Peter has already voted and if I recall correctly Ryan cannot access
Trello - so this might be a waste to bring up - but here is a Trello
card for voting on this issue and tracking progress
https://trello.com/c/3RkTDnIn.
To summarize previous discussion - this would be fantastic to have and
Agreed.
On Mon, Jan 12, 2015 at 10:24 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:
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
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
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 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
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