I have my own genome fasta file containing 1 chromosome with a modified header so that it looks like:

>chr1

ATGCATGC....

I did a FASTQ mapping on it via the galaxy interface and now I end up with a bam file:

9 Bowtie2 on data 6, data 8, and data 7: aligned reads

1.2 GB

format bam 

database ?

I use the visualize button to start the visualization of the dataset. I chose trackster, And view it in a new visualization. I use my fasta file as a reference genome:

Name	Key	Number of chroms/contigs
STPmg315	STPmg315_v1	1

But then I get the error:

Couldn't open /home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len , No such file or directory

I looked into the /chrom/ folder and of course ? does not exist. I am currently running 

python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/

But this ofcourse downloads only known genomes and their chr. information. As I have my own genome I was curious how to continue with this.

I manually created a file in the /chrom/so that it looks like this:

head STPmg315.len 

chr1 1900521

but no luck so far. What else do I have to do to make it work?

Thanks,

Jasper

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