The setting of the R library path has been removed from the scripts. Users must ensure that their R library paths are writable, which is needed to run the install-org-db.R script for organism-specific org.db R packages which are not hosted on Bioconductor.
Updated install-org-db.R Path Handling:
The install-org-db.R script was previously only executable if the main script (GL-DPPD-7110-A_build-genome-annots-tab.R) was run from within the workflow_code directory. Now, the script can be executed from multiple locations:
From the parent directory of workflow_code or GL_RefAnnotTable-A_1.1.0
Directly from the workflow_codeor GL_RefAnnotTable-A_1.1.0 directory.
GL_RefAnnotTable-A_1.1.0 is stored in a variable workflow_version which is now defined at the top of GL-DPPD-7110-A_build-genome-annots-tab.R. This was added to the pipeline documentation.
Removed Library Path Settings from Scripts:
Updated install-org-db.R Path Handling:
The install-org-db.R script was previously only executable if the main script (GL-DPPD-7110-A_build-genome-annots-tab.R) was run from within the workflow_code directory. Now, the script can be executed from multiple locations:
From the parent directory of
workflow_codeorGL_RefAnnotTable-A_1.1.0Directly from the
workflow_codeorGL_RefAnnotTable-A_1.1.0directory.GL_RefAnnotTable-A_1.1.0is stored in a variableworkflow_versionwhich is now defined at the top of GL-DPPD-7110-A_build-genome-annots-tab.R. This was added to the pipeline documentation.