Skip to content

Commit bc7132c

Browse files
author
github-actions
committed
Push generated gbcc2025spatialworkshop
1 parent aff8766 commit bc7132c

File tree

4 files changed

+47
-7
lines changed

4 files changed

+47
-7
lines changed

‎generated/gbcc2025spatialworkshop.container‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
ghcr.io/sydneybiox/gbcc2025_spatial_workshop:latest

‎generated/workshop-toolconf-values.yaml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -112,6 +112,8 @@ configs:
112112
<section name="CDNMWS" id="cdnmws" >
113113
<tool file="interactive/biocworkshop_cdnmws1.xml" />
114114
</section>
115+
<label text="GBCC2025" id="gbcc2025" />
116+
<tool file="interactive/biocworkshop_gbcc2025spatialworkshop.xml" />
115117
</toolbox>
116118
integrated_tool_panel.xml: |
117119
<?xml version='1.0'?>
@@ -239,4 +241,6 @@ configs:
239241
<section name="CDNMWS" id="cdnmws" >
240242
<tool id="interactivetool_biocworkshop_cdnmws1" />
241243
</section>
244+
<label text="GBCC2025" id="gbcc2025" />
245+
<tool id="interactivetool_biocworkshop_gbcc2025spatialworkshop" />
242246
</toolbox>

‎generated/workshop-values-gbcc2025spatialworkshop.yaml‎

Lines changed: 35 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,35 @@
1+
/galaxy/server/tools/interactive/biocworkshop_gbcc2025spatialworkshop.xml:
2+
useSecret: false
3+
applyToJob: true
4+
applyToSetupJob: true
5+
applyToWeb: true
6+
applyToWorkflow: true
7+
applyToNginx: true
8+
tpl: false
9+
content: |
10+
<tool id="interactivetool_biocworkshop_gbcc2025spatialworkshop" tool_type="interactive" name="Making Space Count: Strategies for Analysing Spatial Omics Data" version="0.1">
11+
<description>Introduction to an analytical framework for analysing data from high dimensional spatial omics technologies, using functionality from packages developed by the Sydney Precision Data Science Center</description>
12+
<requirements>
13+
<container type="docker">ghcr.io/sydneybiox/gbcc2025_spatial_workshop:latest</container>
14+
</requirements>
15+
<entry_points>
16+
<entry_point name="gbcc2025spatialworkshop" requires_domain="True">
17+
<port>8787</port>
18+
</entry_point>
19+
</entry_points>
20+
<environment_variables>
21+
<environment_variable name="DISABLE_AUTH">true</environment_variable>
22+
<environment_variable name="HISTORY_ID">$__history_id__</environment_variable>
23+
<environment_variable name="REMOTE_HOST">$__galaxy_url__</environment_variable>
24+
<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
25+
<environment_variable name="API_KEY" inject="api_key" />
26+
</environment_variables>
27+
<command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/GBCC2025_spatial_workshop/vignettes/spatialAnalysis.qmd' ]; then echo '/home/rstudio/GBCC2025_spatial_workshop/vignettes/spatialAnalysis.qmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/spatialAnalysis.qmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init</command>
28+
<inputs>
29+
</inputs>
30+
<outputs>
31+
</outputs>
32+
<tests>
33+
</tests>
34+
<help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/SydneyBioX/GBCC2025_spatial_workshop.</help>
35+
</tool>

‎generated/workshop-values.yaml‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
extraFileMappings:
2-
/galaxy/server/tools/interactive/biocworkshop_biocrstudio321.xml:
2+
/galaxy/server/tools/interactive/biocworkshop_gbcc2025spatialworkshop.xml:
33
useSecret: false
44
applyToJob: true
55
applyToSetupJob: true
@@ -8,13 +8,13 @@ extraFileMappings:
88
applyToNginx: true
99
tpl: false
1010
content: |
11-
<tool id="interactivetool_biocworkshop_biocrstudio321" tool_type="interactive" name="RStudio Bioc 3.21" version="0.1">
12-
<description>Bioconductor 3.21 with R 4.5.1</description>
11+
<tool id="interactivetool_biocworkshop_gbcc2025spatialworkshop" tool_type="interactive" name="Making Space Count: Strategies for Analysing Spatial Omics Data" version="0.1">
12+
<description>Introduction to an analytical framework for analysing data from high dimensional spatial omics technologies, using functionality from packages developed by the Sydney Precision Data Science Center</description>
1313
<requirements>
14-
<container type="docker">ghcr.io/bioconductor/bioconductor:RELEASE_3_21</container>
14+
<container type="docker">ghcr.io/sydneybiox/gbcc2025_spatial_workshop:latest</container>
1515
</requirements>
1616
<entry_points>
17-
<entry_point name="biocrstudio321" requires_domain="True">
17+
<entry_point name="gbcc2025spatialworkshop" requires_domain="True">
1818
<port>8787</port>
1919
</entry_point>
2020
</entry_points>
@@ -25,12 +25,12 @@ extraFileMappings:
2525
<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
2626
<environment_variable name="API_KEY" inject="api_key" />
2727
</environment_variables>
28-
<command detect_errors="aggressive">echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate(getwd()) }, action = 'append')" > /home/rstudio/.Rprofile; export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init</command>
28+
<command detect_errors="aggressive">export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; if [ -f '/home/rstudio/GBCC2025_spatial_workshop/vignettes/spatialAnalysis.qmd' ]; then echo '/home/rstudio/GBCC2025_spatial_workshop/vignettes/spatialAnalysis.qmd' > /tmp/startfile; else echo '/home/rstudio/vignettes/spatialAnalysis.qmd' > /tmp/startfile; fi ; echo "{ 'visual_markdown_editing_is_default': true }" > /etc/rstudio/rstudio-prefs.json ; echo "setwd('/home/rstudio'); setHook('rstudio.sessionInit', function(newSession) { if (newSession) rstudioapi::filesPaneNavigate('\$(dirname \$(cat /tmp/startfile))'); rstudioapi::navigateToFile('\$(cat /tmp/startfile)') }, action = 'append')" > /home/rstudio/.Rprofile; export TEMP=/tmp TMP=/tmp TMPDIR=/tmp TEMPDIR=/tmp; chown -R rstudio /home/rstudio/*; rm /tmp/startfile; chown -R rstudio /home/rstudio/.*; /init</command>
2929
<inputs>
3030
</inputs>
3131
<outputs>
3232
</outputs>
3333
<tests>
3434
</tests>
35-
<help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/Bioconductor/workshop-contributions/issues/107.</help>
35+
<help>This is an autogenerated Bioconductor workshop wrapper. See the source of this workshop or report issues at https://github.com/SydneyBioX/GBCC2025_spatial_workshop.</help>
3636
</tool>

0 commit comments

Comments
 (0)