fixed relative links to tables; added jl to PATH

dge_workflow/dge_star_template.sh

@@ -112,7 +112,7 @@ star_align.sh $igenome $(ls $baseDir/lanereps_pooled/*.fastq.gz)
 
 mcdir $baseDir/dge_analysis
 
-rend.R -e $NGS_TOOLS/dge_workflow/featcounts_deseq.R ../mapped/star_counts_matrix.txt  2>&1  | tee featcounts_deseq.log
+rend.R -e $NGS_TOOLS/dge_workflow/featcounts_deseq.R ../alignments/star_counts_matrix.txt  2>&1  | tee featcounts_deseq.log
 
 
 ## or use just some contrasts of interest

dge_workflow/dge_utils.sh

@@ -26,7 +26,8 @@ export PATH=/home/brandl/bin/subread-1.4.6-p3-Linux-x86_64/bin:$PATH
 #export PATH=/home/brandl/bin/STAR/STAR-STAR_2.4.1d/source:$PATH
 export PATH=/home/brandl/bin/STAR-2.5.0b/source:$PATH
 
-
+export PATH=$PATH:/projects/bioinfo/scripts/joblist_v0.5-SNAPSHOT
+#export PATH=/projects/bioinfo/scripts/joblist_v0.5-SNAPSHOT:$PATH
 #eval "$(jl shortcuts)"
 
 # which tophat;  which bowtie2; which cuffdiff
@@ -453,7 +454,7 @@ dge_create_star_index(){
     cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 10"
     #eval $cmd
     #STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/Chromosomes/*.fa --runThreadN 10
-    jl submit --wait -n 5 -q medium 0n "${project}_star_index" "$cmd"
+    jl submit --wait -t 5 -q medium -n "${project}_star_index" "$cmd"
 
     ## prevent further modification
     chmod -w $(dirname ${star_index})

dge_workflow/featcounts_deseq.R

@@ -367,7 +367,7 @@ deAnnot <- deResults %>%
   left_join(geneInfo)
 
 write.delim(deAnnot, file=paste0(resultsBase, "de_results.txt"))
-#'  [deAnnot](`r paste0(resultsBase, ".dba_results.txt")`)
+#'  [deAnnot](`r paste0(resultsBase, "dba_results.txt")`)
 
 ## also export results which we'll always need for pathways overlays
 deAnnot %>% transmute(
@@ -407,7 +407,7 @@ degs <- deAnnot %>% filter(is_hit)
 #    left_join(geneInfo) %>%
 #    left_join(bindCats)
 degs %>% write.delim(file=paste0(resultsBase, "diffex_genes.txt"))
-#'  [degs](`r paste0(resultsBase, ".diffbind_genes.txt")`)
+#'  [degs](`r paste0(resultsBase, "diffbind_genes.txt")`)
 
 
 #unloadNamespace("dplyr"); require(dplyr)