Bioconductor conference template web site

This repository contains material for the Bioconductor annual conference. View example at https://bioc2022.bioconductor.org/ and the corresponding GitHub repo

1. Make sure Hugo is installed. Check hugo version

hugo version

2. Clone the repository and switch to it

git clone [email protected]:Bioconductor/BioC2022.git
cd BioC2022/

3. Run hugo

rm -rf public; hugo --verbose; hugo server --disableFastRender --verbose

and view the results at http://localhost:1313/

4. Host your site on Netlify, as described here. Use build command hugo, publish directory public, and set advanced variable HUGO_VERSION to your hugo version number, e.g., 0.76.5

Created using modified hugo-universal-theme. See the demo web site, the original github repository and the exampleSite files. Template by Bootstrapious. Ported to Hugo by DevCows. The theme is added as selected files, not as a submodule, for easier modification.

ToDo/Help wanted

• Make schedule as a partial, populated from config.toml. Example - hugo-conference theme.

New template

gdg-x/zeppelin - original conference template, GDG DevFest - demo web site. bcc2020/bcc2020.github.io - modified conference template for the BCC2020 conference

Adding items to schedule table

1. Make changes in the "schedule table" spreadsheet https://docs.google.com/spreadsheets/d/1tGtGffcbCRxQFjE3ej42IcWlN4FJCsuQeZvETt9g0oA/edit#gid=0
2. Run the following command in the terminal in base directory:

Rscript --vanilla 1_create_yaml.R; bash 2_create_abstracts.sh; bash 3_create_tracks.sh

Adding papers for the the schedule

• The only place where we should be adding data for the abstracts and other elements for the schedule table is data/abstracts/.

• The content/abstracts/ directory contains the individual pages for the abstracts. This directory could be ignored as it will be updated with the create_abstracts.sh and create_tracks.sh bash scripts. These scripts convert the elements in data to content pages.

• There are three types of abstracts

general format: day[1-3]_HHMM_type_paper/track#.yaml

1. papers. Name format: day1_1315_longWorkshop_paper25.yaml.
2. tracks. Name format: day1_0900_shortTalksSysEpi_track.yaml.
3. All other elements that will be added to the schedule.

• The abstracts should all contain these fields:

title: ""
paper: ""
session_type: ""
authors: ""
presenting_author: ""
affiliation: ""
abstract: ""
time: ""
github: ""
time: 
twitter: ""
youtube: ""
day: ""
talks: ""

• If any field isn't used, it should remain blank.

• This is the explanation of the fields:

1. title - A string witht he full titlte.
2. paper - number of paper or track. Valid options: paper# or track#. For example, paper2, track1, etc. track is only used for the short talks tracks. There is not defined track number as in the case of the papers, so I'm just adding in order of appearnce in the document shared by Erica.
3. session_type: String with the type. Valid options: "Short talk", "Short talks track", "Package demo", "Workshop".
4. authors: string with the authors separated by comma.
5. presenting_author: author who will present. I'm using the first author.
6. affiliation: string with the affiliation.
7. abstract: string with the abstract. sometimes there are quotes in the text, which should be escaped.
8. github. Haven't used this field. Not sure if this has been provided.
9. twitter - twitter handle without the @.
10. youtube - link to youtube video when available.
11. day - valid options: day1, day2, day3.
12. talks - this field is only for the short talk tracks. this should list the number of the papers under this track. This should be a yaml array. Example: ["paper10", "paper20"]
13. time - the time in 24h format. Example: 1300 for 1 PM.
14. Run the scripts to create the abstracs and tracks files:

## in base driectory
bash create_abstracts.sh
bash create_tracks.sh

Instructions on how to use Rmarkdown code to auto-generate yaml files

• Download the Rmarkdown filee - 01-create-yaml.Rmd in the base Github folder. It also includes a built PDF and HTML for easy viewing of the code.
• Make sure the input file is up to date. Link to the google sheet is here: https://docs.google.com/spreadsheets/d/1tGtGffcbCRxQFjE3ej42IcWlN4FJCsuQeZvETt9g0oA/edit#gid=0
• Once data is updated, export this file as TSV into your computer. Save this file in a folder called "input"
• NOTE - For the "time" column, set format to custom "hh:mm" (IMPORTANT)
• Run the code
• Output files are generated in the "yaml_output" folder