Hi Edward
Select 'view' instead of 'run' in your workflow list. This will give you
a nice (human readable) overview of all the steps, or select the
download option to get an xml describing your workflow.
Regards, Hans
On 09/13/2012 03:20 AM, Edward Hills wrote:
Hi Galaxy team,
I am
On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote:
Hi guys,
Just a quick question about the total size of the genome indexes just made
available via rsync server?
Hi Derrick,
The full size is around 3 TB.
--nate
Cheers,
Derrick
Hi,
I follow this tutorial to configure FTP with galaxy :
wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP
However, even if I can [ log into / upload file to / donwload file to
] my ftp server with my Galaxy account, I can not retrieve these data
on my Galaxy Web server.
It says : Your FTP
Hello David,
I've just committed change set 7656:6aadac8026cb to the Galaxy central
repository that provides the ability to do what you need here. It would be
great if you could try things out and let me know if you run into any problems.
I've been working with nikhil-joshi's
Hi Felix,
Thanks for reporting this error, it has been fixed in revision
7663:cc064ff4249b. Please let us know if you encounter additional issues.
Thanks for using Galaxy,
Dan
On Sep 10, 2012, at 12:23 PM, Felix Homa wrote:
Hello,
We noticed a problem with the tool Filter Fastq. It
Actually, I think that is exactly the issue. I DO have 3:f7a5b54a8d4f
installed. I've run into a related issue before, but didn't fully
understand it.
I believe what happened was:
1) I pushed revision 3:f7a5b54a8d4f to the tool shed which contained the
first revision of version 0.2 of the
Hello Birgit,
I've committed a fix for this issue in change set revision 7668:802413bc137b,
which is currently running on the test tool shed and is currently available
only in the Galaxy central repository. This fix will be include in the ext
Galaxy distribution scheduled for the end of next
Hi David,
I committed a fix for this issue in changeset 7662:c4ced3262d0d, which is
currently available only in the Galaxy central repository. The fix will be
available in the next Galaxy release scheduled for the end of next week.
Thanks for reporting this problem, and sorry for the
Hi Paul,
It seems that you probably did not use the Emboss tools in your local Galaxy
instance before (maybe you have a new instance). If this is the case, you can
install the emboss_datatypes repository and the emboss_5 repository from the
main Galaxy tool shed using the Admin UI features on
Thanks Nate,
D
On Thu, Sep 13, 2012 at 10:43 PM, Nate Coraor n...@bx.psu.edu wrote:
On Sep 12, 2012, at 8:28 PM, Derrick Lin wrote:
Hi guys,
Just a quick question about the total size of the genome indexes just
made available via rsync server?
Hi Derrick,
The full size is around 3
Hello Bjorn,
I've committed your patch in change set revision 7669:5088185a5bca, which is
currently running on the test Galaxy tools shed. The fix will be moved to the
main Galaxy tool shed at the time of the next Galaxy release, currently
scheduled for the end of next week.
Regarding the
Hi Paul,
You have to be running the latest Galaxy dist release from
https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance. Your
repository tip should be e6444e7a1685.
Greg Von Kuster
On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
Hmm, ok this tool shed is all new to me.
Thanks for your help with this. So I updated to the latest version,
but didn't read the instructions about creating a tools directory and
so I have repositories stuck in limbo, like described here:
Galaxy imported a library which already existed in the python system
folder. See the error message below.
Is that because RedHat 6 used a python-marksafe, but Galaxy installation
program did not recognize it? Or Galaxy require a higher version of
markupsafe module?
/home/x/work/galaxy-dist/
Hi Paul,
You should be able to get things working using the same sql command in the
email below. This process will be a new UI feature in the next Galaxy release.
Greg Von Kuster
On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote:
Thanks for your help with this. So I updated to the latest
Ok I just gave up and did a fresh install and it seems to work. Thanks for
your help.
On Thu, Sep 13, 2012 at 7:17 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Paul,
You should be able to get things working using the same sql command in the
email below. This process will be a new UI
hi guys,
I have been trying to clean up some old histories and datasets on our local
galaxy. I have spotted one very old dataset file with big size didn't get
removed no matter what.
I went to check the reports webapp, that dataset isn't on the largest
unpurged data files list (despite it has
So I successfully added the emboss tools to galaxy, but I failed to
create a tool panel section for them.
So I thought I would uninstall them and install them again, this time
creating a tool panel section.
I'm following the instructions here (
Cleaning up the datasets manually is the best suggestion for now. We're
planning to enhance the clean up scripts to automatically delete history export
files soon.
Best,
J.
On Sep 13, 2012, at 10:37 PM, Derrick Lin wrote:
hi guys,
I have been trying to clean up some old histories
The problem is likely your use of the from_work_dir attribute.
I can see by the logging code that you're using an old(er) version of Galaxy,
and it's likely that this attribute isn't functioning correctly in your
instance. We've recently improved the implementation of from_work_dir, and
Thanks Jeremy,
I am sure it's trivial for us to do a manual clean up
Cheers,
D
On Fri, Sep 14, 2012 at 1:05 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote:
Cleaning up the datasets manually is the best suggestion for now. We're
planning to enhance the clean up scripts to automatically delete
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