trying again

PNNL-CompBio · Jul 3, 2024 · 04a7c10 · 04a7c10
1 parent c805fec
commit 04a7c10
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Showing 2 changed files with 8 additions and 5 deletions.
diff --git 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
@@ -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'))