Hi. I am using the tag:
version_stringpath to tool --version/version_string
In my xml file. I would expect the tool version to be printed in the
information window for each dataset but the version field is blank. I
am running the latest Galaxy dist, is there anything else I need to
Hi,
I have some questions about adding new custom tools to my Galaxy instance:
1-How can I reuse workflows?
a.Should I wrap a workflow as a tool?
b.Or can I just add a custom workflow as a workflow step in another
workflow?
2-I noticed that option 1.b above seems to copy
Hi Pieter,
You cannot currently embed on workflow within another, although that
has been suggested as a nice extension to Galaxy.
You can for instance start a new history, run workflow #1 with N tool
steps, then workflow #2 with M tool steps, and save this history as a
new workflow #3 with N+M
Hi Peter,
Thanks for the reply.
Does anyone know how to execute a specific workflow from the command prompt?
E.g. run the workflow as a job? Then I could perhaps write a workflow wrapper
tool to overcome this shortcoming.
Regards,
Pieter.
-Original Message-
From: Peter Cock
Shaun,
version_command is what you want:
version_commandtophat --version/version_command
A couple things to note:
*tool path isn't needed if the tool is in your galaxy user's path;
*your tool must have a --version command line option; if not, you'll
have to modify the
Dear all,
I've a question about FTP upload of data.
The data uploaded via ftp are placed in the directory ftp_upload_dir defined
in universe_wgsi.uni
After the uploading, when a user select the data to import in its history,
galaxy copy the file in the dir file_path (defined in
Perhaps this is a distribution issue. For those who have gotten the Display
at UCSC link to work on a local server or workstation, what linux
distribution and version did you use? Has anyone used this successfully with
Red Hat Enterprise Linux 6.1?
Best,
-Kip
On Fri, Oct 7, 2011 at 6:28 PM,
Kip;
Are these binary BAM or BigWig type files you are having trouble
displaying at UCSC? I don't believe the Paste server has support for the
byte-range requests that UCSC needs, and you need to send files through
the proxy server. I've done this with nginx so don't have direct Apache
experience
Hello Forent,
On Oct 13, 2011, at 2:48 AM, Florent Angly wrote:
But maybe I need a little bit of guidance with this because the example
shown, the user is given a _limited_ number of output datasets to choose
from. The Grinder case seems simple: give the user a field where he can
wrappers are also used when a tool produces several files in an output
folder (i.e. executable takes outdir parameter, not explicitly named outfile
paths) and you would like to move these to the desired paths under files/
(i.e. a composite datatype is not desired) and/or cleanup unnecessary files.
Hi,
i was browsing through the list and found many entries for this issue but not a
definite answer.
We are actually running into this error for simple file uploads from the
internal filesystem.
thanks,
joe
___
Please keep all replies
Hi,
we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools, like
fastqc, stopped working. Are there internal links that we possibly ignored?
Is there a way to adjust the installation via a download or update?
joe
___
Hi Greg,
Thanks for the reply. I believe that how easy it is to write tools
wrappers plays a big role for how widespread Galaxy becomes. I filed an
issue at
https://bitbucket.org/galaxy/galaxy-central/issue/670/better-support-for-multiple-outputs
so that the issue is recorded.
Best,
Florent
Hi, Joe - not sure this will help but here goes: As you know, most
tools expect to find normal executables (like bwa and samtools) on the
execution host path but java packages like FastQC are a special case.
Java based tool wrappers like the Picard tools expect to find the
Picard jar files in
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