Merge remote-tracking branch 'origin/master' into hotfix

docs/releases.rst

@@ -17,3 +17,4 @@ Release Notes
    releases/3_1
    releases/4_0
    releases/4_1
+   releases/4_2

docs/releases/4_2.rst

@@ -0,0 +1,19 @@
+Version 4.2
+===========
+
+Version 4.2.0
+-------------
+
+This is a minor feature release. It adds the following features:
+
+- We added two new modules to pVACview: a :ref:`neofox_module` to visualize
+  NeoFox neoantigen annotations and a :ref:`custom_module` to visualize
+  neoantigen data in a TSV file, for example output files from VaxRank,
+  NeoPredPipe, or antigen.garnish.2.
+- We added a :ref:`vignette <pvacseq_vignette>` to our documentation to provide
+  an extended tutorial on how evaluate neoantigen candidates using pVACview.
+
+This release also fixes the following bug(s):
+
+- When running pVACfuse with Arriba input data, the 3' transcript was not
+  being parsed correctly. This release fixes this issue.

pvactools/tools/pvacview/Dockerfile

@@ -18,7 +18,9 @@ RUN R -e "install.packages(c('shiny',\
   'shinydashboardPlus', \
   'shinycssloaders', \
   'fresh', \
-  'RCurl' ), repos='https://cran.rstudio.com/')"
+  'RCurl', \
+  'shinyWidgets', \
+  'colourpicker'), repos='https://cran.rstudio.com/')"
 
 RUN R -e "devtools::install_github('eclarke/ggbeeswarm', ref='v0.6.1')"