Hi all,
This samtools dependency error is now showing for all my
Test ToolShed repositories using the samtools package:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad
Peter,
From what I've been able to determine, samtools' failure was due to an
error in the testing environment startup process, which in turn caused
errors in a number of tool dependency packages. I've fixed the initial
error, and the next test run should result in a successful samtools
Thanks Dave,
On a slight tangent, is there a way in the ToolShed to see what
other repositories use a given repository as a dependency?
e.g. From http://testtoolshed.g2.bx.psu.edu/view/iuc/package_samtools_0_1_19
it there any way to see what uses samtools 0.1.19?
Cheers,
Peter
On Mon, Apr 21,
The two options I normally use for that are the Repository dependency
definitions and Tool dependency definitions links under the Valid
Galaxy Utilities heading in the left panel, which provide an overview
of all dependencies of the relevant type.
--Dave B.
On Mon 21 Apr 2014 09:39:51 AM
This is due to a mismatch is chromosome names between your hg19.len file (UCSC
naming) and the VCF (Ensembl naming). This should be handled better by Galaxy,
and I’ve created a card for it:
https://trello.com/c/bjmNesZj
In the meantime, I used this command to convert chromosome names for this
Hello all,
This is just a reminder that poster abstracts for the 2014 Galaxy Community
Conference (GCC2014) *are due this Friday. *
Abstracts can be submitted at
https://wiki.galaxyproject.org/Events/GCC2014/Abstracts
Note that posters are reviewed and accepted on a rolling basis, until all
Hi,
I am trying to get DRMAA runner working for my local galaxy cluster. However,
I am having hard time configuring it my system.
So far,
I have installed Torque 2.5.12 and it seems to work as expected.
I installed drmaa_1.0.17 and here is DRMAA_LIBRARY_PATH
Hello
when attempting to create data libraries as admin I am not presented with the
same options listed in the documentation, namely
[cid:image001.png@01CF5DAE.5B451360]
Instead I only get Upload Files and Import datasets from your current
history. I want to use Upload files from filesystem
Hi, Mark,
Perhaps you need to adjusted universe_wsgi.ini where it says:
# Add an option to the admin library upload tool allowing admins to paste
# filesystem paths to files and directories in a box, and these paths will
be
# added to a library. Set to True to enable. Please note the security
#
Nevermind, I found it in universe_wsgi.ini.
Mark
From: Rose Mark USRE
Sent: Monday, April 21, 2014 10:09 PM
To: galaxy-dev
Subject: uploading data libraries options
Hello
when attempting to create data libraries as admin I am not presented with the
same options listed in the documentation,
Hi Simon
I too have been down the long and fruitless task of searching for
details about how to migrate a public (or not so public) galaxy server
to a completely new host.
In the end, I made some assumptions, strapped on my jodhpurs and spurs
and dived in.
Now I don't know whether what
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