fixed MPNST dependencies

PNNL-CompBio · Jun 20, 2024 · 42a48a4 · 42a48a4
1 parent 2559654
commit 42a48a4
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Showing 3 changed files with 3 additions and 1 deletion.
diff --git a/build/docker/Dockerfile.mpnst b/build/docker/Dockerfile.mpnst
@@ -7,6 +7,7 @@ RUN apt-get install -y --allow-unauthenticated build-essential --fix-missing pyt
 RUN python3 -m venv /opt/venv
 RUN /opt/venv/bin/pip3 install --upgrade pip
 
+
 ENV PYTHONPATH "${PYTHONPATH}:/app"
 WORKDIR /app
 

diff --git a/build/mpnst/02_get_drug_data.R b/build/mpnst/02_get_drug_data.R
@@ -1,7 +1,6 @@
 # Load required libraries
 library(data.table)
 # library(biomaRt)# biomart issues still exist
-library(synapser)
 library(dplyr)
 library(stringr)
 library(reticulate)
@@ -22,6 +21,7 @@ PAT <- args[1]
 olddrugfiles <- args[2]
 newdrugfile <- args[3]
 # Log in to Synapse
+library(synapser)
 synLogin(authToken = PAT)
 
 

diff --git a/build/mpnst/requirements.r b/build/mpnst/requirements.r
@@ -3,6 +3,7 @@ install.packages("data.table")
 install.packages("synapser", repos = c("http://ran.synapse.org", "http://cran.fhcrc.org"))
 install.packages('R.utils')
 install.packages("stringr")
+install.packages('reticulate')
 install.packages("tidyr")