cttools-chrysanthemum 0.2.3

CTtools: chrysanthemum transcriptome workflows for prebuilt and custom references

CTtools

CTtools is a private transcriptome workflow toolkit for chrysanthemum projects.

Author: YifanDong

Current Version: 0.2.3 (Released 2026-05-05)

See RELEASE_NOTES_v0.2.3.md for latest updates and CHANGELOG.md for version history.

Design Priority

CTtools encourages users to provide their own reference genome (FASTA), annotation (GFF/GTF) and protein file (PEP) for transparent, reproducible analyses.

Prebuilt species resources are supported as convenience presets, but custom reference workflows are the default recommendation.

Core Capabilities

• Build LSF/bsub scripts for RNA-seq workflows.
• Support two modes:
  • custom: user-provided references (recommended)
  • prebuilt: use registry-managed species resources
• Support stage-level script generation so users can run full workflow or only selected parts.
• Install Conda environments from YAML files.

Stage-Level Execution

You can generate scripts for full pipeline or partial pipeline via --stages.

• prebuilt allowed stages: star, rsem, matrix
• custom allowed stages: agat, rsem_prep, star, rsem, matrix

Auto-Submit Feature (v0.2.2+)

Use --submit flag to automatically submit generated scripts to the HPC cluster via bsub:

# Generate and automatically submit custom workflow
python -m cttools lsf-workflow custom \
	--reference-fasta ./reference.fa \
	--reference-gff ./reference.gff \
	--reads-dir ./raw_reads \
	--out-root ./analysis_output \
	--script-dir ./lsf_scripts \
	--submit

# Generate and automatically submit prebuilt workflow
python -m cttools lsf-workflow prebuilt \
	--species Chrysanthemum_morifolium \
	--reads-dir ./raw_reads \
	--out-root ./analysis_output \
	--script-dir ./lsf_scripts \
	--submit

Standard Examples

# custom full workflow (recommended)
python -m cttools lsf-workflow custom \
	--reference-fasta ./reference.fa \
	--reference-gff ./reference.gff \
	--reads-dir ./raw_reads \
	--out-root ./analysis_output \
	--script-dir ./lsf_scripts

# custom partial workflow (only mapping)
python -m cttools lsf-workflow custom \
	--reads-dir ./raw_reads \
	--out-root ./analysis_output \
	--script-dir ./lsf_scripts \
	--stages star

# prebuilt partial workflow (only matrix generation)
python -m cttools lsf-workflow prebuilt \
	--species cn_diploid_bramble_head \
	--reads-dir ./raw_reads \
	--out-root ./analysis_output \
	--script-dir ./lsf_scripts \
	--stages matrix

# install the software environment
python -m cttools env install \
	--file ./cttools.yml \
	--name cttools \
	--mode create

Environment Installation

CTtools includes a Conda environment installer with complete dependencies.

Starting from v0.2.2, the environment is standardized as cttools.

Starting from v0.2.3, generated LSF scripts no longer source /etc/profile, which avoids the COLORTERM: unbound variable failure on hardened cluster shells.

Recommended command:

python -m cttools env install --file ./cttools.yml --name cttools

Useful options:

• --mode create: create a new environment from the YAML file (default)
• --mode update: update an existing environment
• --prefix /path/to/env: install into a specific prefix instead of a named env
• --dry-run: print the conda command without executing it to preview the operation

The command prints JSON output so it can be used in automation scripts.

Note: If you have an older environment named rsem_env from previous versions, it's recommended to create a new cttools environment to benefit from the latest dependency versions.

Species Naming and Citation Attribution

The built-in prebuilt species registry has been updated to include official naming and citation notes to avoid attribution ambiguity.

• Chrysanthemum morifolium (Cmo), hexaploid cultivar zhongshanzigui
• Chrysanthemum nankingense (Cn_A), diploid haplotype assembly
• Chrysanthemum nankingense (Cn_AB), diploid complete assembly
• Chrysanthemum seticuspe (CsGojo)

Citation notes in registry:

• Song, A., Su, J., Wang, H. et al. Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum. Nat Commun 14, 2021 (2023). DOI: https://doi.org/10.1038/s41467-023-37730-3
• Nakano M, Hirakawa H, Fukai E, et al. Communications Biology, 2021, 4(1):1167

Quick Start

python -m pip install -e .
python -m cttools --help
python -m cttools registry list
python -m cttools env install --file ./cttools.yml --name cttools --dry-run

Repository Layout

• src/cttools/: core package
• resources/: external registry template
• src/cttools/resources/: packaged registry used by default
• docs/: architecture and requirement notes
• tests/: unit and integration tests