Updating STAR from 2.5.2b to 2.7.0f for all RNA-seq references genomes

CCBR · Sep 5, 2019 · d4159d6 · d4159d6
1 parent 37c34bc
commit d4159d6
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Showing 10 changed files with 14 additions and 16 deletions.
diff --git a/Mmul_8.0.1.json b/Mmul_8.0.1.json
@@ -5,7 +5,7 @@
  		"rnaseq": {
  			"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/ref.fa",
  			"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/genes.gtf",
- 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.5.2b/genes-",
+ 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.7.0f/genes-",
 			"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/qualimap_info.txt",
                         "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/karyoplot_gene_coordinates.txt",
  			"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/annotate.genes.txt",
@@ -17,7 +17,7 @@
  			"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/rsemref/Mmul_8.0.1",
  			"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/Mmul_8.0.1.rRNA_interval_list",
  			"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
- 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.5.2b/genes-",
+ 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.7.0f/genes-",
  			"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
  			"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/ref.fa",
  			"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
@@ -29,5 +29,3 @@
  		"ChIPseq": {}
 	}
 }
-
-
diff --git a/canFam3.json b/canFam3.json
@@ -7,7 +7,7 @@
  			"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/genes.gtf",
 			"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/qualimap_info.txt",
                         "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/karyoplot_gene_coordinates.txt",
- 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/STAR/2.5.2b/genes-",
+ 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/STAR/2.7.0f/genes-",
  			"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/annotate.genes.txt",
  			"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/annotate.isoforms.txt",
  			"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/refFlat.txt",
@@ -17,7 +17,7 @@
  			"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/rsemref/canFam3",
  			"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/canFam3.rRNA_interval_list",
  			"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
- 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/STAR/2.5.2b/genes-",
+ 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/STAR/2.7.0f/genes-",
  			"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
  			"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/canFam3_basic/canFam3.fa",
  			"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",

diff --git a/hg19.json b/hg19.json
@@ -162,7 +162,7 @@
     "rnaseq": {
     "GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/ref.fa",
     "GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/genes.gtf",
-    "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/STAR/2.5.2b/genes-",
+    "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/STAR/2.7.0f/genes-",
     "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/annotate.genes.txt",
     "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/qualimap_info.txt",
     "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_basic/karyoplot_gene_coordinates.txt",

diff --git a/hg19_KSHV.json b/hg19_KSHV.json
@@ -6,7 +6,7 @@
  			"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/ref.fa",
  			"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/genes.gtf",
                         "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/qualimap_info.txt",
- 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/STAR/2.5.2b/genes-",
+ 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/STAR/2.7.0f/genes-",
  			"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/annotate.genes.txt",
  			"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/annotate.isoforms.txt",
  			"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/refFlat.txt",
@@ -17,7 +17,7 @@
  			"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/rsemref/hg19_KSHV",
  			"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/hg19_KSHV.rRNA_interval_list",
  			"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
- 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/STAR/2.5.2b/genes-",
+ 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/STAR/2.7.0f/genes-",
  			"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
  			"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg19_KSHV/ref.fa",
  			"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",

diff --git a/hg38.json b/hg38.json
@@ -164,7 +164,7 @@
      "GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/geneinfo.bed",
      "KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/hg.v26/",
      "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/rsemref/hg38",
-     "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/STAR/2.5.2b/genes-",
+     "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/STAR/2.7.0f/genes-",
      "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_basic/hg38.rRNA_interval_list",
 
 

diff --git a/hg38_HPV16.json b/hg38_HPV16.json
@@ -6,7 +6,7 @@
  			"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/ref.fa",
  			"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/genes.gtf",
                         "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/qualimap_info.txt",
- 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/STAR/2.5.2b/genes-",
+ 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/STAR/2.7.0f/genes-",
  			"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/annotate.genes.txt",
  			"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/annotate.isoforms.txt",
  			"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/refFlat.txt",
@@ -17,7 +17,7 @@
  			"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/rsemref/hg38_HPV16",
  			"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/hg38_HPV16.rRNA_interval_list",
  			"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
- 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/STAR/2.5.2b/genes-",
+ 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/STAR/2.7.0f/genes-",
  			"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
  			"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hg38_HPV16/ref.fa",
  			"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",

diff --git a/hs37d5.json b/hs37d5.json
@@ -144,7 +144,7 @@
     "rnaseq": {
     "GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs37d5/ref.fa",
     "GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs37d5/genes.gtf",
-    "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs37d5/STAR/2.5.2b/genes-",
+    "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs37d5/STAR/2.7.0f/genes-",
     "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs37d5/annotate.genes.txt",
     "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs37d5/qualimap_info.txt",
     "ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs37d5/annotate.isoforms.txt",

diff --git a/hs38d1.json b/hs38d1.json
@@ -146,7 +146,7 @@
      "KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/hg.v26/",
      "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs38d1/karyoplot_gene_coordinates.txt",
      "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs38d1/rsemref/hs38d1",
-     "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs38d1/STAR/2.5.2b/genes-",
+     "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs38d1/STAR/2.7.0f/genes-",
      "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/hs38d1/hs38d1.rRNA_interval_list",
 
 

diff --git a/mm10.json b/mm10.json
@@ -129,7 +129,7 @@
      "rnaseq":{
 "GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.fa",
 "GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/genes.gtf",
-"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/STAR/2.5.2b/genes-",
+"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/STAR/2.7.0f/genes-",
 "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/qualimap_info.txt",
 "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/karyoplot_gene_coordinates.txt",
 "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/annotate.genes.txt",

diff --git a/mm9.json b/mm9.json
@@ -96,7 +96,7 @@
         "rnaseq":{
             "GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/ref.fa", 
             "GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/genes.gtf",
-            "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/STAR/2.5.2b/genes-",
+            "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/STAR/2.7.0f/genes-",
             "QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/qualimap_info.txt",
             "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/karyoplot_gene_coordinates.txt",
             "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/annotate.genes.txt",