debug deseq2 R script

tools/deseq2/deseq2.script.R

@@ -2,11 +2,9 @@
 #sink(log)
 #sink(log, type="message")
 library(DESeq2)
-library(edgeR)
 library(apeglm)
 library(BiocParallel)
 library(tximport)
-library(rhdf5)
 library(GenomicFeatures)
 library(ggplot2)
 
@@ -137,41 +135,40 @@ pheatmap(assayNTD[select,], cluster_rows=FALSE, show_rownames=FALSE, cluster_col
 #heatmap(cpmTop,main = "Heatmap",margins = c(10,1))
 dev.off()
 
-speciesData = snakemake@config[["biomaRtDataset"]]
+speciesData = snakemake@params[["biomaRtDataset"]]
+print(speciesData)
+if (speciesData != "None") {
+  # Add annotation with biomaRt
+  library(biomaRt)
+  mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="ensembl.org")
 
-if(speciesData != "None")
-{
-#Add annotation with biomaRt
-library(biomaRt)
-mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="ensembl.org")
-
-species_mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "ensembl.org", dataset = speciesData)
-
-#for the moment the top genes change to significant genes ?
-#what if we have tarnscript ID instead of gene ID ?
-ann <- getBM(filter="ensembl_gene_id",value=rownames(topGenes),attributes=c("ensembl_gene_id","description","transcript_length"),mart=species_mart)
-
-go_ann <- getBM(filter="ensembl_gene_id",value=rownames(topGenes),attributes=c("ensembl_gene_id","description","go_id","name_1006","namespace_1003"),mart=species_mart)
-write.table(go_ann,paste(snakemake@output[["Top_genes"]],"_mqc.tsv",sep="\t")
-
-#test for gene enrichment with gprofiler2
-library(gprofiler2)
-#for the moment the top genes change to significant genes ?
-organisme = gsub("_gene_ensembl", "", speciesData)
-gostres <- gost(query = rownames(topGenes), 
-                organism = organisme, ordered_query = FALSE, 
-                multi_query = FALSE, significant = FALSE, exclude_iea = FALSE, 
-                measure_underrepresentation = FALSE, evcodes = FALSE, 
-                user_threshold = 0.05, correction_method = "g_SCS", 
-                domain_scope = "annotated", custom_bg = NULL, 
-                numeric_ns = "", sources = NULL, as_short_link = FALSE)
-
-
-png(filename = paste0(snakemake@config[["results_dir"]],"/",snakemake@config[["<step_name>__deseq2_output_dir"]],"/gprofiler2_mqc.png"), height=800, width=800)
-gostplot(gostres, capped = TRUE, interactive = TRUE)
-dev.off()
+  species_mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "ensembl.org", dataset = )
+
+  #for the moment the top genes change to significant genes ?
+  #what if we have tarnscript ID instead of gene ID ?
+  ann <- getBM(filter="ensembl_gene_id",value=rownames(topGenes),attributes=c("ensembl_gene_id","description","transcript_length"),mart=species_mart)
+
+  go_ann <- getBM(filter="ensembl_gene_id",value=rownames(topGenes),attributes=c("ensembl_gene_id","description","go_id","name_1006","namespace_1003"),mart=species_mart)
+  write.table(go_ann,paste(snakemake@output[["Top_genes"]],"_mqc.tsv",sep="\t"))
+
+  #test for gene enrichment with gprofiler2
+  library(gprofiler2)
+  #for the moment the top genes change to significant genes ?
+  organisme = gsub("_gene_ensembl", "", speciesData)
+  gostres <- gost(query = rownames(topGenes), 
+                  organism = organisme, ordered_query = FALSE, 
+                  multi_query = FALSE, significant = FALSE, exclude_iea = FALSE, 
+                  measure_underrepresentation = FALSE, evcodes = FALSE, 
+                  user_threshold = 0.05, correction_method = "g_SCS", 
+                  domain_scope = "annotated", custom_bg = NULL, 
+                  numeric_ns = "", sources = NULL, as_short_link = FALSE)
+
+
+  png(filename = paste0(snakemake@config[["results_dir"]],"/",snakemake@config[["<step_name>__deseq2_output_dir"]],"/gprofiler2_mqc.png"), height=800, width=800)
+  gostplot(gostres, capped = TRUE, interactive = TRUE)
+  dev.off()
 
-write.table(gostres$result, paste0(snakemake@config[["results_dir"]],"/",snakemake@config[["<step_name>__deseq2_output_dir"]],"/gprofiler2_mqc.tsv"), sep="\t")
+  write.table(gostres$result, paste0(snakemake@config[["results_dir"]],"/",snakemake@config[["<step_name>__deseq2_output_dir"]],"/gprofiler2_mqc.tsv"), sep="\t")
 
 }
 #cpmTop = cpm_counts[rownames(resSigdf),]

tools/deseq2/deseq2.yaml

@@ -59,7 +59,7 @@
               type: select,
               choices: [
                 None: "None",
-                Mus musculus: "mm_gene_ensembl",
+                Mus musculus: "mmusculus_gene_ensembl",
                 Homo sapiens: "hsapiens_gene_ensembl",
                 Nile tilapia: "oniloticus_gene_ensembl",
                 oniloticus_gene_ensembl: "dmelanogaster_gene_ensembl"
@@ -92,7 +92,8 @@
       tximport: ['Rscript -e ''BiocManager::install("tximport", version = "3.10",Ncpus=8, clean=TRUE);library("tximport")'''],
       rhdf5: ['Rscript -e ''BiocManager::install("rhdf5", version = "3.10",Ncpus=8, clean=TRUE);library("rhdf5")'''],
       GenomicFeatures: ['Rscript -e ''BiocManager::install("GenomicFeatures", version = "3.10",Ncpus=8, clean=TRUE);library("GenomicFeatures")'''],
-      pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap")''']
+      pheatmap: ['Rscript -e ''install.packages("pheatmap",Ncpus=8, clean=TRUE);library("pheatmap")'''],
+      certificates: [apt-get install -y ca-certificates]
     },
   script: deseq2.script.R,
   citations:  {