Bitbucket pipelines
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Bitbucket Pipelines is an integrated CI/CD solution that allows specifying Docker containers and commands to run for each branch. It integrates with Bitbucket repositories and configures via a bitbucket-pipelines.yml file. Compared to Drone.io, it has longer build times per user, customizable builds per branch, and integrates with the Bitbucket UI. The documentation demonstrates configuring pipeline steps and debugging locally by running commands in a Docker container.
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R markdown and Rmdformats
R markdown allows connecting data, code, and text into reports, presentations, and other documents. It works with R, Python, and Bash code. The rmdformats package creates clean HTML documents from R markdown files using different template designs like "readthedown" and "docute". Templates allow formatting code and content into pages, tables of contents, and other features. Parameters control template features such as figure sizes and code folding. Resources for learning more about R markdown and rmdformats were also provided.
File searching tools
This document discusses various file searching tools. It introduces grep for searching files using regular expressions. Faster alternatives to grep like Ag, Ack, and Ripgrep are presented. The document also covers finding files using find or fd, fuzzy filtering with FZF, code searching with ctags or language servers, and summarizes to consider faster tools when possible and leverage editor plugins for code context.
Better BibTeX (BBT) for Zotero
The document discusses Better BibTeX (BBT), an add-on for the desktop version of Zotero. BBT improves on the standard BibTeX file export from Zotero by handling key formatting, duplicates, special characters, and journal abbreviations to produce cleaner BibTeX files that are suitable for use in LaTeX documents on platforms like Overleaf.
Awk primer and Bioawk
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Terminals and Shells
This document discusses terminals and shells. It defines that a shell is a program that interprets commands from a user and executes those commands, while a terminal is a physical device for displaying output and reading input. It provides a brief history of terminals, from telexes and teletypewriters to modern terminal emulators. It also covers terminal configuration, customization, multiplexing using software like tmux and screen, and pseudoterminals. Finally, it discusses different shells, how to choose a shell, shell modes of operation, and shell configuration files like bashrc and profiles.
BioRender & Glossary/Acronym
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Linters in R
Linters in R provides a 3 sentence summary of the document:
The document discusses the R package lintr, which checks R code for adherence to style guidelines, syntax errors, and possible semantic issues. It describes how to install lintr for use with RStudio, Emacs, and Vim and configure which checks or "linters" are applied. The document also gives examples of what lintr checks for, such as syntax, formatting, code quality, and provides information on customizing lintr using a project-specific configuration file.
BioSyntax: syntax highlighting for computational biology
bioSyntax is syntax highlighting software for computational biology. It highlights nucleotides, amino acids, and quality scores in common file formats used in bioinformatics like FASTA, FASTQ, SAM, BAM, VCF, GTF and custom formats. bioSyntax works in many text editors and terminals to help visualize and interpret genomic data. It supports common color schemes and allows customizing colors for specific nucleotides, amino acids or quality scores to highlight features of interest in sequences and alignments.
Get Good With Git
This document provides an overview and introduction to using the version control system Git. It covers basic Git concepts and operations including configuration, the three main states files can be in, committing changes, viewing history and logs, branching, merging, rebasing, tagging, and collaborating remotely. The document also discusses some internals of Git including how objects are stored and how Git and other version control systems originated.
Tech Talk: UCSC Genome Browser
The document discusses the UCSC Genome Browser, an online tool for viewing and interacting with genomic data. It allows users to view multiple data sources simultaneously for a genomic region across many organisms. The document covers basic usage, uploading temporary custom tracks, creating permanent track hubs to host data, and sharing views using saved sessions. Track hubs and sessions allow sharing genomic views and custom data without time limits.
MultiQC: summarize analysis results for multiple tools and samples in a singl...
MultiQC is a tool that aggregates bioinformatics quality control (QC) results from different tools into a single HTML report. It currently supports 73 tools and can integrate QC metrics from preprocessing, alignment, and post-alignment stages. MultiQC generates interactive plots and tables in an customizable report to allow users to compare QC metrics across multiple samples and tools in an flexible manner.
dreamRs: interactive ggplot2
Esquisse is an R package called dreamRs that provides an interactive graphical user interface for creating ggplot2 graphs. The interface allows users to build plots by selecting aesthetic mappings and geoms directly in the UI without writing any code. dreamRs can be launched from within R or installed directly from GitHub, and it offers various customization options for adjusting plot properties through the visual interface.
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Efficient querying of genomic reference databases with gget
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- 2. Bitbucket Pipelines Introduction Setup / Installation Comparison and Motivation Pipelines Configuration Demonstration Debugging Questions ● Bitbucket Pipelines is an integrated CI solution ○ Continuous Integration / Delivery ■ Every change is checked/deployed as automatically as possible ● Allows you to specify a Docker container and a custom list of commands on a per- branch basis ● Integrates nicely with the project on site Introduction
- 3. Bitbucket Pipelines Introduction Setup / Installation Comparison and Motivation Pipelines Configuration Demonstration Debugging Questions ● Hoffman Lab projects already have the ability ● Settings -> Pipelines -> Enable Pipelines ● Create a bitbucket-pipelines.yml file in root directory ○ “Ain’t Markup Language” Setup / Installation
- 4. Bitbucket Pipelines Introduction Setup / Installation Comparison and Motivation Pipelines Configuration Demonstration Debugging Questions Comparison and Motivation Bitbucket Pipelines Drone.IO (hosted) 300 min / user / month (or 2 hours) 15 min / build Customizable Builds Per Branch Specify which branches trigger same build Debug build process locally Debug build process on site No e-mail notifications (yet) E-mail notifications No build status (yet) Visual build status Integrated in project page Separate Website Requires a config file in repo No additional files necessary
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- 7. Bitbucket Pipelines Introduction Setup / Installation Comparison and Motivation Pipelines Configuration Demonstration Debugging Questions Debugging Example taken and modified from: https://bitbucket.org/ian_buchanan/pipeline-example-readthedocs docker run --tty --entrypoint=/bin/bash --memory=2048m --env-file=local.env --volume=${PWD}:/tmp --workdir=/tmp/ dockerimage:tag -i scripttorun.sh
- 8. Bitbucket Pipelines Introduction Setup / Installation Comparison and Motivation Pipelines Configuration Demonstration Debugging Questions Questions
Editor's Notes
- Artifacts Older hosted solutions Exporting Docker Containers