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This repository contains details of the build process and usage for materials from the Bioc2019 conference.

Compiled Workshops Link

https://rebrand.ly/biocworkshops2019

Running workshop materials locally

The workshops (except the CWL workshop) are all installed and ready-to-run inside docker; you will need to install docker on your machine to follow along. We have a base docker image seandavi/bioc_2019 that contains the operating system and base R installation. The workshops and additional package (over 600) are included as a separate download that can be mounted into the container as a volume. To use the entire set of workshop materials, do:

  • Make a directory for the installed packages:

    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:

    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):

    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:

    • username: 'rstudio'
    • password: 'as you set it--bioc above'

Instructions For Workshop Authors

Getting started

To contribute a new workshop, open a BiocWorkshops issue starting with the [Workshop] keyword in the title of the issue. Provide a link to the repository in the issue message body. You may also include GitHub usernames of workshop collaborators. For a successful workshop build, adhere to the following:

  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.

DESCRIPTION

Update the DESCRIPTION file adding packages utilized in your workshop to the Imports field.

Use bioc-devel

BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.

Deadlines for Bioc2019

Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York

  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

About

The official repository of the Bioconductor 2019 Conference Workshops 🎊

bioconductor.github.io/BiocWorkshops2019/

Resources

Readme
Activity
Custom properties

Stars

25 stars

Watchers

13 watching

Forks

14 forks
Report repository

Releases

Packages

Contributors

Languages

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GitHub - Bioconductor/BiocWorkshops2019: The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball: · GitHub
Skip to content
BranchesTags
Repository files navigation
This repository contains details of the build process and usage for materials
from the Bioc2019 conference.
Compiled Workshops Link
https://rebrand.ly/biocworkshops2019
Running workshop materials locally
The workshops (except the CWL workshop) are all installed and
ready-to-run inside docker; you will need to install docker on your machine to
follow along. We have a base docker image seandavi/bioc_2019 that contains
the operating system and base R installation. The workshops and additional package (over 600)
are included as a separate download that can be mounted into the container
as a volume. To use the entire set of workshop materials, do:
  • Make a directory for the installed packages:
    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:
    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):
    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:
    • username: 'rstudio'
    • password: 'as you set it--bioc above'
Instructions For Workshop Authors
Getting started
To contribute a new workshop, open a BiocWorkshops issue starting with
the [Workshop] keyword in the title of the issue. Provide a link to the
repository in the issue message body. You may also include GitHub usernames
of workshop collaborators. For a successful workshop build, adhere to the
following:
  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them
in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or
build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.
DESCRIPTION
Update the DESCRIPTION file adding packages utilized in your workshop to
the Imports field.
Use bioc-devel
BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.
Deadlines for Bioc2019
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
bioconductor.github.io/BiocWorkshops2019/
Resources
Readme
Activity
Custom properties
Stars
25 stars
Watchers
13 watching
Forks
14 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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GitHub - Bioconductor/BiocWorkshops2019: The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball: · GitHub
Skip to content
BranchesTags
Repository files navigation
This repository contains details of the build process and usage for materials
from the Bioc2019 conference.
Compiled Workshops Link
https://rebrand.ly/biocworkshops2019
Running workshop materials locally
The workshops (except the CWL workshop) are all installed and
ready-to-run inside docker; you will need to install docker on your machine to
follow along. We have a base docker image seandavi/bioc_2019 that contains
the operating system and base R installation. The workshops and additional package (over 600)
are included as a separate download that can be mounted into the container
as a volume. To use the entire set of workshop materials, do:
  • Make a directory for the installed packages:
    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:
    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):
    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:
    • username: 'rstudio'
    • password: 'as you set it--bioc above'
Instructions For Workshop Authors
Getting started
To contribute a new workshop, open a BiocWorkshops issue starting with
the [Workshop] keyword in the title of the issue. Provide a link to the
repository in the issue message body. You may also include GitHub usernames
of workshop collaborators. For a successful workshop build, adhere to the
following:
  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them
in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or
build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.
DESCRIPTION
Update the DESCRIPTION file adding packages utilized in your workshop to
the Imports field.
Use bioc-devel
BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.
Deadlines for Bioc2019
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
bioconductor.github.io/BiocWorkshops2019/
Resources
Readme
Activity
Custom properties
Stars
25 stars
Watchers
13 watching
Forks
14 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - Bioconductor/BiocWorkshops2019: The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball: · GitHub
Skip to content
BranchesTags
Repository files navigation
This repository contains details of the build process and usage for materials
from the Bioc2019 conference.
Compiled Workshops Link
https://rebrand.ly/biocworkshops2019
Running workshop materials locally
The workshops (except the CWL workshop) are all installed and
ready-to-run inside docker; you will need to install docker on your machine to
follow along. We have a base docker image seandavi/bioc_2019 that contains
the operating system and base R installation. The workshops and additional package (over 600)
are included as a separate download that can be mounted into the container
as a volume. To use the entire set of workshop materials, do:
  • Make a directory for the installed packages:
    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:
    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):
    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:
    • username: 'rstudio'
    • password: 'as you set it--bioc above'
Instructions For Workshop Authors
Getting started
To contribute a new workshop, open a BiocWorkshops issue starting with
the [Workshop] keyword in the title of the issue. Provide a link to the
repository in the issue message body. You may also include GitHub usernames
of workshop collaborators. For a successful workshop build, adhere to the
following:
  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them
in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or
build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.
DESCRIPTION
Update the DESCRIPTION file adding packages utilized in your workshop to
the Imports field.
Use bioc-devel
BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.
Deadlines for Bioc2019
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
bioconductor.github.io/BiocWorkshops2019/
Resources
Readme
Activity
Custom properties
Stars
25 stars
Watchers
13 watching
Forks
14 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
GitHub - Bioconductor/BiocWorkshops2019: The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball: · GitHub
Skip to content
BranchesTags
Repository files navigation
This repository contains details of the build process and usage for materials
from the Bioc2019 conference.
Compiled Workshops Link
https://rebrand.ly/biocworkshops2019
Running workshop materials locally
The workshops (except the CWL workshop) are all installed and
ready-to-run inside docker; you will need to install docker on your machine to
follow along. We have a base docker image seandavi/bioc_2019 that contains
the operating system and base R installation. The workshops and additional package (over 600)
are included as a separate download that can be mounted into the container
as a volume. To use the entire set of workshop materials, do:
  • Make a directory for the installed packages:
    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:
    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):
    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:
    • username: 'rstudio'
    • password: 'as you set it--bioc above'
Instructions For Workshop Authors
Getting started
To contribute a new workshop, open a BiocWorkshops issue starting with
the [Workshop] keyword in the title of the issue. Provide a link to the
repository in the issue message body. You may also include GitHub usernames
of workshop collaborators. For a successful workshop build, adhere to the
following:
  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them
in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or
build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.
DESCRIPTION
Update the DESCRIPTION file adding packages utilized in your workshop to
the Imports field.
Use bioc-devel
BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.
Deadlines for Bioc2019
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
bioconductor.github.io/BiocWorkshops2019/
Resources
Readme
Activity
Custom properties
Stars
25 stars
Watchers
13 watching
Forks
14 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
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function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
GitHub - Bioconductor/BiocWorkshops2019: The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball: · GitHub
Skip to content
BranchesTags
Repository files navigation
This repository contains details of the build process and usage for materials
from the Bioc2019 conference.
Compiled Workshops Link
https://rebrand.ly/biocworkshops2019
Running workshop materials locally
The workshops (except the CWL workshop) are all installed and
ready-to-run inside docker; you will need to install docker on your machine to
follow along. We have a base docker image seandavi/bioc_2019 that contains
the operating system and base R installation. The workshops and additional package (over 600)
are included as a separate download that can be mounted into the container
as a volume. To use the entire set of workshop materials, do:
  • Make a directory for the installed packages:
    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:
    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):
    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:
    • username: 'rstudio'
    • password: 'as you set it--bioc above'
Instructions For Workshop Authors
Getting started
To contribute a new workshop, open a BiocWorkshops issue starting with
the [Workshop] keyword in the title of the issue. Provide a link to the
repository in the issue message body. You may also include GitHub usernames
of workshop collaborators. For a successful workshop build, adhere to the
following:
  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them
in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or
build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.
DESCRIPTION
Update the DESCRIPTION file adding packages utilized in your workshop to
the Imports field.
Use bioc-devel
BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.
Deadlines for Bioc2019
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
bioconductor.github.io/BiocWorkshops2019/
Resources
Readme
Activity
Custom properties
Stars
25 stars
Watchers
13 watching
Forks
14 forks
Report repository
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GitHub - Bioconductor/BiocWorkshops2019: The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball: · GitHub
Skip to content
BranchesTags
Repository files navigation
This repository contains details of the build process and usage for materials
from the Bioc2019 conference.
Compiled Workshops Link
https://rebrand.ly/biocworkshops2019
Running workshop materials locally
The workshops (except the CWL workshop) are all installed and
ready-to-run inside docker; you will need to install docker on your machine to
follow along. We have a base docker image seandavi/bioc_2019 that contains
the operating system and base R installation. The workshops and additional package (over 600)
are included as a separate download that can be mounted into the container
as a volume. To use the entire set of workshop materials, do:
  • Make a directory for the installed packages:
    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:
    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):
    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:
    • username: 'rstudio'
    • password: 'as you set it--bioc above'
Instructions For Workshop Authors
Getting started
To contribute a new workshop, open a BiocWorkshops issue starting with
the [Workshop] keyword in the title of the issue. Provide a link to the
repository in the issue message body. You may also include GitHub usernames
of workshop collaborators. For a successful workshop build, adhere to the
following:
  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them
in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or
build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.
DESCRIPTION
Update the DESCRIPTION file adding packages utilized in your workshop to
the Imports field.
Use bioc-devel
BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.
Deadlines for Bioc2019
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
bioconductor.github.io/BiocWorkshops2019/
Resources
Readme
Activity
Custom properties
Stars
25 stars
Watchers
13 watching
Forks
14 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
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})();
})();
GitHub - Bioconductor/BiocWorkshops2019: The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball: · GitHub
Skip to content
BranchesTags
Repository files navigation
This repository contains details of the build process and usage for materials
from the Bioc2019 conference.
Compiled Workshops Link
https://rebrand.ly/biocworkshops2019
Running workshop materials locally
The workshops (except the CWL workshop) are all installed and
ready-to-run inside docker; you will need to install docker on your machine to
follow along. We have a base docker image seandavi/bioc_2019 that contains
the operating system and base R installation. The workshops and additional package (over 600)
are included as a separate download that can be mounted into the container
as a volume. To use the entire set of workshop materials, do:
  • Make a directory for the installed packages:
    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space

  • Download and untar entire tar.gz file with all installed packages and materials:
    cd /home/ubuntu/bioc-libs # use the directory from above
wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz
tar -xzf bioc2019-usr-local.tar.gz

  • Run docker locally with (you may or may not need sudo depending on your docker setup):
    # again, use the directory from above
sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \
-p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019

  • Credentials:
    • username: 'rstudio'
    • password: 'as you set it--bioc above'
Instructions For Workshop Authors
Getting started
To contribute a new workshop, open a BiocWorkshops issue starting with
the [Workshop] keyword in the title of the issue. Provide a link to the
repository in the issue message body. You may also include GitHub usernames
of workshop collaborators. For a successful workshop build, adhere to the
following:
  1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example .travis.yml for Continuous Integration against bioc-devel.
  2. Include a standard vignette in the vignettes directory
  3. Put any extra files (images, .bib) in inst/vignettes and reference them
in the vignette using system.file
  4. Number 3 requires package chapter installation before vignette build or
build_vignettes=TRUE when building the package.
  5. Use only one top-level section (#), for the title of your workshop. All other sections must be second-level (##) or lower. You may find the usage section of the Bookdown documentation helpful for background.
  6. Do not use BiocStyle functionality. The style will be based on bookdown/gitbook.
DESCRIPTION
Update the DESCRIPTION file adding packages utilized in your workshop to
the Imports field.
Use bioc-devel
BioC2019 workshops will run on bioc-devel (3.10). That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See Using ‘bioc-devel’ during mid-April to mid-October for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the dummy chapter includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.
Deadlines for Bioc2019
Please be aware of the following deadlines for the Bioconductor 2019 Conference in New York
  • Mon May 27: draft workshop materials submitted as an Issue to this Bioconductor GitHub repo
  • Mon June 10: complete workshop submitted. Only bugfixes / refinements should be made after this point.
  • Mon June 17: All workshops complete and building without error. No new commits to contributor repos will be incorporated.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.
About
The official repository of the Bioconductor 2019 Conference Workshops 🎊
bioconductor.github.io/BiocWorkshops2019/
Resources
Readme
Activity
Custom properties
Stars
25 stars
Watchers
13 watching
Forks
14 forks
Report repository
Releases
Packages
Contributors
Languages