From 5a00d3062cbbc6eead04a60a135d50f8a398b847 Mon Sep 17 00:00:00 2001 From: rhysnewell Date: Fri, 11 Aug 2023 07:43:33 +0000 Subject: [PATCH] add: homebrew setup in actions --- .github/workflows/deploy-docs.yaml | 7 +++++-- docs/citations.md | 2 +- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.github/workflows/deploy-docs.yaml b/.github/workflows/deploy-docs.yaml index a79ec009..a0034af1 100755 --- a/.github/workflows/deploy-docs.yaml +++ b/.github/workflows/deploy-docs.yaml @@ -5,8 +5,8 @@ on: branches: - main paths: - - 'docs/**' - - 'doctave.yml' + - 'docs/**' + - 'doctave.yml' workflow_dispatch: jobs: @@ -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: | diff --git a/docs/citations.md b/docs/citations.md index e12900b9..09d917c3 100755 --- a/docs/citations.md +++ b/docs/citations.md @@ -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