Hi all - I've got a bunch of fatsq files uploaded into a data library in
Galaxy. The underlying files is gzipped however Galaxy strips the .gz from
the filename and displays it as .fastq. When the python wrapper
rgFastQC.py gets called, it correctly sees the fastq.gz file. The wrapper
creates a
Hi Martin - Following up on this - I think your API folder delete commit is :
https://bitbucket.org/galaxy/galaxy-central/commits/8f76a6abc5d7d5c98b6c148c4cfe75cc1c159e90
? I was wondering how to find out more about this API call. Not knowing the
guts of the Galaxy API code much, is it a
To (I think) fix this, I changed line 50 in rgFastQC.py from
infname = self.opts.inputfilename
to
infname = self.opts.input
This will force FastQC to look at the real file and not the renamed
dataset.
On Mon, Jan 12, 2015 at 12:20 PM, Ryan G ngsbioinformat...@gmail.com
wrote:
Yes, I'm doing
Hi Björn,
I'm a bit old fashioned and think I prefer a proper Galaxy tool rather than
a notebook :) so I've set up a temporary demonstration/test site of a
toolfactory generated tool that does what I think I need - can some kind
soul please test it and let me know how it goes ? If it's useful, it
Hi Ryan,
That is the workaround I am using, which means
keeping an uncompressed copy of the FASTQ
file on our main storage from where Galaxy can
see it (for people to use within their histories).
From a long term storage perspective this is not
ideal - so I am keen for better handling of gzipped
Hi Marco,
No problem - I originally copied the metadata access
trick from one of the Galaxy dev-team's tool anyway.
Maybe we need to add this to the wiki...
Peter
On Tuesday, January 13, 2015, Marco Albuquerque
marcoalbuquerque@gmail.com wrote:
Hi Peter,
I was unaware of how to access
Hello,
I'd like to display the unique column content of a file in a combobox to give
the user the possibility to select factor levels for subsequent analyses, e.g.
for combining related factor levels in a meta-analyses.
Unfortunately, I failed to connect the tool that reads out the factor levels
Hi Damion,
I finally got to implement this, see method copy_from_dataset() in this
commit:
https://github.com/afgane/bioblend/commit/bc6b7cb71abb25aa109b85b1ff24e73aadac5ce4
Thanks Nicola!
Damion
Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for
Disease Control
Galaxy is not decompressing the file. The file is linked to on the
filesystem.
On Mon, Jan 12, 2015 at 10:28 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Hi Ryan,
The problem isn't Galaxy stripping the extension, rather
Galaxy is actually decompressing the file as part of the
upload
Ah. Then this is more subtle... are you using the
library import option where Galaxy just symlinks
to existing files? I thought that was not possible
with gzipped files (for the reasons given below).
Perhaps this is not being blocked, leading to the
confused state you're seeing?
Peter
On Mon,
Yes, I'm doing a link to file on file system when doing a library import.
Does this mean I should link to the the uncompressed file?
On Mon, Jan 12, 2015 at 12:14 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
Ah. Then this is more subtle... are you using the
library import option where
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