NGCHM
Next Generation Clustered Heat Maps
Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.
README
Instructions for installing the Simple CHM Loader (SCL) system
Decide on a host and directory to use for the SCL system:
- Users will ssh to the host:directory to request NG-CHMs be installed, uninstalled, etc.
- SCL will execute as 'chmuser' on a system with write access to the NG-CHM server's chmData directory.
- SCL will ssh to scluser@host:directory to obtain requests, data, etc. from users
- 'chmuser' and 'scluser' may be the same or different
Establish a public/private key pair for use by 'chmuser' to login to the SCL host as 'scluser'.
- The SCL system uses many ssh/scp commands to obtain requests etc.
Execute the scl-make-deploy-dir.sh script as 'chmuser' to create the SCL directory on host:
scl-make-deploy-dir.sh scluser@host:path
- A password will not be required if the public/private key pair has
been created and installed properly.
- Most subdirectories of the SCL directory need open permissions to
enable a multitude of users to create and remove directories etc.
- The path to the SCL directory itself can be restricted to allow only a
subset of users access to the system. (scl-make-deploy-dir.sh does
not restrict the path to the SCL directory.)
- It is not possible to prevent users with access to the system from
interfering with each other.
- Conventions can be used to make it unlikely for users to accidentally
interfere with each other. For instance: all NG-CHM names should begin
with the user's initials.
Execute the scl-driver.sh script as 'chmuser':
scl-driver.sh chmData scluser@host:path
- scl-driver.sh must execute as 'chmuser' on a system with write access to
the NG-CHM server's chmData directory
- scl-driver.sh will repeatedly wait for a command from the target system
and execute it
Copy 01-server-protocol-scl.R to your NG-CHM conf.d directory
- This script defines the SCL chmServerProtocol
For each NG-CHM to be accessed using SCL.
- Create a server configuration directory
- Copy example-config.txt to config.txt in that directory and edit as directed
in the file.
- Create an entry in the 'servers' section of your NG-CHM conf.d directory pointing
to the server configuration directory.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
1.0.4 |
rolling linux/jammy R-4.5 | NGCHM_1.0.4.tar.gz |
964.6 KiB |
1.0.4 |
rolling linux/noble R-4.5 | NGCHM_1.0.4.tar.gz |
963.7 KiB |
1.0.4 |
rolling source/ R- | NGCHM_1.0.4.tar.gz |
142.8 KiB |
1.0.4 |
latest linux/jammy R-4.5 | NGCHM_1.0.4.tar.gz |
964.6 KiB |
1.0.4 |
latest linux/noble R-4.5 | NGCHM_1.0.4.tar.gz |
963.7 KiB |
1.0.4 |
latest source/ R- | NGCHM_1.0.4.tar.gz |
142.8 KiB |
1.0.4 |
2026-04-26 source/ R- | NGCHM_1.0.4.tar.gz |
142.8 KiB |
1.0.4 |
2026-04-23 source/ R- | NGCHM_1.0.4.tar.gz |
142.8 KiB |
1.0.4 |
2026-04-09 windows/windows R-4.5 | NGCHM_1.0.4.zip |
981.6 KiB |
1.0.4 |
2025-04-20 source/ R- | NGCHM_1.0.4.tar.gz |
142.8 KiB |