From 972aa219d8ebc025ba1778e8aa08f021c309e2b8 Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Tue, 14 May 2024 14:41:15 -0700 Subject: [PATCH 1/2] added instructions for synapse download --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 06ee96f2..9eed9489 100755 --- a/README.md +++ b/README.md @@ -28,7 +28,15 @@ please see the [schema description](schema/README.md). We have created a build script that executes each step of the build process to enable the creation of a `local` folder with all the requisite folders. -The build requires Python as well as Docker to be installed. +The build requires Python as well as Docker to be installed. To access +the data on Synapse (MPNST, BeatAML proteomics), you will need to +[register for a synapse account](http://synapse.org/register) and then +request access to the [CoderData Build +Team](https://www.synapse.org/#!Team:3503472). Then you will need to +create a [personal authentication +token](https://www.synapse.org/#!PersonalAccessTokens:) with Download +access and then set the `SYNAPSE_AUTH_TOKEN` environment variable to +that token. To build the docker images and run them, simply run (though this will take a while!): ``` From c590a0e855387091840731d33137a55580a55b2b Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Thu, 16 May 2024 12:07:25 -0700 Subject: [PATCH 2/2] this fix didn't get added in! --- build/mpnst/02_get_drug_data.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build/mpnst/02_get_drug_data.R b/build/mpnst/02_get_drug_data.R index 6bb58aa9..5403e8fc 100644 --- a/build/mpnst/02_get_drug_data.R +++ b/build/mpnst/02_get_drug_data.R @@ -72,7 +72,7 @@ print(paste(alldrugs,collapse=',')) ##copy old drug to new drug -olddrugs<-do.call(rbind,lapply(unique(unlist(strsplit(olddrugfiles,split=','))),function(x) read.table(x,header=T,sep='\t',quote='',comment.char='')) +olddrugs<-do.call(rbind,lapply(unique(unlist(strsplit(olddrugfiles,split=','))),function(x) read.table(x,header=T,sep='\t',quote='',comment.char=''))) olddrugs<-unique(olddrugs) print(paste('Read in ',nrow(olddrugs),'old drugs'))