Trackster Error chrom/?.len , No such file or directory

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Trackster Error chrom/?.len , No such file or directory

Jasper Jan Koehorst
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
 bam 
 ?

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:

NameKey Number of chroms/contigs
STPmg315STPmg315_v11

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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Re: Trackster Error chrom/?.len , No such file or directory

Jeremy Goecks
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 <[hidden email]> 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
 bam 
 ?

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:

NameKey Number of chroms/contigs
STPmg315STPmg315_v11

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/