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Environmental Cheminformatics
plan-b
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618f3109
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618f3109
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Mar 23, 2021
by
Todor Kondic
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618f3109
# Environmental Cheminformatics Educational Platform: Plan B
This repository contains a collection of ansible scripts which can be
used to provision an Ubuntu/Debian based virtual machine in a public
cloud. The scripts have been written for a specific Digital Ocean
_droplet_
, but can easily be adapted for something else. And, indeed,
they are now adapted to automate configuration of ECI workstations.
## Access
The desktop environment on the compute node
*alien-one*
is accessible
through VNC protocol. Any VNC viewer can be used. If in doubt, try the
cross-platform TigerVNC viewer
[
available from here for
Windows
](
https://bintray.com/tigervnc/stable/download_file?file_path=vncviewer-1.11.0.exe
)
,
or as a package from your GNU/Linux distribution.
For Mac users,
[
here is the Java version of the viewer
](
https://bintray.com/tigervnc/stable/download_file?file_path=VncViewer-1.11.0.jar
)
.
If you are on Big Sur
[
try this direct download
](
http://tigervnc.bphinz.com/nightly/osx/TigerVNC-1.11.80.dmg
)
.
If you are on Catalina
[
try this direct download
](
https://bintray.com/tigervnc/beta/download_file?file_path=TigerVNC-1.10.90.dmg
)
.
If you are on El Capitan
[
try this direct download
](
https://bintray.com/tigervnc/stable/download_file?file_path=TigerVNC-1.8.0.dmg
)
**Before**
connecting, you need:
-
A X509 certificate file (
`*.pem`
).
-
The IP address of the server.
-
Your username and password.
### Connection instructions
1.
Open the VNC viewer.
2.
Click
`Options`
.
3.
Switch to
`Security`
tab.
4.
Make sure that at least
`TLS with X509 certificates`
is checked.
5.
Make sure that at least
`None`
is checked in the
`Authentication`
section.
6.
Set the
`Path to X509 certificate`
to the location of the X509
certificate file.
7.
Now, click
`OK`
to accept changes and close the
`Options`
tab.
8.
Fill in the IP address of the server in field
`VNC server`
and
append
`:5950`
to it. So, the
`VNC server`
entry should look like
`XXX.XXX.XXX.XXX:5950`
, or
`example.somewhere.biz`
.
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 with Shinyscreen
Shinyscreen is ECI's mass spectrum inspection program. It was written
in R and exists as a R package. In order to run it, it is necessary to
start a R session.
While most students get to know R through R Studio, this development
environment (DE) is by no means the only one that can run R (indeed,
you do not even need a DE to run R: try it yourself, start a command
console and type
`R`
in there). The default choice of R DE on
`alien-one`
currently is GNU Emacs with its
*
Emacs Speaks Statistics
(ESS)
*
mode.
Steps:
1.
Fire up emacs
2.
`Alt-x`
(
`Cmd-x`
for Mac) and
`R`
gets you an R session
3.
If asked, set your start working directory, e.g.
`setwd('/mnt/scratch/user/')`
(where
`user`
is an alias for your username)
4.
Enter
`library(shinyscreen)`
5.
Enter
`options(browser="chromium")`
6.
Enter
`launch()`
To create subdirectories for different Shinyscreen calculations,
use
`dir.create()`
and
`setwd()`
to create and set new working
directories, respectively. This is highly recommended otherwise
you will auto-detect and/or overwrite previous results.
Alternatively, there there are two icons on your desktop that will
start Shinyscreen immediately without a R session. One starts the
~~stable~~outdated version of Shinyscreen. The other runs a
development version (~~you can try it out if you feel
adventurous~~recommended).
### Material needed for the practical
The
*mzML*
data files are in
`/mnt/exchange`
directory.
#### Just in case
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
)
### Some emacs tips
To execute a script in Emacs Ess, you have different shortcuts:
1.
`Ctrl alt x`
: runs a Paragraph
2.
`Ctrl enter`
: similar, but closer to Rstudio in how it
treats collections of sratements
3.
`Ctrl j`
: runs a single line
The above commands are used when you have a separate R script that is
being evaluated in the session. In the session itself, it's just enter
### Converting Shinyscreen MS2 files to MetFrag compatible format
Assuming
`AAs`
is the Shinyscreen project folder, to create files
compatible with MetFrag input format follow these steps:
1.
Navigate to
`AAs`
folder using
`Thunar`
file browser.
2.
Right-click somewhere on the white space in the view showing files and click on
`Open Terminal Here`
.
3.
In the terminal, type
`ls`
. Is there a
`MS2`
folder in there? If yes, then proceed.
4.
Type
`ss2mf`
. This command will create a
`MS2_forMF`
folder containing the MetFrag compatible input files.
README.md
View file @
618f3109
# Environmental Cheminformatics
Educational
Platform: Plan B
# Environmental Cheminformatics Platform: Plan B
This repository contains a collection of ansible scripts which can be
used to provision an Ubuntu/Debian based virtual machine in a public
cloud. The scripts have been written for a specific Digital Ocean
_droplet_
, but can easily be adapted for something else.
_droplet_
, but can easily be adapted for something else. Indeed,
they are now adapted to automate configuration of ECI workstations.
## Access
...
...
@@ -38,7 +39,7 @@ If you are on El Capitan [try this direct download](https://bintray.com/tigervnc
7.
Now, click
`OK`
to accept changes and close the
`Options`
tab.
8.
Fill in the IP address of the server in field
`VNC server`
and
append
`:5950`
to it. So, the
`VNC server`
entry should look like
this
`XXX.XXX.XXX.XXX:5950`
.
`XXX.XXX.XXX.XXX:5950`
, or
`example.somewhere.biz`
.
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`
)
...
...
@@ -77,19 +78,9 @@ you will auto-detect and/or overwrite previous results.
Alternatively, there there are two icons on your desktop that will
start Shinyscreen immediately without a R session. One starts the
stable version of Shinyscreen (used in this course). The other runs a
development version (you can try it out if you feel adventurous).
If you choose this path you are at the mercy of the default file path.
### Material needed for the practical
The
*mzML*
data files are in
`/mnt/exchange`
directory.
#### Just in case
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
)
~~stable~~outdated version of Shinyscreen. The other runs a
development version (~~you can try it out if you feel
adventurous~~recommended).
### Some emacs tips
To execute a script in Emacs Ess, you have different shortcuts:
...
...
@@ -100,16 +91,21 @@ treats collections of sratements
3.
`Ctrl j`
: runs a single line
The above commands are used when you have a separate R script that is
being evaluated in the session. In the session itself, it's just enter
### Converting Shinyscreen MS2 files to MetFrag compatible format
Assuming
`AAs`
is the Shinyscreen project folder, to create files
compatible with MetFrag input format follow these steps:
1.
Navigate to
`AAs`
folder using
`Thunar`
file browser.
2.
Right-click somewhere on the white space in the view showing files and click on
`Open Terminal Here`
.
3.
In the terminal, type
`ls`
. Is there a
`MS2`
folder in there? If yes, then proceed.
4.
Type
`ss2mf`
. This command will create a
`MS2_forMF`
folder containing the MetFrag compatible input files.
being evaluated in the session. In the session itself, it's just enter.
Some venerable Emacs personalities suggest window-based organisation
of Emacs workflow:
1.
Start Emacs.
2.
Resize it to a strip at the bottom of the screen (the
*session*
window), then
`Alt-x R`
.
3.
C-x 5 2 to open a new window (connected to the same session).
4.
Open an existing R script, or start writing a new one.
5.
Commands from above will work and be displayed in the session window.
6.
Switch between the windows with
`C-x 5 o`
.
7.
You can also split windows in panes with
`C-x 2`
,
`C-x 3`
, hide all
but one with
`C-x 1`
, hide this one
`C-x 0`
, ...
8.
Reading the
`Emacs Tutorial`
is not a bad place to start if you
want to delve deeper [note that ECI's Emacs is heavily customised,
so it might not behave as you'd expect].
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