Hi Jen,

Thank you for your response. I seem to have all the relevant entries in the two "*.loc" files you mentioned (paths in all_fasta files and the twobit files are different because of the way we have the files stored. I also converted the 2bit files to .fa and have them available in the same twobit directory).

But the feature extraction is still not working.

Here are the relevant entries in files (I have redacted specific file paths and replaced them with "path_to"):

twobit.loc

hg18    /path_to/twobit/hg18.2bit
hg19    /path_to/twobit/hg19.2bit
mm9    /path_to/twobit/mm9.2bit
mm8    /path_to/twobit/mm8.2bit

all_fasta.loc

hg19full        hg19    Human (Homo sapiens): hg19 Full /path_to/hg19/bwa_path/hg19_all.fa
hg19_chr_only   hg19_chr        Human (Homo sapiens): hg19_chrom_only   /path_to/hg19/bwa_path/hg19.fa
hg18full        hg18    Human (Homo sapiens): hg18 Full /path_to/hg18/bwa_path/hg18_all.fa
hg18_chr_only   hg18_chr        Human (Homo sapiens): hg18_chrom_only   /path_to/hg18/bwa_path/hg18_chrom_only.fa


I assume that the second field in the (all_fasta.loc) file <dbkey> has to match the builds.txt file in the "ucsc" directory. Is that correct? It does in this case. I think I am missing something subtle here.

The "*.loc.sample" files are great but the information contained in those is confusing. I am not sure why there are two examples of the same info (as far as I can tell) in most sample loc files.

Thanks.

On Tue, May 8, 2012 at 6:48 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hi Raja,

This tool uses a <database>.2bit file to extract sequence data when the 'Locally cashed' option is used. The <database> is a genome that you install locally. ".2bit" format was developed by UCSC and they are the source for many genomes in this format already and for tools (compiled and uncompiled) to transform fasta data into/from .2bit format (faTwoToBit and twoBitToFa):
http://hgdownload.cse.ucsc.edu/downloads.html (genomes + source)
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ (compiled utilities)

For the extract tool, the builds list is required:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

You don't actually need to have more NGS set up beyond that. Still, this wiki can help.
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

For example, the <database>.2bit file could be placed with your .fa files like:

/galaxy-dist/tool-data/genome/<databaseA>/seq/<databaseA>.2bit <<
/galaxy-dist/tool-data/genome/<databaseA>/seq/<databaseA>.fa
/galaxy-dist/tool-data/genome/<databaseB>/bowtie/
/galaxy-dist/tool-data/genome/<databaseB>/sam/
/galaxy-dist/tool-data/genome/<databaseB>/seq/<databaseB>.2bit <<
/galaxy-dist/tool-data/genome/<databaseB>/seq/<databaseB>.fa
/galaxy-dist/tool-data/genome/<databaseC>/seq/<databaseC>.2bit <<
/galaxy-dist/tool-data/genome/<databaseC>/seq/<databaseC>.fa
/galaxy-dist/tool-data/genome/<databaseD>/seq/<databaseD>.2bit <<
/galaxy-dist/tool-data/genome/<databaseD>/seq/<databaseD>.fa

Then the .loc file is here:

/galaxy-dist/tool-data/twobit.loc.sample

You will probably have this for all genomes as well:

/galaxy-dist/tool-data/all_fasta.loc.sample

Remove the ".sample" before using these. Instructions for how to populate each are in the files themselves.

The only gtf/gff files associated with this tool would be datasets from the history, so there are no gtf/gff data to stage before using the tool. To have the tool use a particular genome, set the query dataset (interval, bed, gtf) to have the same database identifier as you used for the "<database>" part of the "<database>.2bit" file. (This is why the builds list is required).

If you make changes to data, don't forget to restart your server to see the changes.

Hopefully this helps,

Jen
Galaxy team

On 5/8/12 12:46 PM, Raja Kelkar wrote:

I have two questions that pertain to a local install of galaxy:

1. I have been having trouble getting the “fetch sequences” à “extract
genomic DNA” tool to work. Can someone identify the specific *.loc file
that needs to have the info about the location of the genome sequence files?

I get the following error when I run the extract tool:

/No sequences are available for 'hg19’, request them by reporting this
error./

//

2. What configuration file(s) need to contain locations for the gtf/gff
files?


Thanks.

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