Include kubectl, the official CLI tool,
kubecolor, to improve readability
of kubectl, k9s, a feature rich TUI, and
KDash, a read-only dashboard for
Kubernetes
Create a module to load and configure the connection parameters for the
included tools
Test connecting to a cluster, and retrieve information from the cluster,
using the included tools
Transfer files to and from a cluster using kubectl and termscp
Apache CloudStack integration
Include the Apache CloudStack CLI tool,
CloudMonkey
Create a module to load and configure connection parameters for the included
tool
Connect to a cluster, and retrieve information from the cluster
Several modules are no longer working due to a change in the distribution
mechanism of eRN modules. These modules are marked as broken, and an
alternative module is suggested for each broken module.
casa/1.0_41db96e
fermisciencetools/1.0_e80f75a
gephi/1.0_6da5463
grads/1.0_939f353
guppy/1.0_ef92ed2
julia/1.0_ea102bc
julia/2.0_405e225
New modules were installed for: casa, fermisciencetools, and grads. The
software is the same version as was previously available.
Patched database downloads of funannotate, and included support for
GeneMark. Since the database downloads no longer worked for
funannotate/1.0_1e48052 and funannotate/1.1_121ae18, these modules have
been marked as broken.
An updated version of gephi was not installed.
The status of software on the roadmap is as indicated below:
The documentation needs to be updated to reflect recent changes made to the ern tool.
Create an installer for the eRN. While creating the installer:
include a BOM (bill of materials) of files used in the eRN. The BOM records blake3 checksums for each file.
embed minisign as a base64 encoded payload.
Cryptographically sign and embed the eRN as a tar.xz archive
When installing, the installer must:
Verify the embedded archive, and copy it to the correct location
Include a command in the ern tool to run a self check using the generated BOM.
Cryptographically sign the final release of SIF files with minisign.
Update the module loading algorithm to:
Verify the cryptographic signature of the downloaded SIF file.
During development, continue using sha512 checksums.
Move the SSH configuration files used by the eRN to the user`s SSH directory.
Configure yazi to access the file systems of configured Slurm and PBS clusters.
Write a dialog to collect information to facilitate debugging user issues. Information to be collected:
Relevant command history
Environment variables
Any modules loaded.
Improve module documentation by:
Include a table, under a heading named Revisions, with each row corresponding to a previous version of the module. Each row also includes the version of the installed software and the date the module was released.
Add tooling to manage and mount remote filesystems, such as:
sftp, to access storage on, for example, clusters.
s3, to access files in cloud storage.
Complete tooling to backup projects.
Apply CGroup v2 fixes that affects determining available memory. This depends on the availability of the new cluster for testing.
Software such as Positron, Quarto, and Visual Studio Code can be used with multiple programming languages. The languages relevant for the eRN are Python, R, and Julia. While these languages are available in the eRN as modules, the isolation provided by containers presents one significant problem: shared object files are not accessible between containers. A standard mechanism needs to be developed to manage software that needs access to shared object files to enable all the capabilities. Some options are:
Install all the software into a container. Does not scale, as more software is bundled together, more and more version incompatibilities are encountered.
Development of a user modules: Refactor existing recipes to build modules with the required combination of software, some issues:
Floating licenses were available and therefore Geneious could easily be used on the HPC. Unfortunately, the floating license option was removed by Dotmatics. Workarounds, or alternatives, need to be investigated.
file and directory operations, specifically: cd, pwd, mkdir, mv,
ls, rm, and cp.
viewing file contents, specifically: head, tail, cat, bat, less,
and moor.
using text editors, specifically: nano, micro, and vim.
using keyboard shortcuts when using: bash, fzf, and saving command
snippets for later use.
using yazi as a file manager. mc is no longer used internally.
Create an installer for the eRN.
The installer creates a signed bill of materials that records all files and
their blake3 checksums.
The installer is cryptographically signed and includes an embeded minisign
and xh, this allows the installer to download and verify itself.
A sha256 checksum of the installer is also created.
When loading modules, the helper script is able to verify cryptographically
signed SIF files. If the SIF file is not signed then fallback to the sha512
checksum.
Move the SSH configuration files used by the eRN to the user`s SSH directory.
Configure yazi to access the file systems of configured Slurm and PBS
clusters.
A Revisions heading is included in the documentation of modules, with
multiple versions, and details older versions of the module.
A command is included in the ern tool to run a self check using the
generated bill of materials.
Signal 6P has conflicting license terms, one license on Github, but another
more restrictive license where the software is to be downloaded, additionally
the requesting user did not respond to requests to test dbCAN3 and
EffectorP.