Hi Paul,
Fixes or enhancements to individual tools might be a good place to start -
and you won't need to know as much about the Galaxy internals.
The Galaxy development team look after a lot of tools/wrappers, but of
course there are even more on the Tool Shed written and maintained by other
Hi all,
I'm trying to import an history from the web server to my local server.
First I've chosen Export to File in the history menu and I've seen a
message with an url.
Second in my local server I've created a new history and I chosen Import
from File in my new history menu.
I've pasted the url
In risk of getting a discussion here: a long standing enhancement
request is to highlight the current history item one is currently viewing.
Situation sketch: I often hide the history items panel to study results
(displayed in middle panel) into detail, and when I bring the history
item panel
I thought it was on Trello already. Anyway, for the moment I cannot
acces Trello... When I do I will search and perhaps add it!
Cheers
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
Hi All
Intermediate files in a workflow often make up the large majority of a
workflow's output and, when this is an NGS analysis, this volume can be HUGE.
This is a considerable concern for me as we consider implementing a local
install of galaxy. Storing all of this seems useless (once
Hmm. If that configuration option is set to True, and uncommented, then the
only thing left to check would be to make sure you are logged in as an admin
user.
And, just reply-all, like you did to this mail, and everything will thread to
the list properly.
Thanks!
-Dannon
On Feb 6, 2013,
Hey Mark,
Galaxy by default saves everything, as you've noticed. In workflows, you can
flag outputs after which intermediate (unflagged) steps will be 'hidden' in the
history, but you can't automatically delete them, though this is something
we've wanted to do for a while. Unfortunately it
On Feb 5, 2013, at 7:25 PM, Eric Enns wrote:
Hey,
In our local galaxy install using the latest release january, uploaded
datasets are showing empty. But when you download it the contents are there,
also if you click auto-detect in edit attributes it will remove the empty
status and
Hi,
I am a computer engineer and have to deploy a cloud computing system, like
Hadoop. I want to deploy a local Galaxy system on the Hadoop platform. I know
that Galaxy can run on Cloud such as EC2 from Amazon.
My question is: can Galaxy run on Hadoop? (Not running within a virtual
mechine,
I am an admin user. I guess otherwise I wouldn't have access to Manage
data libraries page.
I have two instances of galaxy, one at server and one locally on my
laptop. And both have the same problem. Can't let the files copy
locally, and it's a problem.
On 02/06/2013 02:10 PM, Dannon Baker
Hi,
Because hadoop is a different computing approach, all the underlying
tools would need to be written for hadoop as well, so currently Galaxy
would not be very useful with only a hadoop cluster as a backend.
However work is underway to allow hadoop jobs to be run alongside
other jobs from a
This is likely a permissions issue: importing your history into another Galaxy
instance requires the history to be accessible. Here's a solution that, while
ugly, should work:
(1) Make the history accessible by going to Share/Publish and clicking the
option to make it accessible.
(2) Export
Hi, thanks for your help.
I've tested your procedure and it doesn't work. I have the same error.
Sorry and thanks for the creation of the card.
Julie
2013/2/6 Jeremy Goecks jeremy.goe...@emory.edu
This is likely a permissions issue: importing your history into another
Galaxy instance requires
Ah, I see the issue: the Cistrome instance cannot be used anonymously (without
login). It's not possible for one Galaxy instance to work with another
instance's history because instances work with objects anonymously rather than
using login credentials.
For now, you can download/copy the
Thanks!
Just one ask : How can I download this compressed history : is it the same
that :
wget url_of_exported_history
and copy the file from this command in a local server ?
Because this file is not an archive but a text file with html code
thanks again.
Julie
2013/2/6 Jeremy Goecks
Adding galaxy-dev list in CC as suggested by Peter.
Il giorno mer, 06/02/2013 alle 16.57 +, Peter Cock ha scritto:
On Tue, Feb 5, 2013 at 11:45 AM, Nicola Soranzo sora...@crs4.it wrote:
Dear Peter,
I have created a simple Galaxy tool for DustMasker of the NCBI BLAST+
suite, which I
Unfortunately using wget won't work in this case. The reason you have access to
the history is your Galaxy cookie, which isn't shared with wget/curl.
You'll need to click on the export link in your Web browser to download the
history to your local computer and then move it to a local server.
Hi Matt,
Here are a couple of things to consider:
1. Fix Select tool to match special characters:
https://trello.com/c/cwrBpNP9
2. Extend history export to include composite dataset objects/files:
https://trello.com/c/oq1ASbkC
There are lots of other ideas, but they tend to be a lot more work.
Hi guys,
When I try to upload a directory of files from a server directory I'm
seeing the error below.
It appears to be trying to write to a temp directory somewhere that
I'm guessing doesn't have enough space? Is there a way I can direct
where it writes to for temporary files like this?
Am I
On Feb 6, 2013, at 2:32 PM, greg wrote:
Hi guys,
When I try to upload a directory of files from a server directory I'm
seeing the error below.
It appears to be trying to write to a temp directory somewhere that
I'm guessing doesn't have enough space? Is there a way I can direct
where
Sorry, I couldn't find a way of posting a reply on the thread. There was
an only option of replying to author.
How can I post my reply so that it appears in publicly visible list?
Yes, I restarted, and in the drop-down, there are only import from
your current history and upload files
Hi, Galaxy developers,
I would like to have the parameters on the web interface to be packed into
sections for a tool. Is there a way to do this? There is a page tag, but
the document says we should avoid using it. Also there is no replacement
tag for page. The problem using the page tag is that
Thanks Nate,
It turns out I already had this as the first line of my job setup file:
export TEMP=/scratch/galaxy
But when I look in that directory, there's plenty of free space, and I
also don't see any recent files there. So I'm wondering if the upload
jobs aren't seeing that for some reason.
Hi Bassam,
First, I am going to post your question to the galaxy-...@bx.psu.edu
mailing list. This is where local and cloud install Galaxy questions can
get the best exposure to the development community.
Next, this isn't necessarily an error. And was the full line really this?
nohup:
On Feb 6, 2013, at 3:00 PM, greg wrote:
Thanks Nate,
It turns out I already had this as the first line of my job setup file:
export TEMP=/scratch/galaxy
But when I look in that directory, there's plenty of free space, and I
also don't see any recent files there. So I'm wondering if
Hmm, I narrowed down the problem some more:
For some reason Python isn't respecting the TEMP environment
variable so it's trying to write to /tmp on whichever node it's
running on.
I really don't understand why Python isn't respecting it. The docs
seem to suggest it should:
Hi Simon,
Significant changes to the way that job run parameters are defined will be
included in a future release. In specific, there'll be no more job runner
URLs, and parameters will be specified with a more robust XML language.
These changes aren't stable enough to go out in the next
Ok, when I ran Python in my last two emails I was running as myself,
not the galaxy user, and only the galaxy user has write permission to
/scratch/galaxy
So that's why Python was ignoring /scratch/galaxy for me. If it
doesn't have write access it tries the next temp directory in its
list.
I'm
Thanks for your reply !
The patch has fixed the problem !
Christophe
Le 30/01/2013 00:58, Derrick Lin a écrit :
Hi, I had the similar issue a while ago, and it's fixed in
https://bitbucket.org/galaxy/galaxy-central/commits/c015b82b3944f967e2c859d5552c00e3e38a2da0
Hope this help
D
On Wed,
Hi All,
Can anybody please add a few words on how can we use the “initial
implementation” which “ exists in the tasks framework”?
-Alex
From: Trello [mailto:do-not-re...@trello.com]
Sent: Wednesday, 6 February 2013 10:58 AM
To: Khassapov, Alex (CSIRO IMT, Clayton)
Subject: 4 new notifications
I am indeed using multiple web processes and I guess I am talking about the "old" admine tool reloader...Is there any other way to do this for your own tools that you just manually place in tools etc.?ThonOn Feb 05, 2013, at 06:22 PM, Dannon Baker dannonba...@me.com wrote:Are you using multiple
Hi Bassam,
I think that your best bet is to explore this command usage in general,
since this is really a unix question and no detail about how you used
this in Galaxy was provided for others to comment on. I am assuming that
you already checked your Galaxy process and found out if it already
Hi Luobin,
This isn't yet possible but is planned: https://trello.com/c/KxlQK0FB
Best,
J.
On Feb 6, 2013, at 2:47 PM, Luobin Yang wrote:
Hi, Galaxy developers,
I would like to have the parameters on the web interface to be packed into
sections for a tool. Is there a way to do this? There
Hello
Everything seems to be working on my local Galaxy
I was talking to my IT guy who did the initial installation and he said that
virtualenv may not have been loaded.
When he did
% yum install python-virtualenv.noarch
He got a not found error.
He did install mercurial and then completed the
I also figured this one out,
My external USB harddrive name had a space in it.
So velvet is running for the first time...
Got my fingers crossed. Thanks for all the help;
I'm sure Ill need some later.
Greg
From: Thyssen, Gregory - ARS
Sent: Tuesday, February 05, 2013 3:34 PM
To:
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