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add: homebrew setup in actions #115

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Aug 11, 2023
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add: homebrew setup in actions #115

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7 changes: 5 additions & 2 deletions .github/workflows/deploy-docs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ on:
branches:
- main
paths:
- 'docs/**'
- 'doctave.yml'
- 'docs/**'
- 'doctave.yml'
workflow_dispatch:

jobs:
Expand All @@ -17,6 +17,9 @@ jobs:
- name: 'Checkout GitHub Action'
uses: actions/checkout@main

- name: 'Setup homebrew'
uses: Homebrew/actions/setup-homebrew@master

- name: 'Build and deploy'
shell: bash
run: |
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2 changes: 1 addition & 1 deletion docs/citations.md
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Expand Up @@ -15,7 +15,7 @@ modules are added to aviary.

## Assembly
- **Flye**: Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology 37, 540–546 (2019). https://doi.org/10.1038/s41587-019-0072-8
- **Circulator**: Hunt, M. et al. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology 16, 294 (2015). https://doi.org/10.1186/s13059-015-0849-0
- **Circlator**: Hunt, M. et al. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biology 16, 294 (2015). https://doi.org/10.1186/s13059-015-0849-0
- **Racon**: Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27, 737–746 (2017). https://doi.org/10.1101/gr.214270.116
- **Pilon**: Walker, B. J. et al. Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLOS ONE 9, e112963 (2014). https://doi.org/10.1371/journal.pone.0112963
- **metaSPAdes**: Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017). metaSPAdes: a new versatile metagenomic assembler. Genome research, 27(5), 824-834. https://doi.org/10.1101/gr.213959.116
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