I was wondering if there was a way to export a dataset to the file
system? Basically I think it would be advantageous if someone could copy
a dataset to an "export" folder, they could then FTP this data away or
work with it locally?
Thanks for the help,
Your galaxy instance does not have to be accessible from outside. The
GALAXY_URL is send to the external datasource to create a new url that your
browser understands and that galaxy will use to retrieve the data prepared
by the service. E.g.
http://localhost/galaxy/tool_id=1?url=http://externaldata/dat1.txt. You only
have to make sure that galaxy is able to reach the external service.
On Mar 12, 2011 1:08 PM, "Martin Senger" <martin.senger(a)gmail.com> wrote:
I am not sure if I understand correctly how the external data sources (i.e.
BioMart) are integrated into Galaxy. However, I believe that the Galaxy
sends an HTTP request to the external data source with the parameter
GALAXY_URL - and this URL is used later by the external data source to send
parameters for a subsequent request resubmission. Without going to further
details (about sync and async method), it seems to me that in any case the
URL given in GALAXY_URL must be a publicly available URL (available from/by
the external source).
1) But what if I am running my own Galaxy behind a firewall that does not
allow access from the outside?
2) If I cannot make our firewall open, is there a way (perhaps in the Galaxy
configuration) to change the host name that Galaxy is using when creating
its GALAXY_URL parameter? That would allow me have a "third-party" URL where
Galaxy and external data sources can communicate together.
Many thanks for any help,
I installed Galaxy on my own linux machine. I would like to perform analysis
on local RNAseq files since they are too big to upload. How do we add files
from a local directory or a network share?
A L B E R T
is there a way to clean fastq files (filter Poly-A etc.) with Galaxy?
Haven't found anything so far. Also if you generally know good tools plz
Have seen lots of stuff for fasta and qual files but not for fastq.
I'm experiencing some strange problems with the fastq groomer.
Trying to groom my files I get the following error:
"Traceback (most recent call last):
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in
if __name__ == "__main__": main()
File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main
for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ):
File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 452, in __iter__
File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 448, in next
File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 142, in assert_sequence_quality_lengths
assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len )
AssertionError: Invalid FASTQ file: quality score length (63) does not match sequence length (36)"
I've double checked the file and it should be ok.
dear Galaxy users,
I would like to import genotyping data in Rgenetics and I can't succeed.
I have ped file and map file, I try to import them in lped format but it didn't work ...
Anybody with experience can help me to solve this issue ?
Many thanks in advance,
----- Forwarded message from Noushin Ghaffari <noushin.ghaffari(a)gmail.com> -----
Date: Mon, 7 Mar 2011 09:09:13 -0600
From: Noushin Ghaffari <noushin.ghaffari(a)gmail.com>
Subject: Question about FTP
Dear Galaxy team,
Firstly, thank you very much for the great tools.
I am working on a large dataset and need to upload it to Galaxy via FTP. I
but I cannot login. I used my email, my public name on Galaxy and just
simple my name, but none of them worked. Can you please help me to know how
can I login to upload my file?
Here is my inofrmation:
public name: me-on-galaxy
I appreciate you help and time in advance.
----- End forwarded message -----
I am new to Galaxy (but not to EMBOSS :-)) - so I may be doing something
stupid. Sorry if I do. I am referring to my own local Galaxy installation.
1) I noticed that most of the emboss graphical programs (e.g. plotorf) are
executed from/by the perl interpreter, e.g.:
emboss_single_outputfile_wrapper.pl plotorf -sequence ...
These programs are working fine.
2) There are few other programs that could produce a graphical output
(freak, hmoment, iep) but they don't because the toggle "-plot" is not used
in their command line. Therefore, strictly speaking, they are also working
fine (producing tables instead of graphs).
3) But there are two programs, prettyplot and pepnet, that are called
without any wrapper (no perl interpreter), e.g.
pepnet -sequence ...
and they produce graph (as PNG), indeed, but this graphical result is not
shown in Galaxy. Instead, I am getting there an image showing just the text
of a URL (attached). And metadata/report on this result says:
114: prettyplot on data 1
format: png, database: ?
I do not know why there is an "empty" remark - because the PNG file is
created, and it is a PNG file, it is just not shown in the Galaxy.
I wonder what I have wrongly configured...?
Thanks for any help,