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Environmental Cheminformatics
plan-b
Commits
615f8fb5
Unverified
Commit
615f8fb5
authored
Feb 28, 2021
by
Todor Kondic
Browse files
Shortcuts for running shinyscreen new and old
parents
29511525
c6df32df
Changes
14
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README.md
View file @
615f8fb5
...
...
@@ -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
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615f8fb5
...
...
@@ -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
0 → 100644
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615f8fb5
(
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
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...
...
@@ -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
0 → 100755
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615f8fb5
#!/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
0 → 100644
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615f8fb5
#!/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
0 → 100644
View file @
615f8fb5
require
(
shinyscreen
)
options
(
browser
=
"chromium"
)
options
(
shiny.launch.browser
=
T
)
launch
()
files/home/user/.local/bin/run-ss.R
0 → 100755
View file @
615f8fb5
require
(
shinyscreen
)
options
(
browser
=
"chromium"
)
app
(
shiny_args
=
list
(
launch.browser
=
T
))
files/home/user/Desktop/newss.desktop
0 → 100644
View file @
615f8fb5
[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
0 → 100644
View file @
615f8fb5
[Desktop Entry]
Name=Shinyscreen (stable ;-) )
Comment=Mass-spectrum Prescreening Program
Icon=r
Exec=oldss.sh
Type=Application
Terminal=false
main.yml
View file @
615f8fb5
...
...
@@ -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
View file @
615f8fb5
...
...
@@ -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
0 → 100644
View file @
615f8fb5
-
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
View file @
615f8fb5
...
...
@@ -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
}}"
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