update species file for hg38_chr19_only genome

species/kundaje.conf

@@ -71,6 +71,24 @@ reg2map_bed	= /mnt/data/pipeline_genome_data/hg38/ataqc/hg38_celltype_compare_su
 roadmap_meta	= /mnt/data/pipeline_genome_data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt
 ENCODE_assembly = GRCh38
 
+[hg38_chr19_chrM] # hg38 with chr19 and chrM only
+chrsz	= /mnt/data/pipeline_genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes
+seq_dir = /mnt/data/pipeline_genome_data/hg38/seq
+gensz	= hs
+bwa_idx	= /mnt/data/pipeline_genome_data/hg38_chr19_chrM/bwa_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta
+bwt2_idx	= /mnt/data/pipeline_genome_data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta
+ref_fa	= /mnt/data/pipeline_genome_data/hg38_chr19_chrM/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta
+blacklist	= /mnt/data/pipeline_genome_data/hg38_chr19_chrM/hg38.blacklist.bed.gz
+# data for ATAQC
+tss_enrich	= /mnt/data/pipeline_genome_data/hg38/ataqc/hg38_gencode_tss_unique.bed.gz
+dnase	= /mnt/data/pipeline_genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz
+prom	= /mnt/data/pipeline_genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz
+enh	= /mnt/data/pipeline_genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz
+reg2map	= /mnt/data/pipeline_genome_data/hg38/ataqc/hg38_dnase_avg_fseq_signal_formatted.txt.gz
+reg2map_bed	= /mnt/data/pipeline_genome_data/hg38/ataqc/hg38_celltype_compare_subsample.bed.gz
+roadmap_meta	= /mnt/data/pipeline_genome_data/hg38/ataqc/hg38_dnase_avg_fseq_signal_metadata.txt
+ENCODE_assembly = GRCh38
+
 [dm3] # installed by install_genome_data.sh
 chrsz	= /mnt/data/pipeline_genome_data/dm3/dm3.chrom.sizes
 seq_dir = /mnt/data/pipeline_genome_data/dm3/seq