Just a heads up, I'm sure we the IUC will have Tool Shed packages
prepared for the samtools 1.3 etc release shortly.
However, I'm less clear what Galaxy itself is doing for sorting BAM
files - noting the original "samtools sort" API has been withdrawn.
Peter
-- Forwarded message ---
Hi Peter,
thanks for forwarding.
Afaik, we are using the pysam API for sorting extracting metadata since
a few releases.
So hopefully this will not be a problem.
Ciao,
Bjoern
Just a heads up, I'm sure we the IUC will have Tool Shed packages
prepared for the samtools 1.3 etc release shortly.
Hello all,
About a year ago I stated wrapping the "samtools bam2fq" command
from samtools v1.1 for use in Galaxy:
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_bam2fq
That uncovered a number of bugs in "samtools bam2fq" which have
resulted in two new commands "samtools fastq"
Thanks Youri,
That's the bit of code I was worrying about (BAM grooming). I've filed an
issue for this:
https://github.com/galaxyproject/galaxy/issues/1336
Peter
On Wed, Dec 16, 2015 at 9:47 AM, Y. Hoogstrate
wrote:
> Great news Peter,
>
> This is how Galaxy seems to do it:
>
> comma
Hello,
Does anyone know how to start my Galaxy instance with the history panel and
tool panel collapsed by default?
I used to do it by editing the galaxy/templates/base/base_panels.mako script
and adding
lp.do_toggle();
and
rp.do_toggle();
inside the if sections of %if self.has_left_panel:
Good morning Carl,
I had to go down to the last option -- but it WORKED
MD_zip
Thanks,
Bob
- Original Message -From: Carl Eberhard To:
rbrown1422@comcast.netCc: Eric Rasche , galaxy-dev
Sent: Tue, 15 Dec 2015 20:10:14 -
(UTC)Subject: Re: [galaxy-dev] How does one run Jav
