Hi Raja,

Can you check that your fields are tab separated and not spaces (they are 
spaces below, but that could be a copy and paste artifact)?


Thanks for using Galaxy,

Dan


On May 9, 2012, at 9:45 AM, Raja Kelkar wrote:

> 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 <j...@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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> -- 
> Jennifer Jackson
> http://galaxyproject.org
> 
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