Hi Alexander,
Am 19.06.2015 um 01:44 schrieb Alexander Vowinkel:
> Hi,
>
> when I 'produce' a bam file in my output, I can download the bam file and a
> corresponding bai file.
>
> I am now wondering where does the bai file come from?
From Galaxy! :)
Galaxy has a concept of datatypes and metada
The response speed is awesome!
On github Eric answered:
https://github.com/galaxyproject/tools-iuc/blob/0887009a23d176b21536c9fd8a18c4fecc417d4f/tools/bedtools/multiCov.xml
> see L12 of that file for where the bai file is stored.
That explains a lot. Very precise example. Thank you!
What I'm s
Hi,
when I 'produce' a bam file in my output, I can download the bam file and a
corresponding bai file.
I am now wondering where does the bai file come from?
When is it being generated, what code is used for that?
When I do multiple actions with my bam file - is the index generated every
time? (o
Hi,
in
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros,
macros are defined with
[...]
But when I look in IUC macros, I find the following:
[...]
Which one is the current standard?
Best,
Alexander
___
I have opened a fix for this here -
https://github.com/galaxyproject/galaxy/pull/371. Sorry about that and
thank you for the detailed bug report.
-John
On Thu, Jun 18, 2015 at 11:17 AM, Ryan G wrote:
> In scripts/functional_tests.py, line 71, the change is causing a directory
> called "test-data
Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4,
which downloads bowtie binaries from depot.galaxyproject.org
http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.4-linux-x86_64.tgz
Jobs submitted on our setup, running as a 'real user' (not galaxy use
Hi all,
The table_recalibration tool cannot be installed through tool_shed. There seems
to be a broken link for the repository.
(https://toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/gatk_table_recalibration/0.0.5)
Here is the most recent log from the "Automated tool test results"
(We discussed this over IRC, but responding to the list posting for
posterity/searchability)
The JSON.pm file isn't found in your PERL5LIB path because the original
version of my JBrowse tool failed to specify the full dependency list and
assumed you had some perl modules manually installed.
The
In scripts/functional_tests.py, line 71, the change is causing a directory
called "test-data,https://github.com/galaxyproject/galaxy-
test-data.git" to get created. I'm not sure that's the intention of this
fix.
default_galaxy_test_file_dir is assigned to test_dir, then never used
again. test_di
We’re going to try this one now: https://connect.johnshopkins.edu/r283zwzv0yi
On Jun 18, 2015, at 11:09 AM, Hans-Rudolf Hotz wrote:
> sorry my (copy paste) mistake
>
> https://connect.johnshopkins.edu/galaxyadmins201506/
>
>
> On Jun 18, 2015, at 5:08 PM, Christian Brenninkmeijer
> wrote:
sorry my (copy paste) mistake
https://connect.johnshopkins.edu/galaxyadmins201506/
On Jun 18, 2015, at 5:08 PM, Christian Brenninkmeijer
wrote:
> Does anyone have a link to the meeting?
> Page below only has a general link not to this meeting.
> From: galaxy-dev [galaxy-dev-boun...@lists.gala
Does anyone have a link to the meeting?
Page below only has a general link not to this meeting.
From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of
Hans-Rudolf Hotz [hansrudolf.h...@fmi.ch]
Sent: Thursday, June 18, 2015 4:03 PM
To: Galaxy Dev
Hi everyone, the online meetup will (hopefully) start in a few minutes at:
https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_06_18
Regards, Hans-Rudolf
On Jun 15, 2015, at 3:47 PM, Dave Clements wrote:
> Hello all,
>
> The June 2015 online GalaxyAdmins meetup will be this
Thanks Bjoern
My initial install didn't pick up the Perl dependencies correctly, but I
re-installed and now the install seems to have the required modules but is
missing something in the environment variables. Specifically I get an error
import JSON.pm, see below. Note that the
jbrowse/1.11.6/iuc/
Peter,
I'm in a hurry ... have a look at
https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse
Developed by IUC member Eric Rasche.
Cheers,
Bjoern
On 18.06.2015 10:00, Peter van Heusden wrote:
I've tried that - I've added the Environment Modules for the relevant
tools to the l
I've tried that - I've added the Environment Modules for the relevant tools
to the local_env.sh file, so they're there in the environment when Galaxy
runs. These tools are scheduled via our cluster, however, so I don't think
the environment passes across to them. They depend on these Galaxy
package
On 06/18/2015 09:06 AM, Peter van Heusden wrote:
Hi there
I'm trying to visualise some of our genome data using Trackster. Initial
input is 790,000 lines of GFF3. When I try and create the visualisation,
I get errors from two tools:
Convert GFF to Interval Index on data 3
-- an out of memory
Hi there
I'm trying to visualise some of our genome data using Trackster. Initial
input is 790,000 lines of GFF3. When I try and create the visualisation, I
get errors from two tools:
Convert GFF to Interval Index on data 3
-- an out of memory error - I'll try and fix this by upping the memory
l
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