Hi Peter,
Thanks to you and all the other responders who were so helpful! This did
solve my problem right away.
Best regards,
Scott
On Fri, Feb 26, 2016 at 3:13 PM, Peter Cock
wrote:
> Hi Scott,
>
> Galaxy itself requires samtools (to deal with BAM files), separately
> from any Tool Dependenc
Hi Scott,
Galaxy itself requires samtools (to deal with BAM files), separately
from any Tool Dependency within the tool calling framework.
Right now there is no mechanism for datatype definitions to declare a
dependency (e.g. on a binary like samtools, or a Python library).
Probably samtools sho
, February 26, 2016 6:01 PM
To: Scott Szakonyi
Cc: Galaxy Dev Mailing List
Subject: Re: [galaxy-dev] Difficulty uploading BAM files
Hello Scott,
you do need a samtools binary on GALAXY's PATH.
This is not samtools installed from the toolshed.
Best,
Marius
On 26 February 2016 at 18:49, Scott Sza
I too had trouble with BAM files as
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py
Line 201
class Bam( Binary ):
...
def _get_samtools_version( self ):
...
samtools_exec = which('samtools')
Assumes samtools is installed on the server and was not finin
Hello Scott,
you do need a samtools binary on GALAXY's PATH.
This is not samtools installed from the toolshed.
Best,
Marius
On 26 February 2016 at 18:49, Scott Szakonyi
wrote:
> Hi,
>
> I'm having trouble uploading BAM files in our development environment.
> Other files types are uploading wit
