From 0bfbf8e511d2e3fb2804c17af6f73146b8cd2830 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 23 Jul 2019 16:24:32 +0200 Subject: [PATCH 1/4] wip --- _config.yml | 17 +++++++++++++++++ _data/people.yml | 23 +++++++++++++++++++++++ _includes/header.html | 10 ++++++++++ _includes/home_news_events.html | 3 +++ assets/css/main.scss | 24 ++++++++++++++++++++++++ index-annotation.md | 4 ++++ 6 files changed, 81 insertions(+) diff --git a/_config.yml b/_config.yml index e3d5291ae..74cfebb97 100644 --- a/_config.yml +++ b/_config.yml @@ -112,6 +112,14 @@ team_sites: url: "https://galaxy.pasteur.fr/" galaxy_server: "https://galaxy.pasteur.fr/" blurb: "" + annotation: + name: Genome Annotation + subdomain: true + url: /annotation/ + private_news: true + url: "https://annotation.usegalaxy.eu/" + galaxy_server: "https://annotation.usegalaxy.eu/" + blurb: "" header_links: main: @@ -163,6 +171,15 @@ header_links: url: /pasteur/people - name: Publications url: /pasteur/publications + annotation: + - name: News + url: /annotation/news + - name: Events + url: /annotation/events + - name: People + url: /annotation/people + - name: Publications + url: /annotation/publications # Exclude from processing. # The following items will not be processed, by default. Create a custom list diff --git a/_data/people.yml b/_data/people.yml index 94da64343..9b041e1b7 100644 --- a/_data/people.yml +++ b/_data/people.yml @@ -192,3 +192,26 @@ erasmusmc: email: s.horsman@erasmusmc.nl phone: +31(0) 70 32460 location: Ee-1579 + +annotation: + erasche: + name: Helena Rasche + title: B.Sc. Biochem., Technician + email: hxr@informatik.uni-freiburg.de + phone: +49(0) 761 - 203 54128 + location: "Build.: 079, Room: -1005a" + location_link: "https://goo.gl/maps/zEL3g3KVE8Q2" + gitter: erasche + orcid: 0000-0001-9760-8992 + galaxyadmin: true + + abretaud: + name: Anthony Bretaudeau + gitter: abretaud + bio: BIPAA/GenOuest + + nathandunn: + name: Nathan Dunn + gitter: nathandunn + location: Oregon, United States + bio: Lawrence Berkeley National Lab diff --git a/_includes/header.html b/_includes/header.html index ba1180d1b..517d469e5 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -42,9 +42,19 @@ Member Sites diff --git a/_includes/home_news_events.html b/_includes/home_news_events.html index f346edab9..fbfb52e84 100644 --- a/_includes/home_news_events.html +++ b/_includes/home_news_events.html @@ -1,5 +1,8 @@ {% assign page_dir = page.dir | split:'/' %} {% assign key = page_dir[1] | default: page.site %} +{% if include.key %} + {% assign key=include.key %} +{% endif %} {% assign key_length = key | size %}
diff --git a/assets/css/main.scss b/assets/css/main.scss index af1932144..8b0a69cbf 100644 --- a/assets/css/main.scss +++ b/assets/css/main.scss @@ -323,6 +323,30 @@ body.location-pasteur { } +body.location-annotation { + .navbar { + background-color: green !important; + border: 0px !important; + } + + .navbar .navbar-brand, .navbar .navbar-nav > li > a { + color: white !important; + } + + .navbar .navbar-brand:hover, .navbar .navbar-brand:focus, + .navbar .navbar-nav > li > a:hover, .navbar .navbar-nav > li > a:focus { + color: #aaa !important; + } + + .nav > li > a:hover, .nav > li > a:focus { + background-color: transparent !important; + } + + .nav .open > a, .nav .open > a:hover, .nav .open > a:focus { + background-color: transparent !important; + color: white; + } +} .tooltable { td:nth-child(1) { width: 15%; diff --git a/index-annotation.md b/index-annotation.md index 6899f9051..822d8c5d3 100644 --- a/index-annotation.md +++ b/index-annotation.md @@ -2,10 +2,14 @@ layout: subsite-galaxy subdomain: annotation gitter: galaxy-genome-annotation/Lobby +site: annotation --- Welcome to **Galaxy for Genome Annotation** -- a platform to annotate, curate, and publish genomic data GGA Logo + +{% include home_news_events.html key=annotation %} + *Coming soon* From ba62f960b861392b0b8eb3bc7a7315e3eadb7b58 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 23 Jul 2019 16:50:51 +0200 Subject: [PATCH 2/4] borders --- assets/css/main.scss | 24 +++++++++++++++--------- 1 file changed, 15 insertions(+), 9 deletions(-) diff --git a/assets/css/main.scss b/assets/css/main.scss index 8b0a69cbf..5d0bd68a8 100644 --- a/assets/css/main.scss +++ b/assets/css/main.scss @@ -168,15 +168,6 @@ img { } -.border-freiburg { - border-left: 5px solid #2c3143 !important; -} -.border-erasmusmc { - border-left: 5px solid #f17925 !important; -} -.border-deNBI, .border-denbi { - border-left: 5px solid rgb(0, 174, 236) !important; -} @import "people"; @import "404"; @import "news"; @@ -222,6 +213,12 @@ img { } +.border-freiburg { + border-left: 5px solid #2c3143 !important; +} +.border-deNBI, .border-denbi { + border-left: 5px solid rgb(0, 174, 236) !important; +} body.location-freiburg { .navbar { background-color: #2c3143 !important; @@ -247,6 +244,9 @@ body.location-freiburg { } } +.border-erasmusmc { + border-left: 5px solid #f17925 !important; +} body.location-erasmusmc { .navbar { background-color: #f17925 !important; @@ -272,6 +272,9 @@ body.location-erasmusmc { } } +.border-belgium{ + border-left: 5px solid #1b2944 !important; +} body.location-belgium { .navbar { background-color: #1b2944 !important; @@ -323,6 +326,9 @@ body.location-pasteur { } +.border-annotation { + border-left: 5px solid green !important; +} body.location-annotation { .navbar { background-color: green !important; From 17d966d318a92caf6a78f83fc1b8c5ee708f336b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 23 Jul 2019 16:51:04 +0200 Subject: [PATCH 3/4] annotation progress --- _bibliography/annotation.bib | 0 _events/2019-05-13-Westerdijk.md | 24 ++++++++++++++++++++++++ _posts/2019-07-22-ismb.md | 13 +++++++++++++ annotation/events.md | 6 ++++++ annotation/galaxy/gxevents.md | 3 +++ annotation/galaxy/gxnews.md | 3 +++ annotation/galaxy/index.md | 6 ++++++ annotation/index.md | 9 +++++++++ annotation/news.md | 5 +++++ annotation/people.md | 4 ++++ annotation/publications.md | 7 +++++++ 11 files changed, 80 insertions(+) create mode 100644 _bibliography/annotation.bib create mode 100644 _events/2019-05-13-Westerdijk.md create mode 100644 _posts/2019-07-22-ismb.md create mode 100644 annotation/events.md create mode 100644 annotation/galaxy/gxevents.md create mode 100644 annotation/galaxy/gxnews.md create mode 100644 annotation/galaxy/index.md create mode 100644 annotation/index.md create mode 100644 annotation/news.md create mode 100644 annotation/people.md create mode 100644 annotation/publications.md diff --git a/_bibliography/annotation.bib b/_bibliography/annotation.bib new file mode 100644 index 000000000..e69de29bb diff --git a/_events/2019-05-13-Westerdijk.md b/_events/2019-05-13-Westerdijk.md new file mode 100644 index 000000000..9d4ad061d --- /dev/null +++ b/_events/2019-05-13-Westerdijk.md @@ -0,0 +1,24 @@ +--- +site: annotation +tags: [training] +title: "Galaxy Workshop @ Fungal Biodiversity Institute Utrecht" +starts: 2019-05-13 +ends: 2019-05-16 +organiser: + name: Westerdijk Fungal Biodiversity Institute + email: +location: + name: Westerdijk Fungal Biodiversity Institute + street: Uppsalalaan 8 + postal: 3584CT + city: Utrecht + country: The Netherlands +supporters: +--- + +We will cover: + +- Galaxy +- QC & Mapping +- Genome Annotation with Maker +- 16S Metagenomics with Mothur diff --git a/_posts/2019-07-22-ismb.md b/_posts/2019-07-22-ismb.md new file mode 100644 index 000000000..52b767fbd --- /dev/null +++ b/_posts/2019-07-22-ismb.md @@ -0,0 +1,13 @@ +--- +site: annotation +title: GGA @ ISMB +tags: [talk] +supporters: + - denbi + - elixir +author: erasche +--- + +We will present the work of the GGA in the past years at ISMB/ECCB 2019 in Basel, Switzerland. + +You can [view a copy of the presentation](https://docs.google.com/presentation/d/1hJyI1sbfxAzzgoJ5E4eHNicSbYzBDaVwTwfOlOLiV3c/edit#slide=id.g5d8be916d1_0_182) online. diff --git a/annotation/events.md b/annotation/events.md new file mode 100644 index 000000000..8bb63c8b6 --- /dev/null +++ b/annotation/events.md @@ -0,0 +1,6 @@ +--- +# You don't need to edit this file, it's empty on purpose. +# Edit theme's home layout instead if you wanna make some changes +# See: https://jekyllrb.com/docs/themes/#overriding-theme-defaults +layout: event_list +--- diff --git a/annotation/galaxy/gxevents.md b/annotation/galaxy/gxevents.md new file mode 100644 index 000000000..315a55fc8 --- /dev/null +++ b/annotation/galaxy/gxevents.md @@ -0,0 +1,3 @@ +--- +layout: event_list-galaxy +--- diff --git a/annotation/galaxy/gxnews.md b/annotation/galaxy/gxnews.md new file mode 100644 index 000000000..bcd7d95b0 --- /dev/null +++ b/annotation/galaxy/gxnews.md @@ -0,0 +1,3 @@ +--- +layout: news_list-galaxy +--- diff --git a/annotation/galaxy/index.md b/annotation/galaxy/index.md new file mode 100644 index 000000000..ab957b389 --- /dev/null +++ b/annotation/galaxy/index.md @@ -0,0 +1,6 @@ +--- +layout: external-galaxy +--- + + +{% include home_news_events-galaxy.html %} diff --git a/annotation/index.md b/annotation/index.md new file mode 100644 index 000000000..64384bd5b --- /dev/null +++ b/annotation/index.md @@ -0,0 +1,9 @@ +--- +layout: home +title: Genome Annotation +--- + + + +{% include home_news_events.html %} +{% include home_done.html %} diff --git a/annotation/news.md b/annotation/news.md new file mode 100644 index 000000000..23f0d69c8 --- /dev/null +++ b/annotation/news.md @@ -0,0 +1,5 @@ +--- +layout: news_list +title: News +--- + diff --git a/annotation/people.md b/annotation/people.md new file mode 100644 index 000000000..f623a4e17 --- /dev/null +++ b/annotation/people.md @@ -0,0 +1,4 @@ +--- +# intentionally blank. Please edit _data/people.yml +layout: people +--- diff --git a/annotation/publications.md b/annotation/publications.md new file mode 100644 index 000000000..d4ab35cae --- /dev/null +++ b/annotation/publications.md @@ -0,0 +1,7 @@ +--- +layout: default +--- + +# Our publications + +{% bibliography --file annotation %} From 09c938c8a8bd95f1e7c8b5c89a81edd689af61f8 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Tue, 23 Jul 2019 16:54:55 +0200 Subject: [PATCH 4/4] hmm --- annotation/galaxy/index.md | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/annotation/galaxy/index.md b/annotation/galaxy/index.md index ab957b389..4e3af30cb 100644 --- a/annotation/galaxy/index.md +++ b/annotation/galaxy/index.md @@ -1,6 +1,15 @@ --- -layout: external-galaxy +layout: subsite-galaxy +subdomain: annotation +gitter: galaxy-genome-annotation/Lobby +site: annotation --- +
-{% include home_news_events-galaxy.html %} +Welcome to **Galaxy for Genome Annotation** -- a platform to annotate, curate, and publish genomic data + +GGA Logo + + +{% include home_news_events.html %}