From 42a48a4386ba3ec93ab1d46d4281224b5d5c1cf8 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 20 Jun 2024 10:20:56 -0700 Subject: [PATCH] fixed MPNST dependencies --- build/docker/Dockerfile.mpnst | 1 + build/mpnst/02_get_drug_data.R | 2 +- build/mpnst/requirements.r | 1 + 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/build/docker/Dockerfile.mpnst b/build/docker/Dockerfile.mpnst index 2461abe8..c35978cc 100755 --- 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 index 27b238c6..fffd103b 100644 --- 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 index bcb8d20b..160a55bc 100755 --- 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")