Hi Lance,
Thank you for finding this issue and a bigger thanks for the patch. We've
updated FreeBayes in the toolshed with your patch. Please let us know if you
encounter further issues.
Thanks!
Dan
On Sep 11, 2012, at 5:08 PM, Lance Parsons wrote:
> Today I ran into a new issues with inst
Today I ran into a new issues with installing a specific version of
Freebayes. It turns out to be an issue with how git deals with
submodules, something I'm only just learning about myself. In order to
ensure that FreeBayes is built with the correct versions of all of the
various submodules f
Thanks for information Greg. Actually, it turned out to be two things
causing my issues:
1) My copy of tool-data/sam_fa_indices.loc.sample was not owned by the
galaxy user (though it was writable by that user). This caused the
exception which caused the installation to get "stuck" at "cloning
Hi Lance,
You'll need to execute the following sql manually in your Galaxy database.
update tool_shed_repository set status = 'New' where status = 'Cloning';
Next, you'll have to update your production Galaxy instance code base to at
least changeset 2531e085f262 (the human-readable changeset re
Thanks for the explanation. That makes sense. I went ahead and
installed the new version along with dependencies in my development
environments and all went well. Then in production, the installation
seems to have failed and I'm now stuck with freebayes in the "cloning"
status. I tried to de
Hi Lance,
This has to do with the way that the updating currently works. Since the
migrated version is 0.0.2, the automatic update will only update that
particular Tool version (newest version of 0.0.2). To get 0.0.3, you need to
install it as a new tool. This way you are able to have both vers
Thanks for the quick turnaround Dan. Much appreciated. When I tried to
test updating Freebayes from the toolshed, I get a message that no
updates are available. Perhaps it takes some time before they are
recognized? Or am I missing something?
Lance
Daniel Blankenberg wrote:
Hi Lance,
Tha
Hi Lance,
Thank you for the pull request. I think this is an excellent way to handle
patches until the toolshed itself provides a better mechanism, particularly for
the devteam owned repositories; other repository owners may prefer different
methods of providing patches, but they can be contact
I have been using the FreeBayes tool in our local Galaxy instance for
some time. As FreeBayes is a rapidly evolving tool, it has been very
helpful to have Daniel Blankenberg work on keeping an updated wrapper.
Recently, I've run into a rather troublesome bug in FreeBayes
(https://github.com/e
I just tried via command line and re-did the steps that Galaxy attempted on the
same files. I got through the samtools sorting of the bam file without a
problem, but then soon saw the same error when I tried executing freebayes
itself:
[perin@variome 000]$ freebayes --fasta-reference
/share/a
Juan,
I'm not sure of a likely cause of this error off the top of my head. Have you
tried running Freebayes from the command line on the same data input? That
might be an easy way to explore what particular options with the newer version
of Freebayes that you have are causing issues, or perha
This fix got me further, however I'm now getting the following error, which is
now more confusing...
[bam_sort_core] merging from 40 files...
BGZF ERROR: unable to open file 1.0
BGZF ERROR: unable to open file 1.0
Could not open input BAM files
Juan
On Apr 1, 2011, at 1:53 PM, Dannon Baker wrot
Juan,
What version of freebayes are you running? The freebayes configuration in the
galaxy repository was written with the .4 series in mind, and it appears that
the options have changed with the .6 series. We'll update the tool config, but
in the meanwhile you could probably get it working a
I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment of
solid data. I keep getting the following error:
[bam_sort_core] merging from 40 files...
freebayes: invalid option -- Y
did you mean --bam ?
I'm not sure where this is set in the code to try to debug things. I'm
won
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