Hi Ciara,
Galaxy supports compressed files like gz [1] by default.
Keep in mind that large files like yours are not guaranteed to upload
properly, please use other techniques to get your data in galaxy.
For example with FTP:
http://wiki.g2.bx.psu.edu/FTPUpload
Hope that helps,
Bjoern
[1]
Thanks for the quick reply.
I've already checked how to configure our Galaxy instance for FTP upload,
but due to security reasons, I cannot use that option. I read the wiki for
Data Libraries and found that uploading via filesystem path can be used
for putting files with size greater than 2GB in
HELLO !
I just updated our local galaxy instance and just wanted to try the new IGV
display application. When I try to display a BAM file whith the local IGV,
I encounter the following message :
HTTP and FTP access to BAM files require byte-range support
Has anyone encountred the same probleme?
Hello Kwon,
Most of this sounds correct. The only issue is with compressed files.
Galaxy uses uncompressed liftOver data at our site and this is how we
instruct that it be set up (see
galaxy-central/tool-data/liftOver.loc.sample).
Would you be able to run a test to see if uncompressing
Hi all,
I did manage to log in now after the postgres installation by re-registering.
However my workflow is gone. Is there a file stored in galaxy by default which
I can reupload to retrieve my workflow?.
Also it seems that I am no longer able to upload files. It's only a 300kb test
file
In your workflows, are you using Input Dataset steps? Galaxy uses these
steps to know how to map datasets to do special things like this. If you're
not currently using them, just open the workflow editor and add input dataset
steps (it's at the very bottom of the tool list) connected to the
When using the 'upload via filesystem path' option for data libraries, Galaxy
will use the file as is without decompressing it. In practice, this means
that you'll need to decompress it before uploading it to a library because
Galaxy tools expect the dataset to be uncompressed.
This is, of
I did manage to log in now after the postgres installation by re-registering.
However my workflow is gone. Is there a file stored in galaxy by default
which I can reupload to retrieve my workflow?.
Moving to a new database will make all your previous data inaccessible as it's
no longer in
Thank you for explaining it further, Jeremy. We'll keep that in mind next
time we use that method. Anyway, I'm sorry for this redundant post, but I'm
getting an error every time I am uploading a file into a data library using
my non-admin user account. Galaxy says that there is no valid file
Hi Jen,
Thanks for looking into this. I have unzipped all the .gz files so that the
directory contains all .chain files. The liftover.loc file has also been
modified to refer to all the .chain files instead, as such:
http://pastebin.com/xSKGvUtG
I still run into the same error if I try to run
When I merged brad chapmans code into galaxy-central two 0099 migration files
are created.
I got things working by moving the ngs lims one to 0104 , but now i think i'll
be in for a problem when a new 104 is created...
What's the right way to solve this?
Brad
--
Brad Langhorst
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