How to add new genome
Download genome of interest into MySQL data directory (/var/lib/mysql for OpenSUSE).
rsync -avzP rsync://hgdownload.cse.ucsc.edu/mysql/dm3/ ./dm3/
chown -R mysql.mysql ./dm3
Download a corresponding fasta files into /wardrobe/indices/dm3, unzip and make one file, for example
mkdir -p /wardrobe/indices/dm3 cd /wardrobe/indices/dm3 ncftpget ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/chromosomes/* zcat *.gz >>dm3.fa
Make a bowtie index than copy it into /wardrobe/indices
bowtie-build dm3.fa dm3 cp dm3* ../
To make STAR to pay attention to annotation it has to be provided in gtf format. One way to get right annotation is from UCSC genome browser Table Browser function. Save file into /wardrobe/indices/gtf/dm3_refseq.gtf
mkdir -p /wardrobe/indices/STAR/dm3 cd /wardrobe/indices/STAR/dm3 STAR --runMode genomeGenerate --genomeDir ./ --genomeFastaFiles ../../dm3/dm3.fa --runThreadN 48 --sjdbGTFfile ../../gtf/dm3_refseq.gtf --sjdbOverhang 100
Download a ribosomal sequence in fasta format then make a bowtie index with the prefix ribo and organism bowtie-build ribo.fasta ribo_dm3 and put index files into /wardrobe/indices/
Run next SQL command in command line mysql tool or in MySQL Workbench.
INSERT INTO ems.`genome` VALUES(genome,db,findex,annotation,annottable,gsize)
('D. melanogaster v3','dm3','dm3','dm3_refseq_genes','refGene','1.2e8');
Where db is UCSC genome browser database name dm3 in my case and findex is the base name used in bowtie-build and directory name after STAR/.