minor patch to highlight quarto dependency

sigven · Aug 3, 2024 · dd092d9 · dd092d9
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -17,8 +17,7 @@ Description: oncoEnrichR performs annotation and prioritization of genesets
     patterns in human tumor samples), STRING/BioGRID (protein-protein interaction networks), 
     curated protein complexes (CORUM/Compleat/ComplexPortal/hu.MAP2), 
     COMPARTMENTS (subcellular compartments), 
-    Human Protein Atlas (tissue and cell-type specific expression patterns and 
-    prognostic associations), CellChatDB (ligand-receptor interactions),
+    Human Protein Atlas (prognostic gene expression associations), CellChatDB (ligand-receptor interactions),
     DoRothEA (regulatory interactions), synthetic lethality predictions, 
     and Gene Ontology/MSigDB/REACTOME/KEGG/NetPath 
     (functional enrichment/over-representation analysis with respect to gene 

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ Web-based access to **oncoEnrichR** is available at [**https://oncotools.elixir.
 
 ## News
 
--   August 2nd 2024 [**1.5.0 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-0)
+-   August 3rd 2024 [**1.5.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-0)
 -   August 16th 2023: [**1.4.2 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-2)
 -   June 18th 2023: [**1.4.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-1)
 -   February 21st 2023 [**1.4.0 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-0)

diff --git a/data_processing_code/RELEASE_NOTES.txt b/data_processing_code/RELEASE_NOTES.txt
@@ -1,6 +1,6 @@
-##ONCOENRICHR_DB_VERSION = 20240801
+##ONCOENRICHR_DB_VERSION = 20240803
 name	url	description	version	key	resource_type	license
-oncoEnrichR	https://github.com/sigven/oncoEnrichR	R package for functional interrogation of genesets in the context of cancer	v1.5.0	oncoEnrichR	software	MIT
+oncoEnrichR	https://github.com/sigven/oncoEnrichR	R package for functional interrogation of genesets in the context of cancer	v1.5.1	oncoEnrichR	software	MIT
 clusterProfiler	https://guangchuangyu.github.io/software/clusterProfiler/	A universal enrichment tool for interpreting omics data (R package)	v4.12.0	clusterProfiler	software	Artistic-2.0
 OmnipathR	https://omnipathdb.org/	Access to datasets on prior molecular knowledge: gene regulatory interactions, enzyme-PTM relationships, protein complexes, protein annotations etc.	v3.11.10	omnipathr	software	MIT
 hu.MAP	http://humap2.proteincomplexes.org/	Human Protein Complex Map	v2.0	humap2	db	CC0 1.0

diff --git a/data_processing_code/data_raw.R b/data_processing_code/data_raw.R
@@ -21,7 +21,7 @@ db_updates[['omnipath_regulatory']] <- F
 db_updates[['subcelldb']] <- F
 db_updates[['ligand_receptor_db']] <- F
 
-oe_version <- "1.5.0"
+oe_version <- "1.5.1"
 
 data_raw_dir <-
   "/Users/sigven/project_data/packages/package__oncoEnrichR/db/raw"

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -45,15 +45,15 @@ RUN cd cmake-3.20.0 && ./bootstrap && make && make install
 ## PINNED versions of all packages can be found in /renv.lock (JSON format)
 RUN R -e "install.packages(repos = NULL, 'https://cloud.r-project.org/src/contrib/renv_1.0.7.tar.gz', lib = '/usr/lib/R/library/')"
 COPY renv.lock /
-COPY oncoEnrichR_1.5.0.tar.gz /
+COPY oncoEnrichR_1.5.1.tar.gz /
 
 #RUN R -e "library(renv)"
 
 RUN R -e "library(renv); renv::restore(prompt = F, library = '/usr/lib/R/library/')"
 WORKDIR /
 
 ## PINNED version - oncoEnrichR
-RUN R -e "install.packages(repos = NULL, 'oncoEnrichR_1.5.0.tar.gz', lib = '/usr/lib/R/library/')"
+RUN R -e "install.packages(repos = NULL, 'oncoEnrichR_1.5.1.tar.gz', lib = '/usr/lib/R/library/')"
 
 ## PINNED VERSION: pandoc (for HTML report generation)
 RUN wget https://github.com/jgm/pandoc/releases/download/2.13/pandoc-2.13-1-amd64.deb && \
@@ -72,5 +72,5 @@ RUN gdebi --non-interactive quarto-linux-amd64.deb
 RUN rm -f quarto-linux-amd64.deb
 
 RUN rm -rf /root/.cache
-RUN rm -rf /oncoEnrichR_1.5.0.tar.gz
+RUN rm -rf /oncoEnrichR_1.5.1.tar.gz
 RUN rm -rf /cmake-3.20.0*
diff --git a/inst/templates/quarto/_documentation_workflow.qmd b/inst/templates/quarto/_documentation_workflow.qmd
@@ -6,7 +6,7 @@
 ::: {.callout-important}
 ## Citation policies for usage of report contents
 
-We encourage users of _oncoEnrichR_ to properly cite no only the software but also the underlying data sources and other software tools used in the analysis. Below, we provide a guide as to the recommended citations for the various output modules of the report.
+We encourage users of _oncoEnrichR_ to properly cite not only the software, but also the underlying data sources and other software tools used in the analysis. Below, we provide a guide as to the underlying citations for the various output modules of the report.
 :::
 
 :::: {.columns}

diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -4,6 +4,17 @@ toc:
   depth: 3
 template:
   bootstrap: 5
+  bslib:
+    info: "#014587"
+    dropdown-link-hover-bg: "#014587"
+    dropdown-link-hover-color: "white"
+    dropdown-link-active-color: "white"
+    navbar-light-color: "white"
+    navbar-light-brand-color: "white"
+    navbar-link-hover-color: "white !important"
+    nav-link-hover-color: "white !important"
+    navbar-light-brand-hover-color: "white !important"
+    navbar-link-color: "white"
   includes:
     in_header: |
        <script async src="https://www.googletagmanager.com/gtag/js?id=G-N4MB4571K5"></script>
@@ -18,6 +29,12 @@ authors:
   Sigve Nakken:
     href: "https://github.com/sigven"
 navbar:
+  link-color: "white"
+  light-color: "white"
+  light-brand-color: "white"
+  light-hover-color: "white !important"
+  type: light
+  bg: info
   structure:
     left:  [home, installation, running, articles, changelog]
     right: [reference, search, github]

diff --git a/pkgdown/index.md b/pkgdown/index.md
@@ -85,7 +85,7 @@ See also the [output views](articles/output.html) that addresses each of the que
 
 ## News
 
--   August 2nd 2024: [**1.5.0 release**](articles/CHANGELOG.html#version-1-5-0)
+-   August 3rd 2024: [**1.5.1 release**](articles/CHANGELOG.html#version-1-5-1)
 -   August 16th 2023: [**1.4.2 release**](articles/CHANGELOG.html#version-1-4-2)
 -   June 18th 2023: [**1.4.1 release**](articles/CHANGELOG.html#version-1-4-1)
 -   February 21st 2023: [**1.4.0 release**](articles/CHANGELOG.html#version-1-4-0)

diff --git a/vignettes/CHANGELOG.Rmd b/vignettes/CHANGELOG.Rmd
@@ -7,6 +7,13 @@ vignette: >
   %\usepackage[UTF-8]{inputenc}
 ---
 
+## Version 1.5.1
+
+* Date: 2024-08-03
+
+* Updates
+  * Minor patch that highlights `quarto` as package dependency in installation instructions
+
 ## Version 1.5.0
 
 * Date: 2024-08-02

diff --git a/vignettes/installation.Rmd b/vignettes/installation.Rmd
@@ -9,7 +9,11 @@ vignette: >
 
 ## Requirements/dependencies
 
-* _oncoEnrichR_ requires R (>= version 4.1)
+*  R (>= version 4.1)
+*  **quarto CLI**
+   - Downloads available for different platforms here: [https://github.com/quarto-dev/quarto-cli/releases](https://github.com/quarto-dev/quarto-cli/releases)
+   - When installing on Linux, make sure you include `quarto` in your PATH variable, see instructions [here](https://quarto.org/docs/download/tarball.html)
+   - Ensure that quarto is correctly installed through `quarto check`
 
 ## Installation of oncoEnrichR with R commands