Hi Lilach,
Regarding the cloud instance, you can load data from the public main
instance of Galaxy just like any other URL. On the "Get Data -> Upload
Data" form on your cloud instance , paste in the URLs of the datasets
from main. The URL can be captured by right-clicking on a dataset's disk
icon and then "Copy link location" (on a Mac; do the equivalent if using
a PC).
It is generally better to transfer one URL per job, if the data is
large, since jobs have a certain amount of time to complete. If you lump
together several large file URLs into one job, there could be a chance
that it could time out. It is fine to execute several jobs concurrently.
Best,
Jen
Galaxy team
On 6/27/12 6:51 AM, Lilach Friedman wrote:
Hi Jennifer,
Is there a way to directly upload my files from the public Galaxy to
my cloud Galaxy instance (in AWS)? Or should I download them first to
my computer, and then to upload them? (It takes a lot of time because
of the low uploading speed).
Thanks,
Lilach
2012/6/26 Jennifer Jackson <j...@bx.psu.edu <mailto:j...@bx.psu.edu>>
Hello Lilach,
Currently, the human reference genome indexed for the GATK-beta
tools is 'hg_g1k_v37'. The GATK-beta tools are under active
revision by our team, so we expect there to be little to no change
to the beta version on the main public instance until this is
completed.
Attempting to convert data between different builds is not
recommended. These tools are very sensitive to exact inputs, which
extends to naming conventions, etc. The best practice path is to
start and continue an analysis project with the same exact genome
build throughout.
If you want to use the hg19 indexes provided by the GATK project,
a cloud instance is the current option (using a hg19 genome as a
'custom genome' will exceed the processing limits available on the
public Galaxy instance). Following the links on the GATK tools can
provide more information about sources, including links on the
GATK web site which will note the exact contents of the both of
these genome versions, downloads, and other resources.
Hopefully this helps to clear up any confusion,
Best,
Jen
Galaxy team
On 6/21/12 7:50 AM, Lilach Friedman wrote:
Hi Jennifer,
Thank you for this reply.
I made a new BWA file, this time using the hg19(full) genome.
However, when I am trying to use DepthOfCoverage, the reference
genomr is stucked on the hg_g1k_v37 (this is the only option to
select), and I cannot change it to hg19(full). Most probably,
because I selected hg_g1k_v37 in the previous time I tried to use
DepthOfCoverage.
It seems as a bug? How can I change it?
Thanks,
Lilach
2012/6/18 Jennifer Jackson <j...@bx.psu.edu <mailto:j...@bx.psu.edu>>
Hi Lilach,
The problem with this analysis probably has to do with a
mismatch between the genomes: the intervals obtained from
UCSC (hg19) and the BAM from your BWA (hg_g1k_v37) run.
UCSC does not contain the genome 'hg_g1k_v37' - the genome
available from UCSC is 'hg19'.
Even though these are technically the same human release, on
a practical level, they have a different arrangement for some
of the chromosomes. You can compare NBCI GRCh37
<http://www.ncbi.nlm.nih.gov/genome/assembly/2758/>with UCSC
hg19 <http://genome.ucsc.edu>for an explanation. Reference
genomes must be /exact/ in order to be used with tools - base
for base. When they are exact, the identifier will be exact
between Galaxy and the source (UCSC, Ensembl) or the full
Build name will provide enough information to make a
connection to NCBI or other.
Sometimes genomes are similar enough that a dataset sourced
from one can be used with another, if the database attribute
is changed and the data from the regions that differ is
removed. This may be possible in your case, only trying will
let you know how difficult it actually is with your analysis.
The GATK pipeline is very sensitive to exact inputs. You will
need to be careful with genome database assignments, etc.
Following the links on the tool forms to the GATK help pages
can provide some more detail about expected inputs, if this
is something that you are going to try.
Good luck with the re-run!
Jen
Galaxy team
On 6/18/12 4:42 AM, Lilach Friedman wrote:
Hi,
I am trying to used Depth of Coverage to see the coverages
is specific intervals.
The intervals were taken from UCSC (exons of 2 genes),
loaded to Galaxy and the file type was changed to intervals.
I gave to Depth of Coverage two BAM files (resulted from
BWA, selection of only raws with the Matching pattern:
XT:A:U, and then SAM-to-BAM)
and the intervals file (in advanced GATK options).
The consensus genome is hg_g1k_v37.
I got the following error message:
An error occurred running this job: /Picked up
_JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main
##### ERROR
------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version
1.4-18-g80a4ce0):
##### ERROR The invalid argume
/Is it a bug, or did I do anything wrong?
I will be grateful for any help.
Thanks!
Lilach/
/
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--
Jennifer Jackson
http://galaxyproject.org
--
Jennifer Jackson
http://galaxyproject.org
--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
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:
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To manage your subscriptions to this and other Galaxy lists,
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