Hi,
I agree that *.loc files should be consolidated or, at least, we should
have proper documentation about which loc file is required for each tool...
Took me quite some time to find that solution.
I would suggest can we have a open wiki where these things are
annotated. ie: if I find a "trick" or a shortcut to something, shouldn't
we have a centralised place to share it with the community, rather than
having Nate and co waste their precious time answering over and over the
same questions?
Mailing lists are cool, but sometimes heavy to search and to find the
proper answers..
my 2p or maybe I missed something...
Cheers,
Fred
On 10/05/2012 15:35, Raja Kelkar wrote:
Hi Fred,
Thanks for the tip on the alignseq file. It did work (I do now have
sequence that came back from the tool, will have to check if it correct).
Anyone have a logical explanation?
Perhaps these myriad loc files can be streamlined down to something
simple in future.
Thanks.
Dan: The entries I had in local loc files were all tab delimited.
On Wed, May 9, 2012 at 4:49 PM, Federico De Masi <[email protected]
<mailto:[email protected]>> wrote:
Hi,
I was having the same issue just today and my solution was to add:
seq mm9 /path_to/twobit/mm9.2bit
in the alignseq.loc file as .nib has been replaced by 2bit.
Plus all necessaty entries in all_fasta.loc and twobit.loc
That worked :)
Hope this helps.
Fred
On 09/05/2012 22:40, Daniel Blankenberg wrote:
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
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> 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
<http://hgdownload.cse.ucsc.__edu/downloads.html
<http://hgdownload.cse.ucsc.edu/downloads.html>> (genomes +
source)
http://hgdownload.cse.ucsc.____edu/admin/exe/linux.x86_64/
<http://hgdownload.cse.ucsc.__edu/admin/exe/linux.x86_64/
<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
<http://wiki.g2.bx.psu.edu/__Admin/Data%20Integration>
<http://wiki.g2.bx.psu.edu/__Admin/Data%20Integration
<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
<http://wiki.g2.bx.psu.edu/__Admin/NGS%20Local%20Setup>
<http://wiki.g2.bx.psu.edu/__Admin/NGS%20Local%20Setup
<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 <http://galaxyproject.org/>
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_____________________________________________________________
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in your mail client. To manage your subscriptions to this
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--
Federico De Masi, PhD,
Assistant Professor
The Technical University of Denmark - DTU
Center for Biological Sequence Analysis - CBS
Kemitorvet 208/002
DK-2800 KGS. LYNGBY, DENMARK
Telephone: (+45) 45 25 24 21 <tel:%28%2B45%29%2045%2025%2024%2021>
Fax: (+45) 45 93 15 85 <tel:%28%2B45%29%2045%2093%2015%2085>
http://rg.cbs.dtu.dk
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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--
Federico De Masi, PhD,
Assistant Professor
The Technical University of Denmark - DTU
Center for Biological Sequence Analysis - CBS
Kemitorvet 208/002
DK-2800 KGS. LYNGBY, DENMARK
Telephone: (+45) 45 25 24 21
Fax: (+45) 45 93 15 85
http://rg.cbs.dtu.dk
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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