diff --git a/subdomains/singlecell/parse_tools_to_produce_yml_files.py b/subdomains/parse_tools_to_produce_yml_files.py similarity index 100% rename from subdomains/singlecell/parse_tools_to_produce_yml_files.py rename to subdomains/parse_tools_to_produce_yml_files.py diff --git a/subdomains/singlecell/Evil_scientist.jpeg b/subdomains/singlecell/Evil_scientist.jpeg deleted file mode 100644 index 2d793572..00000000 Binary files a/subdomains/singlecell/Evil_scientist.jpeg and /dev/null differ diff --git a/subdomains/singlecell/annotation-overview.png b/subdomains/singlecell/annotation-overview.png deleted file mode 100644 index 0bdeaa80..00000000 Binary files a/subdomains/singlecell/annotation-overview.png and /dev/null differ diff --git a/subdomains/singlecell/assembly-overview.png b/subdomains/singlecell/assembly-overview.png deleted file mode 100644 index 61cf705c..00000000 Binary files a/subdomains/singlecell/assembly-overview.png and /dev/null differ diff --git a/subdomains/singlecell/conclusion.html b/subdomains/singlecell/conclusion.html deleted file mode 100644 index f2a0c340..00000000 --- a/subdomains/singlecell/conclusion.html +++ /dev/null @@ -1,165 +0,0 @@ -
-

What's happening in {{ nationality }} Single Cell and Spatial Omics research?

- -
-
-

What do you think of the {{ site_name }}?

- -
- - - - - - - - diff --git a/subdomains/singlecell/custom.css b/subdomains/singlecell/custom.css deleted file mode 100644 index e69de29b..00000000 diff --git a/subdomains/singlecell/footer.html b/subdomains/singlecell/footer.html deleted file mode 100644 index fa4d580e..00000000 --- a/subdomains/singlecell/footer.html +++ /dev/null @@ -1,119 +0,0 @@ - diff --git a/subdomains/singlecell/intro.html b/subdomains/singlecell/intro.html deleted file mode 100644 index 023b0cc3..00000000 --- a/subdomains/singlecell/intro.html +++ /dev/null @@ -1,46 +0,0 @@ -
-

- - Welcome to the Galaxy {{ site_name }} {{ lab_name }}! -

-

- Access Single Cell Omics analysis tutorials, tools, and workflows that let you analyse data without programming experience or private infrastructure. -

-

- Word cloud of common single cell tools including Seurat and Scanpy -

-

-
- - How does this page relate to Galaxy {{ site_name }}? - -

- -
diff --git a/subdomains/singlecell/lab_test.yml b/subdomains/singlecell/lab_test.yml deleted file mode 100644 index 6a4c8267..00000000 --- a/subdomains/singlecell/lab_test.yml +++ /dev/null @@ -1,34 +0,0 @@ -# Test this locally with: -# http://127.0.0.1:8000/lab/export?content_root=http://localhost:8000/static/home/labs/genome/main.yml - -# Request this on site.usegalaxy.org.au with: -# https://site.usegalaxy.org.au/lab/export?content_root=https://site.usegalaxy.org.au/static/home/labs/genome/main.yml - -# Use these variables in HTML templates like: -# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}" -# To make the content more generic and reusable across sites -site_name: Australia -lab_name: Single Cell Lab -analysis_name: Single Cell -nationality: Australian -galaxy_base_url: https://singlecell.usegalaxy.org.au # Use for rendering tool/workflow URLs. Trailing '/' will be removed. -subdomain: singlecell -root_domain: usegalaxy.org.au - -# Custom content relative to this file URL -header_logo: static/logo_single_cell.svg -custom_css: static/custom.css -intro_html: templates/intro.html -conclusion_html: templates/conclusion.html -footer_html: templates/footer.html - - -# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements. -# Either: -# 1. Relative to this file URL -# 2. Full URL to fetch globally centralized content -sections: - - 1_beginner.yml - - 2_intermediate.yml - - 3_advanced.yml - - 4_community.yml diff --git a/subdomains/singlecell/logo.png b/subdomains/singlecell/logo.png deleted file mode 100644 index ea8b9ffa..00000000 Binary files a/subdomains/singlecell/logo.png and /dev/null differ diff --git a/subdomains/singlecell/logo_single_cell.svg b/subdomains/singlecell/logo_single_cell.svg deleted file mode 100644 index 43540c2b..00000000 --- a/subdomains/singlecell/logo_single_cell.svg +++ /dev/null @@ -1,276 +0,0 @@ - - - - - - - - - - - - - - - - image/svg+xml - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/subdomains/singlecell/main.yml b/subdomains/singlecell/main.yml new file mode 100644 index 00000000..baaaf267 --- /dev/null +++ b/subdomains/singlecell/main.yml @@ -0,0 +1,44 @@ +# Request this as a webpage with: +# https://site.usegalaxy.org.au/lab/export?content_root=https://raw.githubusercontent.com/nomadscientist/galaxy_codex/subdomain_unification/subdomains/singlecell/main.yml + + +# ----------------------------------------------------------------------------- +# Use these variables in HTML templates like: +# "Welcome to the Galaxy {{ site_name }} {{ lab_name }}" +# To make the content more generic and reusable across sites + +# These will be rendered like "Welcome to the Galaxy {{ site_name }} {{ lab_name }}!" +site_name: SITE_NAME +lab_name: Single Cell Lab +analysis_name: Single Cell +nationality: NATIONALITY # e.g. Australian, Canadian, etc. + +# Used for rendering tool/workflow links. Trailing '/' will be removed. +galaxy_base_url: https://singlecell.usegalaxy.org.au +subdomain: singlecell +root_domain: usegalaxy.org.au + +# More variables here... +support_url: https://help.usegalaxy.org.au + +# ----------------------------------------------------------------------------- +# Custom content relative to this file URL + +header_logo: static/logo_single_cell.svg +custom_css: static/custom.css +intro_md: templates/intro.html +conclusion_md: templates/conclusion.html +footer_md: templates/footer.html + + +# Data (Tools, Workflows etc.) to be rendered into sections/tabs/accordion elements. +# Either: +# 1. Relative to this file URL +# 2. Full URL to fetch globally centralized content +sections: + - sections/1_beginner.yml + - sections/2_intermediate.yml + - sections/3_advanced.yml + - sections/4_community.yml + +# ----------------------------------------------------------------------------- diff --git a/subdomains/singlecell/scripts/parse_tools_to_produce_yml_files.py b/subdomains/singlecell/scripts/parse_tools_to_produce_yml_files.py deleted file mode 100644 index 57b48a6a..00000000 --- a/subdomains/singlecell/scripts/parse_tools_to_produce_yml_files.py +++ /dev/null @@ -1,35 +0,0 @@ -# coding: utf-8 -import yaml -import io -import os -import re -import argparse - -parser = argparse.ArgumentParser(description='Create installation yaml files from a Yaml file containing the panel_view/Toolkit data') -parser.add_argument('--tk', action="store", dest='toolkit', help='Path of the toolkit.yaml file') # Toolkit.yaml file -parser.add_argument('--yml-folder', action="store", dest='dest', help='Folder containing the yml files with tool installed in the target instance') # Folder containing the .yml and yml.lock containing the tools installed in the target instance -args = parser.parse_args() - -print(args.toolkit) -print(args.dest) - -with open(args.toolkit, 'r') as stream: - data_loaded = yaml.safe_load(stream) - -for i in range(3,len(data_loaded['items'])-2): - section=data_loaded['items'][i]['id'] - name=data_loaded['items'][i]['name'] - f = open(section+".yml", "w") - f.write("tool_panel_section_label: "+name+"\ntools:\n") - for j in data_loaded['items'][i]['items']: #for loop on toolkit sections - path=j['id'] - infos=path.replace('toolshed.g2.bx.psu.edu/repos/',"") - pattern=re.compile(r"([^\/]+)\/([^\/]+)\/") # extract the owner (group1) and the name of the tool (group2) - for match in pattern.finditer(infos): #for each tool in the seection - owner=match.group(1) - tool=match.group(2) - installed = os.popen('grep -r "'+tool+'" '+args.dest).read() #verify the tool is not already installed - if installed=='': ## if tool not installed - f.write("- name: "+tool+"\n") - f.write(" owner: "+owner+"\n") - f.close() diff --git a/subdomains/singlecell/1_beginner.yml b/subdomains/singlecell/sections/1_beginner.yml similarity index 100% rename from subdomains/singlecell/1_beginner.yml rename to subdomains/singlecell/sections/1_beginner.yml diff --git a/subdomains/singlecell/2_intermediate.yml b/subdomains/singlecell/sections/2_intermediate.yml similarity index 100% rename from subdomains/singlecell/2_intermediate.yml rename to subdomains/singlecell/sections/2_intermediate.yml diff --git a/subdomains/singlecell/3_advanced.yml b/subdomains/singlecell/sections/3_advanced.yml similarity index 100% rename from subdomains/singlecell/3_advanced.yml rename to subdomains/singlecell/sections/3_advanced.yml diff --git a/subdomains/singlecell/4_community.yml b/subdomains/singlecell/sections/4_community.yml similarity index 100% rename from subdomains/singlecell/4_community.yml rename to subdomains/singlecell/sections/4_community.yml diff --git a/subdomains/singlecell/static/Evil_scientist.jpeg b/subdomains/singlecell/static/Evil_scientist.jpeg deleted file mode 100644 index 2d793572..00000000 Binary files a/subdomains/singlecell/static/Evil_scientist.jpeg and /dev/null differ diff --git a/subdomains/singlecell/static/annotation-overview.png b/subdomains/singlecell/static/annotation-overview.png deleted file mode 100644 index 0bdeaa80..00000000 Binary files a/subdomains/singlecell/static/annotation-overview.png and /dev/null differ diff --git a/subdomains/singlecell/static/assembly-overview.png b/subdomains/singlecell/static/assembly-overview.png deleted file mode 100644 index 61cf705c..00000000 Binary files a/subdomains/singlecell/static/assembly-overview.png and /dev/null differ diff --git a/subdomains/singlecell/static/logo.png b/subdomains/singlecell/static/logo.png deleted file mode 100644 index ea8b9ffa..00000000 Binary files a/subdomains/singlecell/static/logo.png and /dev/null differ diff --git a/subdomains/singlecell/static/test b/subdomains/singlecell/static/test deleted file mode 100644 index a2eed705..00000000 --- a/subdomains/singlecell/static/test +++ /dev/null @@ -1 +0,0 @@ -test of "/" for folder diff --git a/subdomains/singlecell/test b/subdomains/singlecell/test deleted file mode 100644 index a2eed705..00000000 --- a/subdomains/singlecell/test +++ /dev/null @@ -1 +0,0 @@ -test of "/" for folder