Hi,
Thanks for your answers. I understand that permit to load or create
"unsorted bam" (or sorted by name) can create bug with lot of tools
and it's difficult to restrict this manipulation just for few tools.
But I don't understand one thing. Why can I download from the toolshed
a tool which permi
We also encountered this issue.
As I understood it: if Galaxy gets a BAM file (either through upload or
generated by a tool), it will generate metadata and indexing is part of that.
This only works if the BAM file is coordinate sorted, otherwise it fails
(although there is nothing wrong with th
Indeed, this would be the right approach.
But so far the current strategy is quite imputed also in tools.
E.g. BWA from devteam automatically sorts the bam afterwards - wanted or
not.
2015-07-17 11:59 GMT-05:00 Ryan G :
> I would think the correct approach would be to allow any bam file and if a
I would think the correct approach would be to allow any bam file and if a tool
requires a coordinate sorted bam and one is not provided it would make sense
for the tool to fail with an error.
Does galaxy itself require a coordinate sorted bam or this this so the majority
of tools can functi
I'm not the right person to respond to this but since no one else has
I will explain my limited (probably incorrect) understanding of the
problem and what needs to be done. I believe Galaxy assumes all bam
files are coordinated sorted by default - so Galaxy's bam datatype
would be better thought of
Hi all,
My galaxy is the last update and I work with samtools 1.2.
I have a bug with the sorting and the upload of bam file.
This bug appears only when I try to upload bam sorted by name or when
I try to sort by name.
When I work with bam sorted by coordinate, there is no problem.
So, when I try
