Update shelley installation & README

[eileen-xue]

Description

Fixed

• Update tools to the latest version PR #13.
• Update README based on feedback Issue #14.

Changed

• Rename Shelley and update installation to use uv.

Type of change

• Bug fix
• New feature / tool addition
• Version update (tool or image)
• Configuration change (Ansible, Packer, OpenStack)
• Documentation only
• Other: Update shelley installation method

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Version updates

Tool	Variable	Old	New	Source
Singularity	singularity_version	4.4.1	4.5.0	https://github.com/sylabs/singularity/releases/tag/v4.5.0
Go	go_version	1.26.1	1.26.4	https://go.dev/dl/
Nextflow	nextflow_version	25.10.4	26.04.4	https://github.com/nextflow-io/nextflow/releases/tag/v26.04.4
nf-core	nfcore_version	3.5.2	4.0.2	https://pypi.org/project/nf-core/
RStudio	rstudio_version_full	2023.12.1-402	2026.06.0-242	https://www.rstudio.com/wp-content/downloads.json
RStudio	rstudio_version	2023.12.1	2026.06.0	https://www.rstudio.com/wp-content/downloads.json
Jupyter (timestamp)	jupyter_version	2026.04	2026.07	(timestamp - not an upstream version)

Image version (build/openstack-bioshell.pkr.hcl)

• Bumped image_version to reflect changes in this PR
• No image version bump needed (docs/config only)
• Other: No image version bump (pre-release updates)

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Changelog

• Updated CHANGELOG.md with a summary of changes under the correct version heading
• No changelog entry needed (e.g. internal refactor, typo fix)

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Checklist

• My changes follow the existing conventions in this repo
• I have reviewed the diff and removed any unintended changes
• Any new tools or version pins are documented in the relevant Ansible vars file