install additional packages

wbaopaul · Nov 27, 2019 · 68bf898 · 68bf898
1 parent 7bbacfb
commit 68bf898
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Showing 3 changed files with 8 additions and 3 deletions.
diff --git a/configure_user.txt b/configure_user.txt
@@ -130,7 +130,7 @@ SPLIT_BAM2CLUSTER = TRUE
 #######################################
 ## TF footprinting analysis ##
 #######################################
-DO_FOOTPRINT = TRUE
+DO_FOOTPRINT = FALSE
 
 ## comparing two clusters:
 cluster1_fp = 0   ## cluster name

diff --git a/scripts/install/Docker/install_Rpackages_docker.R b/scripts/install/Docker/install_Rpackages_docker.R
@@ -14,7 +14,7 @@ for(pk in pks){
     }
 }
 
-bioc.pks = c('RColorBrewer','pheatmap','motifmatchr', 'chromVAR', 'SummarizedExperiment', 'BiocParallel', 'DESeq2', 'edgeR', 'matrixStats', 'cicero', 'farver')
+bioc.pks = c('RColorBrewer','pheatmap','motifmatchr', 'chromVAR', 'SummarizedExperiment', 'BiocParallel', 'DESeq2', 'edgeR', 'matrixStats', 'cicero', 'farver', 'org.Mm.eg.db', 'org.hs.eg.db', 'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19', 'BSgenome.Mmusculus.UCSC.mm10', 'BSgenome.Mmusculus.UCSC.mm9', 'clusterProfiler')
 
 for(pk in bioc.pks){
     if(!require(pk, character.only = T)) {  
@@ -27,3 +27,8 @@ if(!require(chromVARmotifs)) {
     message(paste('Install chromVARmotifs...'))
     devtools::install_github("GreenleafLab/chromVARmotifs", upgrade = 'never', force = T)
 }
+
+if(!require(cisTopic)) {  
+    message(paste('Install cisTopic...'))
+    devtools::install_github("aertslab/cisTopic", upgrade = 'never', force = T)
+}
diff --git a/scripts/install/install_Rpackages.R b/scripts/install/install_Rpackages.R
@@ -14,7 +14,7 @@ for(pk in pks){
     }
 }
 
-bioc.pks = c('RColorBrewer','pheatmap','motifmatchr', 'chromVAR', 'SummarizedExperiment', 'BiocParallel', 'DESeq2', 'edgeR', 'matrixStats', 'cicero', 'farver')
+bioc.pks = c('RColorBrewer','pheatmap','motifmatchr', 'chromVAR', 'SummarizedExperiment', 'BiocParallel', 'DESeq2', 'edgeR', 'matrixStats', 'cicero', 'farver', 'BSgenome.Hsapiens.UCSC.hg38', 'clusterProfiler')
 
 for(pk in bioc.pks){
     if(!require(pk, character.only = T)) {