "emacs-bbdb"
+   "emacs-use-package"
+   "emacs-ag"
+   "emacs-magit"
+   "emacs-org"
+   "emacs-org-ref"
+   "emacs-paredit"
+   "emacs-ess"
+   "emacs-company"
+   "emacs-ivy"
+   "emacs-counsel"
+   "emacs-geiser"
+   "emacs-guix"
+   "emacs-zenburn-theme"
+   "emacs-solarized-theme"
+   "emacs-cyberpunk-theme"
+   "emacs-atom-one-dark-theme"
+   "emacs-polymode"
+   "emacs-polymode-org"
+   "emacs-polymode-ansible"
+   "emacs-csv"
+   "emacs-smartparens"
+   ;; "emacs-elpy"
+   "emacs-wgrep"
+   "emacs-emojify"
+   "emacs-rust-mode"
+   "emacs-flycheck-rust"
+
+   ;; X
+   "xterm"
+   "rxvt-unicode"
+   "evince"
+   "xdg-utils"
+   "xdg-user-dirs"
+   "pango"
+   "libxft"
+   "cairo"
+
+   ;; TeX
+   "gs-fonts"
+   "texlive"
+   ;; "gs-fonts"
+   ;; "texlive-charter"
+   ;; "texlive-fonts-stmaryrd"
+   ;; "texlive-txfonts"
+   ;; "texlive-amsfonts"
+   ;; "texlive-fonts-latex"
+   ;; "texlive-latex-psnfss"
+   ;; "texlive-latex-type1cm"
+   ;; "texlive-latex-ms"
+   ;; "texlive-fontinst"
+   ;; "texlive-metafont-base"
+   ;; "texlive-latex-fontspec"
+   ;; "texlive-hyph-utf8"
+   ;; "lyx"
+   ;; "texlive-bin"
+   ;; "texlive-base"
+   ;; "texlive-latex-tools"
+   ;; "texlive-latex-base"
+   ;; "texlive-latexconfig"
+   ;; "texlive-dvips"
+   ;; "texlive-fonts-latex"
+   ;; "texlive-latex-babel"
+   ;; "texlive-latex-graphics"
+   ;; "texlive-amsfonts"
+   ;; "texlive-fonts-ec"
+   ;; "texlive-dvips"
+   ;; "texlive-bibtex"
+   ;; "texlive-latex-fancyhdr"
+   ;; "texlive-latex-enumitem"
+   ;; "texlive-latex-ifplatform"
+   ;; "texlive-latex-koma-script"
+   ;; "texlive-url"
+   ;; "texlive-latex-framed"
+   ;; "texlive-latex-geometry"
+   ;; "texlive-latex-hyperref"
+
+   ;;Fonts
+   "unicode-emoji"
+   "fontconfig"
+   "font-dejavu"
+   "font-gnu-freefont"
+   "font-ubuntu"
+   "font-terminus"
+   "font-liberation"
+   "font-inconsolata"
+   "font-gnu-unifont"
+   "font-public-sans"
+   "font-misc-misc"
+   "font-awesome"
+   "font-hack"
+   "font-iosevka"
+   "font-iosevka-term"
+   "font-iosevka-term-slab"
+   "font-iosevka-sparkle"
+   "font-iosevka-slab"
+   "font-iosevka-etoile"
+   "font-iosevka-aile"
+   "font-google-noto"
+
+   ;;Python
+   "python-requests"
+   "python-ruamel.yaml"
+   "python-matplotlib"
+   "python-numpy"
+   "python-scipy"
+
+   ;; Java
+   "openjdk:out"
+   "openjdk:jdk"
+   ;; Perl
+   "perl-yaml-libyaml"
+
+   ;; Guile
+   "guile-readline"
+
+   ;; R
+   "r"
+   "r-curl"
+   "r-ellipsis"
+   "r-remoter"
+   "r-sass"
+   "r-bslib"
+   "r-cachem"
+   "r-future"
+   "r-rmarkdown"
+   "r-knitr"
+   "r-roxygen2"
+   "r-rcolorbrewer"
+   "r-data-table"
+   "r-gplots"
+   "r-devtools"
+   "r-usethis"
+   "r-shiny"
+   "r-shinyfiles"
+   "r-shinydashboard"
+   "r-flexdashboard"
+   "r-handsontable"
+   "r-shinyfiles"
+   "r-cowplot"
+   "r-withr"
+   "r-massbank"
+   "r-chemmass"
+   "r-resolution"
+   "r-msnbase"
+   "r-pander"
+   "r-rstatix"
+   "r-shinyscreen"))

files/home/user/.config/guix/channels.scm

@@ -12,6 +12,7 @@
        (channel
          (name 'guix)
          (url "https://git.savannah.gnu.org/git/guix.git")
+	 (commit "10b909a0249fd53d589890b357232db4165690f5")
 	 ;; (commit "2b5a81dfd3f7a633f4137d31060d0fa82c5e89f6")
          ;; (commit "66c31d5072c846ab86026c5f696ea55a08723ac")
 	 

files/home/user/.local/bin/newss.sh

+#!/bin/sh
+
+# Clear environment, source the profile containing the new shinyscreen
+# and run it.
+
+env -i HOME="$HOME"\
+    USER="$USER"\
+    DISPLAY=":50"\
+    PATH=/usr/local/sbin/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin\
+    bash -c "source  '$HOME'/.prof-ss/etc/profile
+             '$HOME'/.prof-ss/bin/Rscript '$HOME'/.local/bin/run-ss.R"

files/home/user/.local/bin/oldss.sh

+#!/bin/sh
+
+# Clear environment, source the profile containing the new shinyscreen
+# and run it.
+
+Rscript ~/.local/bin/run-olds.R
+
+             

files/home/user/.local/bin/run-olds.R

+require(shinyscreen)
+options(browser="chromium")
+options(shiny.launch.browser=T)
+launch()

files/home/user/.local/bin/run-ss.R

+require(shinyscreen)
+options(browser="chromium")
+app(shiny_args=list(launch.browser=T))

files/home/user/Desktop/newss.desktop

+[Desktop Entry]
+Name=Shinyscreen (devel)
+Comment=Mass-spectrum Prescreening Program
+Icon=r
+Exec=newss.sh
+Type=Application
+Terminal=false

files/home/user/Desktop/oldss.desktop

+[Desktop Entry]
+Name=Shinyscreen (stable ;-) )
+Comment=Mass-spectrum Prescreening Program
+Icon=r
+Exec=oldss.sh
+Type=Application
+Terminal=false

main.yml

@@ -12,7 +12,6 @@
     - name: Set hostname.
       ansible.builtin.hostname:
         name: "{{ inventory_hostname }}"
-
     - name: Copy profiles.
       tags: profile
       copy:
@@ -24,6 +23,7 @@
 
     - include: tasks/apt.yml
     - include: tasks/users.yml
+      tags: users
     - include: tasks/ufw.yml
     - include: tasks/spaces.yml
       tags: spaces
@@ -33,6 +33,8 @@
       tags: visual
     - include: tasks/emacs.yml
       tags: emacs
+    - include: tasks/r-setup.yml
+      tags: r-setup
 
 
 

tasks/guix.yml

@@ -51,6 +51,13 @@
   copy:
     src: files/etc/guix_manifest.scm
     dest: /etc/guix_manifest.scm
+  tags: guix-inst-pkg
+
+- name: Copy "new shinyscreen" package manifest.
+  copy:
+    src: files/etc/guix_new_shinyscreen_manifest.scm
+    dest: /etc/guix_new_shinyscreen_manifest.scm
+  tags: guix-inst-pkg
 
 - name: Install packages.
   command:
@@ -62,3 +69,19 @@
   register: result
   until: result.rc == 0
   loop: "{{ users }}"
+
+- name: Create new shinyscreen profile.
+  command:
+    cmd: >
+      /usr/bin/bash -l -c
+      'guix package -c4 
+      -m /etc/guix_new_shinyscreen_manifest.scm
+      -p "/home/{{ item.login }}/.prof-ss"
+      --fallback'
+  tags: guix-inst-pkg
+  become_user: "{{ item.login }}"
+  retries: 20
+  delay: 5
+  register: result
+  until: result.rc == 0
+  loop: "{{ users }}"

tasks/r-setup.yml

+- name: Copy newss.sh
+  copy:
+    src: files/home/user/.local/bin/newss.sh
+    dest: /home/{{ item.login }}/.local/bin/newss.sh
+    owner: "{{ item.login }}"
+    mode: 0744
+  loop: "{{ users }}"
+
+- name: Copy run-ss.R
+  copy:
+    src: files/home/user/.local/bin/run-ss.R
+    dest: /home/{{ item.login }}/.local/bin/run-ss.R
+    owner: "{{ item.login }}"
+    mode: 0744
+  loop: "{{ users }}"
+
+- name: Copy newss.desktop
+  copy:
+    src: files/home/user/Desktop/newss.desktop
+    dest: /home/{{ item.login }}/Desktop/newss.desktop
+    owner: "{{ item.login }}"
+    mode: 0744
+  loop: "{{ users }}"
+
+
+- name: Copy oldss.sh
+  copy:
+    src: files/home/user/.local/bin/oldss.sh
+    dest: /home/{{ item.login }}/.local/bin/oldss.sh
+    owner: "{{ item.login }}"
+    mode: 0744
+  loop: "{{ users }}"
+
+- name: Copy run-olds.R
+  copy:
+    src: files/home/user/.local/bin/run-olds.R
+    dest: /home/{{ item.login }}/.local/bin/run-olds.R
+    owner: "{{ item.login }}"
+    mode: 0744
+  loop: "{{ users }}"
+
+- name: Copy oldss.desktop
+  copy:
+    src: files/home/user/Desktop/oldss.desktop
+    dest: /home/{{ item.login }}/Desktop/oldss.desktop
+    owner: "{{ item.login }}"
+    mode: 0744
+  loop: "{{ users }}"
+
+  
+
+
+

tasks/users.yml

@@ -35,3 +35,12 @@
   ignore_errors: yes
   when: item.sshkey
   loop: "{{ users }}"
+
+- name: Create local bin.
+  file:
+    path: "/home/{{ item.login }}/.local/bin"
+    state: directory
+    recurse: yes
+    owner: "{{ item.login }}"
+    mode: 0750
+  loop: "{{ users }}"