Hi Ross, thanks for the reply! I ran FastQC from the command line, and it did
give the proper output. Furthermore, FastQC generating the proper output when I
run it from Galaxy. However, Galaxy is having trouble accessing the files. If I
go into the filesystem, I can find all of the files in
I try it with a script for galaxy service, but it did not work. I
successfully did it with one daemon file for each process...
2011/8/26 Nate Coraor n...@bx.psu.edu
By default, PasteScript is looking for a section named [server:main].
With this config, you can
There's a Tophat2 wrapper in galaxy-central right now that you're welcome to
try, but it's still under development and may be buggy and is still subject to
(potentially) major changes. I'd guess that Tophat2 support will make it to
beta near the end of this month and be available on the public
For larger files, or if complete downloads seem to be a problem, using
curl at a command or Terminal prompt is a great option. The syntax is:
% curl -O 'copied-link-from-dataset-disc-icon'
I am trying to share my files/history in Galaxy/Cistrome with my
colleague, but the 'Share with user' link gives the following error.
Could you please help me, am i doing something wrong or is there a bug
in the system?
input file example in galaxy:WASH7P 0.305384KLHL17 6.4404GLTPD1
22.8633PUSL122.9327CPSF3L 0.446421SAMD11 0.0267019
then the error message complaint is on the tile column.After updating R to
latest version the grouping function is no longer working. I have been
Thank you for your answer. Although using curl command might be a good
solution to overcome the incomplete downloads issue, this solution might
not be enough user-oriented (as I don't think our users are familiar with
using the command line). Anyway, we have developed a tool
Did you have special characters (é, à,...) in the email of the person
you try to share with?
If so, try whitout this special characters (è - e or à - a), it should
Le 07/06/2012 16:26, Päivi Pihlajamaa a écrit :
I am trying to share my files/history in
On Jun 1, 2012, at 4:36 AM, julie dubois wrote:
After several post in an Apache Forum, I've solve any problem of my apache
configuration to enable load balancer configuration.
It seems work but when I launch my galaxy application, I arrive in this web
I am helping a research group to use Galaxy on our clusters. Unfortunately I
have no previous experience with Galaxy, but learning along the way. We are
almost there, but cannot figure out one particular issue. This is about
configuration of Galaxy, so I thought developers list is
It's not important how the files get there, they could be moved via ftp, scp,
cp, smb - whatever.
Galaxy will use that directory to import from no matter how the files arrive.
I found that confusing at first too.
On Jun 7, 2012, at 1:55 PM, Mehmet Belgin wrote:
Thank you for your fast reply! Looks like library_import_dir is for admins
and there is another library option for users. I will try with that one and see
if the files appear in the GUI.
Mehmet Belgin, Ph.D.
On May 22, 2012, at 11:18 AM, Peter Cock wrote:
On Tue, May 22, 2012 at 4:14 PM, Sarah Diehl di...@immunbio.mpg.de wrote:
Thanks Peter! It's very likely that I have the exact same problem, because I
also have CentOS and needed to compile Python.
In that case make sure you've done this:
Sorry to say I'm unable to explain this problem with your local
instance - it works fine on all of mine and on main.
What do you see when you type
in the root of your Galaxy clone?
The current tip is
If this is an up to date clone and you
I appreciate you taking the time to help! I'm almost positive it's a local
configuration issue, like you said, but without knowing how Galaxy generates or
parses its internal links (in the form of [Galaxy web address]/datasets/[16
character hash]/display/[filename] ) it's tough to know how to
The configuration suggested at
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy is what you
followed to set your proxy up?
That obfuscated link hash element is generated from internal database
ids to help secure against malicious users viewing specific datasets -
I'm trying to write a test for Galaxy and it fails on the result of the test
differing from the expected output. As the output of diff (below) lists
nothing but local_file data, I'm assuming that the issue is that no output is
being generated by the test. The test config is a series
I have put together a project that builds heavily on mi-deployment
that does some of what you want to do (and probably a bunch of things
you don't), but you could hopefully pull out just the parts you need.
The idea behind the project is to build really cheap cloud galaxy
I have read through the documentation a couple times, but I still have
a few questions about the recent tool shed enhancements.
At MSI we have a testing environment and a production environment and
I want to make sure the tool versions and configurations don't get out
of sync, I would also like
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