Hi everyone,
I tried to create an AMI with my tools integrated on Galaxy, but by default it
mounts the snapshots with the tools from Galaxy. How I can change the snapshots
mounted by default? i.e. before I start a cluster.
Thanks,Jose ___
t; You can probably modfiy /home/galaxy/.sge_request to make it work for now,
> but for portability of tools I'd still recommend the tag.
> Changes to .sge_request will not be persisted after shutdown, so you'll have
> to redo it with each new cluster.
>
> On Jun 13, 2
Dependencies" section. Many of the other tools on the
> cloud volume use the 'env.sh' method discussed there. For example, blast has
> the 'blast' package requirement, and in the /mnt/galaxyTools/blast/default
> directory you'll find an 'env.sh' f
Hi Galaxy Team,
I'm modifying my Galaxy CloudMan instance by adding custom tools. I've
installed my tools under the /mnt/galaxyTools/tools folder and I've modified
the .bashrc files from the sgeadmin and galaxy users to add the needed paths to
the PATH and PYTHONPATH variables. When I'm in Gala
,Jose
> Subject: Re: [galaxy-dev] Error copying files from job_working_directory
> From: n...@bx.psu.edu
> Date: Thu, 19 Apr 2012 12:16:05 -0400
> CC: galaxy-dev@lists.bx.psu.edu
> To: josenavasmol...@hotmail.com
>
> On Apr 16, 2012, at 9:03 PM, Jose Navas wrote:
>
> >
Hi everybody,
I was searching through the Galaxy code and I find the solution: the function
responsible for copying files is using shutil.copy function, which only allows
copy files. I've modified this function to use shutil.copytree in case of
file_name is a directory. I can send you the code
Hello,
I've integrated a tool into my Galaxy instance, but when I run the tool I get
this error:
galaxy.objectstore CRITICAL 2012-04-16 11:25:56,697 Error copying
/home/galaxy/galaxy-dist/database/job_working_directory/000/307/dataset_431_files/unweighted_unifrac_2d_continuous
to
/home/gala
Hi Galaxy developers,
I'm adding a tool to my Galaxy instance which generates some directories in the
directory $output.files_path, but when I look in
database/files/000/dataset_X_files/ directory, the directories has been copied
as an empty plain text files.
There is any option in unive
i.ini you can set the following option (to false) to
> disable this:
>
> # Sanitize All HTML
> # By default, all tool output served as 'text/html' will be sanitized
> # thoroughly. This can be disabled if you have special tools that require
> # unaltered output.
>
Hi Galaxy developers,
I have a tool that generates an html output which executes some javascript
functions that are defined in a *.js file. I put this file under the
$output1.files_path but when I display the html file in the galaxy browser, it
doesn't executes the Javascript. What can I do to
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