diff --git a/.github/workflows/database-update.yml b/.github/workflows/database-update.yml index 9d26ea3..e33de41 100644 --- a/.github/workflows/database-update.yml +++ b/.github/workflows/database-update.yml @@ -58,11 +58,11 @@ jobs: run: | docker run -v $PWD:/tmp sgosline/srp-exposome - name: List files cwd - run: ls -la + run: ls -la /tmp/ - name: Copy files to artifact run: | mkdir expo-files - mv /tmp/sigGeneStats.csv expo-files + mv /tmp/*.csv expo-files - name: upload artifact uses: actions/upload-artifact@v2 with: @@ -82,6 +82,8 @@ jobs: - name: Run zfexp python command run: | docker run -v $PWD:/tmp sgosline/srp-zfexp + - name: List files cwd + run: ls -lah /tmp/ - name: Copy files to artifact run: | mkdir exp-files @@ -107,6 +109,6 @@ jobs: with: name: expo-files - name: List files cwd - run: ls -lah + run: ls -lah /tmp/ #zipfiles push to figshare diff --git a/zfExp/parseGexData.R b/zfExp/parseGexData.R index 8895e6c..4f18595 100644 --- a/zfExp/parseGexData.R +++ b/zfExp/parseGexData.R @@ -15,6 +15,7 @@ schema<-data.frame(Project=c(), data.dir<-'https://raw.githubusercontent.com/PNNL-CompBio/srpAnalytics/main/data/zfExp' +out.dir='/tmp/' generateGeneExamples<-function(genelist,chems){ library(ggplot2) @@ -230,6 +231,6 @@ main<-function(args=c()){ } -out.dir='/tmp/' -ret = main(args<-c('../data/zfExp/ZF_gex.xlsx','../data/chemicalIdMapping.csv','../data/zfExp/allianceGenomeInfo.csv')) + +main()#args<-c('../data/zfExp/ZF_gex.xlsx','../data/chemicalIdMapping.csv','../data/zfExp/allianceGenomeInfo.csv'))