You'll need to set your dataset's database/dbkey to your custom reference genome before you can visualize it. We have enhancements planned so that this error doesn't happen in the future.
Best, J. On Dec 5, 2013, at 7:56 AM, Jasper Jan Koehorst <jasper.koeho...@wur.nl> wrote: > 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 > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
