I wanted to remove all the non-standard reads (reads from non-standard
chromosomes) from a bam file. I used Slice bam and the bed file contained all
of the chromosome lengths for chr1-22, x, and y. But all I get back in the bam
file are the unaligned chromosomes.
What am I doing wrong?
Jean
Galaxy Community,
Based on popular demand, we are pleased to announce another Galaxy training
event for this year. BioTeam and the Galaxy Team are offering a training
session that will focus on analyzing NGS Data using Galaxy. In addition to
learning about the NGS related Galaxy features, you
Hi Rico,
This should be fixed in 10742:3de162c29e7e.
Thanks for reporting this,
Greg Von Kuster
On Sep 27, 2013, at 12:18 PM, Richard Burhans wrote:
> Greg,
>
> I was mistaken. It wasn't a GET, it was a POST. Here's the POST request:
>
> POST
> /admin_toolshed/prepare_for_install?include
Greg,
I was mistaken. It wasn't a GET, it was a POST. Here's the POST
request:
POST /admin_toolshed/prepare_for_install?
includes_tools_for_display_in_tool_panel=True&encoded_repo_info_dicts=72
2fdbb60840f8caa6f7dd248a9f08b927df4325%
3A7b22746573745f6c6f6e675f757269223a205b22746573742074
The link for datasets is dead:
http://screencast.g2.bx.psu.edu/usinggalaxy_datasets/flow.html
thanks,
Kevin___
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and other Gal
Make the precedence a config option. Otherwise I agree.
In addition, I still like the idea I suggested earlier of dependency provider
plugins. Then you could (for example) have one that uses 'modules' and skips
env.sh entirely.
On Sep 26, 2013, at 9:15 PM, John Chilton wrote:
> I was not even
Hi all,
This is a slight change to my usual theme of completely missing
nightly test results ;)
Looking at
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/70e7dcbf6573
(Main Tool Shed) or
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/aecdffbc08fc
(Test Tool Shed) toda
Il giorno ven, 20/09/2013 alle 10.25 -0500, John Chilton ha scritto:
> On Fri, Sep 20, 2013 at 9:08 AM, Nicola Soranzo wrote:
> >> First step is to create a new dynamic job destination, this is
> >> demonstrated in job_conf.xml in the above changeset. This demonstrates
> >> the new style job_conf
On Thu, Sep 26, 2013 at 10:27 PM, John Chilton wrote:
> My recommendation would be make the tool dependency install work on as
> many platforms as you can and not try to optimize in such a way that
> it is not going to work - i.e. favor reproduciblity over performance.
Reproducibility versus spee
