got single dataset build to work with script

Author: sgosline

build.out

@@ -39,9 +39,9 @@ ENV MPLCONFIGDIR=/app/tmp/matplotlib
 RUN mkdir -p /app/tmp/matplotlib
 
 # Add necessary files to the container
-ADD build/mpnstPDX/requirements.txt .
-ADD build/mpnstPDX/requirements.r .
-ADD build/mpnstPDX/* ./
+ADD build/mpnstpdx/requirements.txt .
+ADD build/mpnstpdx/requirements.r .
+ADD build/mpnstpdx/* ./
 ADD build/utils/* ./
 
 # installing python libraries

build/docker/Dockerfile.mpnstPDX

@@ -44,6 +44,7 @@ services:
         HTTPS_PROXY: ${HTTPS_PROXY}
     platform: linux/amd64
     image: mpnst:latest
+    
   mpnstpdx:
     build:
       context: ../../

build/docker/docker-compose.yml

@@ -1,2 +1,10 @@
-Rscript 02_get_drug_data.R $SYNAPSE_AUTH_TOKEN $1 /tmp/mpnst_drugs.tsv
+#!/bin/bash
+set -euo pipefail
+
+trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR
+
+echo "Running 02_get_drug_data.R with /tmp/mpnst_drugs.tsv and $1."
+Rscript 02_get_drug_data.R /tmp/mpnst_drugs.tsv $1
+
+echo "Running build_drug_desc.py."
 /opt/venv/bin/python3 build_drug_desc.py --drugtable /tmp/mpnst_drugs.tsv --desctable /tmp/mpnst_drug_descriptors.tsv.gz

build/mpnst/build_drugs.sh

@@ -30,7 +30,7 @@ synLogin(authToken = PAT)
 # Read the sample mapping CSV and genes.csv
 samples_df <- fread(patients)|>
     dplyr::select(improve_sample_id,common_name,model_type)|>
-                                        distinct()#"mpnst/synapse_NF-MPNSTPDX_samples.csv")
+                                        distinct()#"mpnst/synapse_NF-MPNSTpdx_samples.csv")
 
 pdx_samps<-subset(samples_df,model_type=='patient derived xenograft')
 tumor_samps<-subset(samples_df,model_type=='tumor')
@@ -41,7 +41,7 @@ manifest<-synapser::synTableQuery("select * from syn53503360")$asDataFrame()|>
                                                              dplyr::rename(common_name='Sample')
 
 
-##for now we only have tumor and PDX data
+##for now we only have tumor and pdx data
 ##they each get their own sample identifier
 pdx_data<-manifest|>dplyr::select(common_name,starts_with("PDX"))|>
     left_join(pdx_samps)|>
@@ -83,7 +83,7 @@ proteomics<-do.call('rbind',lapply(setdiff(pdx_data$Proteomics,c('',NA,"NA")),fu
                                         # }
 }))
 
-fwrite(proteomics,'/tmp/mpnstPDX_proteomics.csv.gz')
+fwrite(proteomics,'/tmp/mpnstpdx_proteomics.csv.gz')
 
 
 #### FIRST WE GET RNASeq Data
@@ -108,7 +108,7 @@ rnaseq<-do.call('rbind',lapply(setdiff(pdx_data$RNASeq,c(NA,"NA")),function(x){
                                         # }
 }))
 
-fwrite(rnaseq,'/tmp/mpnstPDX_transcriptomics.csv.gz')
+fwrite(rnaseq,'/tmp/mpnstpdx_transcriptomics.csv.gz')
 
 
 
@@ -136,7 +136,7 @@ wes<-do.call(rbind,lapply(setdiff(pdx_data$`Mutations`,c(NA,"NA")),function(x){
                                         # }
 }))
 
-fwrite(wes,'/tmp/mpnstPDX_mutations.csv.gz')
+fwrite(wes,'/tmp/mpnstpdx_mutations.csv.gz')
 
 
 print(paste("getting CNV"))
@@ -190,6 +190,6 @@ cnv<-do.call(rbind,lapply(setdiff(pdx_data$CopyNumber,c(NA,"NA")),function(x){
                                         # }
 }))
 
-fwrite(cnv,'/tmp/mpnstPDX_copy_number.csv.gz')
+fwrite(cnv,'/tmp/mpnstpdx_copy_number.csv.gz')
 
 ##TODO: get proteomics!!!

build/mpnstPDX/01_mpnst_get_omics.R

@@ -162,7 +162,7 @@ pdx_data<-rbind(old_data,new_data)
 fwrite(pdx_data,'/tmp/curve_data.tsv',sep='\t')
 
 ##TODO: create new curve fitting script in python
-pycmd = '/opt/venv/bin/python calc_pdx_metrics.py --input /tmp/curve_data.tsv --outprefix /tmp/mpnstPDX'
+pycmd = '/opt/venv/bin/python calc_pdx_metrics.py --input /tmp/curve_data.tsv --outprefix /tmp/mpnstpdx'
 print('running curve fitting')
 #system(pycmd)
 

build/mpnstPDX/03_get_drug_response_data.R

@@ -1 +1 @@
-cp $1 /tmp/mpnstPDX_samples.csv
+cp $1 /tmp/mpnstpdx_samples.csv

build/mpnstPDX/build_samples.sh

@@ -8,4 +8,6 @@ install.packages("data.table")
 install.packages("synapser", repos = c("http://ran.synapse.org", "https://cloud.r-project.org"))
 install.packages("R.utils")
 install.packages("stringr")
-install.packages("tidyr")
+install.packages("tidyr")
+install.packages('readr')
+install.packages("readxl")