Hi All,
New to galaxy here. I'm having an issue uploading bam files into a local
instance of galaxy. I understand that it requires samtools, and I installed
the appropriate dependency from the toolshed. However, I get the following
error:
Traceback (most recent call last):
File "/home/galaxy/ga
Hi Nathan,
is samtools executable in the environment path?
Scott
> On Dec 31, 2014, at 1:49 PM, Nathan Kipniss wrote:
>
> Hi All,
>
> New to galaxy here. I'm having an issue uploading bam files into a local
> instance of galaxy. I understand that it requires samtools, and I installed
> t
So I checked, and it is not. (type not found).
I will try some of the methods suggested on the admin/config wiki. (
https://wiki.galaxyproject.org/Admin/Config/ToolDependencies)
But something I am confused over is why did the install not go "properly"
through the toolshed? Or am I missing somethin
Unfortunately the ToolShed dependency only provides samtools to individual
Galaxy tools that declare a dependency on it. However, it allows multiple
versions of samtools to be available to different (versions of) Galaxy
tools.
This does NOT provide a samtools on $PATH for Galaxy itself, and it nee
Hi Nathan,
please try the following.
ln -s /path/to/your/shed_tools/samtools/0.1.19/devteam/what/ever/
/path/to/your/shed_tools/samttools/default
The important part is that it is samtools < 1.0 and that the default
link is a link to the folder in which you find the env.sh file.
I hope this will
