tidy up binneR env file

MetaboHUB-MetaToul-FluxoMet · Jul 22, 2024 · 0c3bfb8 · 0c3bfb8
1 parent 3fd65c6
commit 0c3bfb8
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 9 deletions.
diff --git a/cylc-src/bioreactor-workflow/envs/wf-binner.yml b/cylc-src/bioreactor-workflow/envs/wf-binner.yml
@@ -3,16 +3,12 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - r-base=4.3.1
-  - r-essentials=4.3
   - r-remotes=2.4
-  - r-furrr=0.3.1
-  - r-ggthemes=5.1.0
+  - r-essentials=4.3
   - r-optparse=1.7.4
-  - r-tidyselect=1.2.1
-  - r-rcpp=1.0.12
+  - r-ggthemes=5.1.0
+  - r-furrr=0.3.1
   - bioconductor-mzr=2.36
-  - bioconductor-rhdf5lib=1.24
 
 # Inside R, install the binneR package from GitHub
-# remotes::install_github('aberHRML/binneR')
+# conda activate wf-binner && Rscript -e "remotes::install_github('aberHRML/binneR', upgrade='never')"
diff --git a/docs/source/getting_started/installation.rst b/docs/source/getting_started/installation.rst
@@ -96,7 +96,7 @@ Bioinformatics tools are installed in separate Conda environments, for isolation
 purposes. For binneR, you'll need to install it from the R console::
 
     $ for file in wf-*.yml; do conda env create -f $file; done
-    $ conda activate wf-binner && Rscript -e "remotes::install_github('aberHRML/binneR', dependencies=FALSE, upgrade_dependencies=FALSE)"
+    $ conda activate wf-binner && Rscript -e "remotes::install_github('aberHRML/binneR', upgrade='never')"
     $ conda deactivate
 
 .. _installation.influxdb: