rnaseq-cwl-training.git
5 months agoRemove software carpentries logo main
Peter Amstutz [Wed, 27 Apr 2022 15:51:52 +0000 (11:51 -0400)]
Remove software carpentries logo

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

5 months agoShow arvados sections by default, instead of generic ones.
Peter Amstutz [Tue, 26 Apr 2022 18:45:38 +0000 (14:45 -0400)]
Show arvados sections by default, instead of generic ones.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

5 months agoRemove text stating this was produced by Software Carpentries
Peter Amstutz [Tue, 26 Apr 2022 18:27:09 +0000 (14:27 -0400)]
Remove text stating this was produced by Software Carpentries

refs #18696

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

7 months agoMake URL into a link
Peter Amstutz [Tue, 1 Feb 2022 19:30:29 +0000 (14:30 -0500)]
Make URL into a link

7 months agoFix embed of Explorer.png
Peter Amstutz [Tue, 1 Feb 2022 19:28:13 +0000 (14:28 -0500)]
Fix embed of Explorer.png

7 months agoFix tabs, improve setup documentation to be explicit about vscode
Peter Amstutz [Tue, 1 Feb 2022 18:14:24 +0000 (13:14 -0500)]
Fix tabs, improve setup documentation to be explicit about vscode

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

7 months agoFix formatting of solution
Peter Amstutz [Mon, 31 Jan 2022 17:16:31 +0000 (12:16 -0500)]
Fix formatting of solution

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

8 months agoFix link, add explicit solution to exercise
Peter Amstutz [Mon, 31 Jan 2022 14:59:49 +0000 (09:59 -0500)]
Fix link, add explicit solution to exercise

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

8 months agoAdd links to solution
Peter Amstutz [Thu, 27 Jan 2022 16:05:25 +0000 (11:05 -0500)]
Add links to solution

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

8 months agoMore information about Docker
Peter Amstutz [Thu, 27 Jan 2022 15:45:45 +0000 (10:45 -0500)]
More information about Docker

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

8 months agoSupplemental material on creating Docker images
Peter Amstutz [Wed, 26 Jan 2022 22:06:18 +0000 (17:06 -0500)]
Supplemental material on creating Docker images

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

10 months agoMerge pull request #9 from common-workflow-lab/ALuesink-patch-1
Peter Amstutz [Tue, 16 Nov 2021 15:48:38 +0000 (10:48 -0500)]
Merge pull request #9 from common-workflow-lab/ALuesink-patch-1

Fixed typo in line 99

10 months agoMerge pull request #6 from ALuesink/patch-1
Peter Amstutz [Tue, 16 Nov 2021 15:48:20 +0000 (10:48 -0500)]
Merge pull request #6 from ALuesink/patch-1

Added links to YAML and CWL array

10 months agoFixed type in line 99
ALuesink [Tue, 16 Nov 2021 15:44:19 +0000 (16:44 +0100)]
Fixed type in line 99

10 months agoAdded links to YAML and CWL array
ALuesink [Thu, 11 Nov 2021 15:40:29 +0000 (16:40 +0100)]
Added links to YAML and CWL array

12 months agoMerge pull request #5 from common-workflow-lab/jekyll-tabs-fix
Peter Amstutz [Wed, 1 Sep 2021 16:57:51 +0000 (12:57 -0400)]
Merge pull request #5 from common-workflow-lab/jekyll-tabs-fix

Replace jekyll-tabs plugin with custom code

16 months agoRemove redundant js code from Ep 3 file
Luna [Fri, 28 May 2021 18:29:33 +0000 (14:29 -0400)]
Remove redundant js code from Ep 3 file

16 months agoReplace jekyll-tabs plugin with custom code
Luna [Fri, 28 May 2021 15:33:11 +0000 (11:33 -0400)]
Replace jekyll-tabs plugin with custom code

17 months agoDelete FUNDING.yml
Michael R. Crusoe [Wed, 7 Apr 2021 08:37:25 +0000 (10:37 +0200)]
Delete FUNDING.yml

was overriding the CWL organization FUNDING instructions

19 months agoTweak solution
Peter Amstutz [Wed, 17 Feb 2021 00:32:29 +0000 (19:32 -0500)]
Tweak solution

19 months agoFix lesson 02 exercise
Peter Amstutz [Wed, 17 Feb 2021 00:29:19 +0000 (19:29 -0500)]
Fix lesson 02 exercise

19 months agoFix links again
Peter Amstutz [Wed, 17 Feb 2021 00:12:13 +0000 (19:12 -0500)]
Fix links again

19 months agoDon't use link
Peter Amstutz [Wed, 17 Feb 2021 00:00:17 +0000 (19:00 -0500)]
Don't use link

19 months agoTry fixing solution links again
Peter Amstutz [Tue, 16 Feb 2021 23:55:31 +0000 (18:55 -0500)]
Try fixing solution links again

19 months agoFix solution links
Peter Amstutz [Tue, 16 Feb 2021 23:43:22 +0000 (18:43 -0500)]
Fix solution links

19 months agoMark as beta
Peter Amstutz [Tue, 16 Feb 2021 23:41:00 +0000 (18:41 -0500)]
Mark as beta

19 months agoUpdates based on practice run.
Peter Amstutz [Tue, 16 Feb 2021 23:40:26 +0000 (18:40 -0500)]
Updates based on practice run.

19 months agoAdd tabs, arvados specific instructions & links to solutions
Peter Amstutz [Thu, 4 Feb 2021 19:36:56 +0000 (14:36 -0500)]
Add tabs, arvados specific instructions & links to solutions

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

19 months agoPut a little text into readme
Peter Amstutz [Mon, 1 Feb 2021 15:55:13 +0000 (10:55 -0500)]
Put a little text into readme

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoGeospatial *imaging*
Peter Amstutz [Fri, 29 Jan 2021 22:15:07 +0000 (17:15 -0500)]
Geospatial *imaging*

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoFix image link
Peter Amstutz [Fri, 29 Jan 2021 22:12:11 +0000 (17:12 -0500)]
Fix image link

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoUpdate the front page
Peter Amstutz [Fri, 29 Jan 2021 22:08:34 +0000 (17:08 -0500)]
Update the front page

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoRemove symlinks
Peter Amstutz [Fri, 29 Jan 2021 21:52:38 +0000 (16:52 -0500)]
Remove symlinks

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoTurn the "run the workflow again" instructions into exercises.
Peter Amstutz [Fri, 29 Jan 2021 15:45:38 +0000 (10:45 -0500)]
Turn the "run the workflow again" instructions into exercises.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoSecond pass. Lots of work.
Peter Amstutz [Thu, 28 Jan 2021 22:47:28 +0000 (17:47 -0500)]
Second pass.  Lots of work.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoFormatting & content WIP
Peter Amstutz [Tue, 26 Jan 2021 22:41:21 +0000 (17:41 -0500)]
Formatting & content WIP

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoMigrating to carpentries WIP
Peter Amstutz [Tue, 26 Jan 2021 21:36:18 +0000 (16:36 -0500)]
Migrating to carpentries WIP

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agowordsmithing
Peter Amstutz [Tue, 26 Jan 2021 21:10:21 +0000 (16:10 -0500)]
wordsmithing

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoFix typos
Peter Amstutz [Tue, 26 Jan 2021 20:05:09 +0000 (15:05 -0500)]
Fix typos

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoAdd more background to lesson 1.
Peter Amstutz [Tue, 26 Jan 2021 19:45:32 +0000 (14:45 -0500)]
Add more background to lesson 1.

Add answers to each section.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoGet rid of separate script file
Peter Amstutz [Mon, 25 Jan 2021 22:29:20 +0000 (17:29 -0500)]
Get rid of separate script file

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoPaste content of script into lesson1
Peter Amstutz [Mon, 25 Jan 2021 22:29:10 +0000 (17:29 -0500)]
Paste content of script into lesson1

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoRemove vscode specific instructions.
Peter Amstutz [Mon, 25 Jan 2021 22:27:20 +0000 (17:27 -0500)]
Remove vscode specific instructions.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoAdd lesson 6
Peter Amstutz [Mon, 25 Jan 2021 22:22:11 +0000 (17:22 -0500)]
Add lesson 6

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoformatting
Peter Amstutz [Mon, 25 Jan 2021 21:01:42 +0000 (16:01 -0500)]
formatting

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoFormatting
Peter Amstutz [Mon, 25 Jan 2021 20:58:41 +0000 (15:58 -0500)]
Formatting

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoMore text for lesson 5. Working on formatting.
Peter Amstutz [Mon, 25 Jan 2021 20:55:58 +0000 (15:55 -0500)]
More text for lesson 5.  Working on formatting.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoDone with 1st draft of lesson 4, working on lesson 5
Peter Amstutz [Fri, 22 Jan 2021 22:35:42 +0000 (17:35 -0500)]
Done with 1st draft of lesson 4, working on lesson 5

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoStill working on it.
Peter Amstutz [Tue, 19 Jan 2021 23:01:28 +0000 (18:01 -0500)]
Still working on it.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoRunning is lesson 2.
Peter Amstutz [Mon, 18 Jan 2021 22:51:10 +0000 (17:51 -0500)]
Running is lesson 2.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

20 months agoStarting the lesson.
Peter Amstutz [Fri, 15 Jan 2021 20:31:23 +0000 (15:31 -0500)]
Starting the lesson.

20 months agoInitial commit
Peter Amstutz [Fri, 15 Jan 2021 20:08:49 +0000 (15:08 -0500)]
Initial commit

20 months agoAdd incubator option for carpentry field. (#542)
Trevor Keller [Mon, 11 Jan 2021 16:32:06 +0000 (11:32 -0500)]
Add incubator option for carpentry field. (#542)

Closes #541

20 months agoadd missing parenthesis
François Michonneau [Fri, 8 Jan 2021 21:34:07 +0000 (16:34 -0500)]
add missing parenthesis

20 months agoGitHub Actions: cache required R packages (#534)
François Michonneau [Fri, 8 Jan 2021 16:18:15 +0000 (17:18 +0100)]
GitHub Actions: cache required R packages (#534)

20 months agopin ubuntu version to 20.04 (#540)
François Michonneau [Fri, 8 Jan 2021 16:15:59 +0000 (17:15 +0100)]
pin ubuntu version to 20.04 (#540)

Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com>
20 months agoinclude @zkamvar suggestions
François Michonneau [Wed, 6 Jan 2021 14:21:13 +0000 (15:21 +0100)]
include @zkamvar suggestions

Co-authored-by: Zhian N. Kamvar <zkamvar@gmail.com>
20 months agoalso delete _site
François Michonneau [Fri, 18 Dec 2020 16:42:55 +0000 (17:42 +0100)]
also delete _site

20 months agodeploy R-based lessons without using another action
François Michonneau [Fri, 18 Dec 2020 16:02:33 +0000 (17:02 +0100)]
deploy R-based lessons without using another action

20 months agodeploy from "website" action
François Michonneau [Fri, 18 Dec 2020 14:26:14 +0000 (15:26 +0100)]
deploy from "website" action

20 months agoavoid ansi color characters from being printed
Zhian N. Kamvar [Wed, 6 Jan 2021 02:08:35 +0000 (18:08 -0800)]
avoid ansi color characters from being printed

21 months agoMerge pull request #537 from maxim-belkin/caution-blockquote
Zhian N. Kamvar [Tue, 22 Dec 2020 19:05:47 +0000 (11:05 -0800)]
Merge pull request #537 from maxim-belkin/caution-blockquote

bin/lesson_check.py: allow 'caution' blockquote

21 months agobin/lesson_check.py: allow 'caution' blockquote
Maxim Belkin [Tue, 22 Dec 2020 17:25:06 +0000 (11:25 -0600)]
bin/lesson_check.py: allow 'caution' blockquote

21 months agobin/lesson_check.py: allow 'language-*' code blocks (#532)
Toby Hodges [Mon, 21 Dec 2020 19:21:47 +0000 (20:21 +0100)]
bin/lesson_check.py: allow 'language-*' code blocks (#532)

21 months agopermissive checks for pre-alpha lessons
Zhian N. Kamvar [Fri, 18 Dec 2020 16:16:56 +0000 (08:16 -0800)]
permissive checks for pre-alpha lessons

This will fix #533

21 months agoNo need for User Agent string
Zhian N. Kamvar [Thu, 17 Dec 2020 23:46:52 +0000 (15:46 -0800)]
No need for User Agent string

21 months agoSpeed up builds of R-based lessons
Zhian N. Kamvar [Thu, 17 Dec 2020 19:46:31 +0000 (11:46 -0800)]
Speed up builds of R-based lessons

R-based lessons might take a while to build because packages need to be compiled from source. RStudio Package Manager has compiled versions of packages for ubuntu distros starting with 16.04: https://packagemanager.rstudio.com/client/#/repos/1/overview

I've added the necessary magic in the actions yaml to make it work.

21 months agoIgnore .jekyll-metatada
Kilian [Thu, 17 Dec 2020 11:03:48 +0000 (12:03 +0100)]
Ignore .jekyll-metatada

21 months agolesson.scss: wildcard selectors for code blocks
Maxim Belkin [Fri, 20 Nov 2020 14:42:26 +0000 (08:42 -0600)]
lesson.scss: wildcard selectors for code blocks

21 months ago404 page for better learner experience
Maxim Belkin [Tue, 24 Nov 2020 21:06:38 +0000 (15:06 -0600)]
404 page for better learner experience

21 months agoadd control structure
Zhian N. Kamvar [Mon, 7 Dec 2020 17:54:36 +0000 (09:54 -0800)]
add control structure

21 months agorun R-based lessons in forks
Zhian N. Kamvar [Mon, 7 Dec 2020 17:47:46 +0000 (09:47 -0800)]
run R-based lessons in forks

This is a modification for #501

21 months agoaccept any base filename for Rmd episodes
Toby Hodges [Tue, 8 Dec 2020 18:09:16 +0000 (19:09 +0100)]
accept any base filename for Rmd episodes

21 months agoFix Ruby style
Maxim Belkin [Tue, 24 Nov 2020 22:41:26 +0000 (16:41 -0600)]
Fix Ruby style

21 months agoset CRAN url if default is "@CRAN@"
Zhian N. Kamvar [Wed, 2 Dec 2020 17:35:13 +0000 (09:35 -0800)]
set CRAN url if default is "@CRAN@"

This will fix #526

22 months agoMatlab -> MATLAB
Toby Hodges [Mon, 9 Nov 2020 10:33:14 +0000 (11:33 +0100)]
Matlab -> MATLAB

22 months ago_config.yml: mention Carpentries Incubator
Maxim Belkin [Thu, 5 Nov 2020 14:57:54 +0000 (08:57 -0600)]
_config.yml: mention Carpentries Incubator

22 months agoremoving contractions from CONTRIBUTING (#512)
Christina K [Mon, 2 Nov 2020 10:14:44 +0000 (04:14 -0600)]
removing contractions from CONTRIBUTING (#512)

23 months agodrop patch version, fix at v1
François Michonneau [Wed, 28 Oct 2020 14:03:09 +0000 (15:03 +0100)]
drop patch version, fix at v1

23 months agobump ruby version (as specified in github-pages v209)
François Michonneau [Wed, 28 Oct 2020 13:44:35 +0000 (14:44 +0100)]
bump ruby version (as specified in github-pages v209)

23 months agolesson.scss: no borders around unrecognized code (#510)
Maxim Belkin [Thu, 22 Oct 2020 04:34:27 +0000 (21:34 -0700)]
lesson.scss: no borders around unrecognized code (#510)

23 months agoupdate expected reference filename (#508)
Toby Hodges [Wed, 21 Oct 2020 16:20:39 +0000 (18:20 +0200)]
update expected reference filename (#508)

23 months agoadd warning code block
François Michonneau [Tue, 20 Oct 2020 06:16:35 +0000 (08:16 +0200)]
add warning code block

23 months agoRevert "Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages"
François Michonneau [Tue, 20 Oct 2020 05:16:30 +0000 (07:16 +0200)]
Revert "Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages"

This reverts commit 2c6b97e57dce86830bdbde8d9f8a871c0b46a035, reversing
changes made to 53e991355f617c108912a21eae00cfe46823aca4.

23 months agoadd warning blockquote
François Michonneau [Wed, 7 Oct 2020 07:55:41 +0000 (09:55 +0200)]
add warning blockquote

23 months agoMerge branch 'gh-pages' of github.com:carpentries/styles into gh-pages
François Michonneau [Tue, 20 Oct 2020 05:06:26 +0000 (07:06 +0200)]
Merge branch 'gh-pages' of github.com:carpentries/styles into gh-pages

23 months agoadd default repository to install_required_packages() (#509)
Zhian N. Kamvar [Mon, 19 Oct 2020 06:45:35 +0000 (23:45 -0700)]
add default repository to install_required_packages() (#509)

23 months agoupdate link to discuss mailing list (#507)
Toby Hodges [Thu, 8 Oct 2020 09:06:10 +0000 (11:06 +0200)]
update link to discuss mailing list (#507)

2 years agolesson.scss: styling for DIVs for embedding Youtube videos (#503)
Maxim Belkin [Mon, 21 Sep 2020 13:45:18 +0000 (06:45 -0700)]
lesson.scss: styling for DIVs for embedding Youtube videos (#503)

2 years agoGH Website action: rename + don't use lesson directory (#504)
Maxim Belkin [Mon, 21 Sep 2020 13:22:51 +0000 (06:22 -0700)]
GH Website action: rename + don't use lesson directory (#504)

When 'Website' action tests a lesson, it checks out repositories into the current working directory: 'lesson' directory doesn't exist.
As a result, steps that use "lesson" as the working directory fail.

2 years agoGitHub Action: website.yml: don't run in forks (#501)
Maxim Belkin [Wed, 2 Sep 2020 16:18:48 +0000 (11:18 -0500)]
GitHub Action: website.yml: don't run in forks (#501)

2 years agoGitHub Actions: better workflow and job names (#500)
Maxim Belkin [Tue, 25 Aug 2020 08:17:56 +0000 (03:17 -0500)]
GitHub Actions: better workflow and job names (#500)

2 years agoGitHub Actions: website (#488)
Maxim Belkin [Tue, 25 Aug 2020 08:16:36 +0000 (03:16 -0500)]
GitHub Actions: website (#488)

2 years agoSync styles first (#494)
François Michonneau [Sat, 22 Aug 2020 05:11:22 +0000 (07:11 +0200)]
Sync styles first (#494)

Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com>
2 years agoremove unused code highlight classes (#498)
François Michonneau [Thu, 20 Aug 2020 12:56:01 +0000 (14:56 +0200)]
remove unused code highlight classes (#498)

2 years agoadd three more common languages (#497)
Henry Schreiner [Wed, 19 Aug 2020 16:27:24 +0000 (12:27 -0400)]
add three more common languages (#497)

2 years agofix: tighten definitions of highlighter (#496)
Henry Schreiner [Wed, 19 Aug 2020 14:48:29 +0000 (10:48 -0400)]
fix: tighten definitions of highlighter (#496)

2 years agoGitHub Actions: check lesson template (#489)
Maxim Belkin [Fri, 14 Aug 2020 16:34:28 +0000 (11:34 -0500)]
GitHub Actions: check lesson template (#489)

Co-authored-by: Maxim Belkin <maxim.belkin@gmail.com>
Co-authored-by: François Michonneau <francois.michonneau@gmail.com>
2 years agofix variable name
François Michonneau [Thu, 13 Aug 2020 05:51:56 +0000 (07:51 +0200)]
fix variable name

2 years agoonly display Episodes drop-down if we have episodes to show (#491)
François Michonneau [Tue, 11 Aug 2020 14:36:48 +0000 (16:36 +0200)]
only display Episodes drop-down if we have episodes to show (#491)