new mouse RNASeq and ChIPSeq indexes included in json files

CCBR · Aug 30, 2018 · 888b362 · 888b362
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commit 888b362
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Showing 2 changed files with 36 additions and 38 deletions.
diff --git a/mm10.json b/mm10.json
@@ -121,20 +121,23 @@
     "VEPGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/genome.fa",
 },
      "rnaseq":{
-"GENOMEFILE": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/ref.fa",
-"GTFFILE": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes.gtf",
-"STARDIR": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes-",
-"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/dev/Mm10_M12_genes.txt",
-"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/dev/Mm10_M12_isoforms.txt",
-"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatMm10_M12.txt",
-"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCm38_mm10_RefSeq.bed",
-"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/dev/mm.vM12.gencode.gtf.pre.bed",
+"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/ref.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-",
+"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/annotate.genes.txt",
+"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/annotate.isoforms.txt",
+"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/refFlat.txt",
+"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/genes.ref.bed",
+"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/geneinfo.bed",
 "KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/mm.vM12/",
-"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/mouse_gencode",
-"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/gencode.vM12.annotation.rRNA.interval_list",
+"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/rsemref/mm10",
+"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.rRNA_interval_list",
+
+
+
 "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
 "FUSIONGTFFILE": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes.gtf",
-"STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M12/genes-",
+"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/STAR/2.5.2b/genes-",
 # "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode",
 # "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/dev/rsemref/mouse_gencode.transcripts.fa",
 #"SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/mouse_gencode.transcripts.fa",
@@ -247,24 +250,18 @@
     "MUTECTSNP": ""
 },
         "ChIPseq":{
-            "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/dev/Mm10_genes.txt",
-            "BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCm38_mm10_RefSeq.bed",
-            "BLACKLISTBWAINDEX":"/data/CCBR_Pipeliner/db/PipeDB/lib/mm10.blacklist_chrM_plus.fa",
-            "BWA": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa",
+            "BLACKLISTBWAINDEX":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10.blacklist.chrM",
+            "BWA": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10",
+            "BOWTIE2INDEX": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10",
             "CHROMS": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10",
                        "chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19",
                        "chrX","chrY","chrM"],
-            "EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/mm10_UCSCexons.bed",
             "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
-	    "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
+	        "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
             "FASTAWITHADAPTERSETD": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.consolidated.fa",
-            "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa",
-            "GENOMEFILE": "/fdb/STAR_2.4.2a/GENCODE/Gencode_mouse/release_M4/ref.fa",	 
-            "GTFFILE": "/fdb/STAR_2.4.2a/UCSC/mm10/genes.gtf",
+            "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/ref.fa",
             "KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
-            "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/SS_mouse_exome_mm10_reformat.bed",
-            "REFLEN":"/data/CCBR_Pipeliner/db/PipeDB/lib/mm10.len",
-            "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/gencode.vM12.annotation.rRNA.interval_list",
+            "REFLEN":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/indexes/mm10.fa.sizes",
             }, 
 
 

diff --git a/mm9.json b/mm9.json
@@ -94,17 +94,17 @@
         },
 
         "rnaseq":{
-            "GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/ref.fa", 
-            "GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/genes.gtf",
-            "STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/genes-",
-            "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/Mm9_M1_genes.txt",
-            "ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/Mm9_M1_isoforms.txt",
-            "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/refFlat_mm9_M1.txt",
-            "BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/mm9_refseq.bed",
-            "GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/mm9_M1_geneinfo.bed",
+            "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-",
+            "ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/annotate.genes.txt",
+            "ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/annotate.isoforms.txt",
+            "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/refFlat.txt",
+            "BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/genes.ref.bed",
+            "GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/geneinfo.bed",
             "KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/mm9.M1/",
-            "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/mm9_M1/mm9_M1",
-            "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/lib/STAR_indices/2.5.2b/GENCODE/Gencode_mouse/release_M1/mm9_M1.rRNA.interval_list",
+            "RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/rsemref/mm9",
+            "RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/mm9_M1.rRNA.interval_list",
 
             },
 
@@ -166,17 +166,18 @@
         },
 
         "ChIPseq":{
-            "BWA": "/fdb/igenomes/Mus_musculus/UCSC/mm9/Sequence/BWAIndex/genome.fa",
-            "BLACKLISTBWAINDEX":"/data/CCBR_Pipeliner/db/PipeDB/lib/mm9.blacklist_chrM.fa",
+            "BWA": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9",
+            "BOWTIE2INDEX": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9",
+            "BLACKLISTBWAINDEX":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9.blacklist.chrM",
             "CHROMS": ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10",
                        "chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19",
                        "chrX","chrY","chrM"],
             "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
-	    "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
+	        "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
             "FASTAWITHADAPTERSETD": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.consolidated.fa",
-            "GENOME": "/fdb/igenomes/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa",
+            "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/ref.fa",
             "KRAKENBACDB": "/fdb/kraken/20170202_bacteria",
-            "REFLEN":"/data/CCBR_Pipeliner/db/PipeDB/lib/mm9.len",            
+            "REFLEN":"/data/CCBR_Pipeliner/db/PipeDB/Indices/mm9_basic/indexes/mm9.fa.sizes",            
         }, 
     }
 }