HI Jennifer,
Thanks for the kind email reply. I think what you wrote "pull from central
individual changesets as desired" should be the way that I like to try out.
The question is do you know the patch name for the nglims? Or I need to talk to
the nglims developers as you mentioned in your emai
Hi Peter,
This is the correct list to post to (not owner, that is just for list
subscription questions).
http://wiki.galaxyproject.org/MailingLists
Galaxy-dist is the stable release repository. Galaxy-central is the
active development repository. Depending on how risk-tolerant your
project i
When Galaxy reads and updates the integrated_tool_panel.xml file,
tools in multiple sections can be lost.
1) Install tool shed repository A into section A
2) Install tool shed repository B into section B
3) Edit integrated_tool_panel.xml to put a tool from repository B
in
Hi Matt,
Have a look here:
http://wiki.galaxyproject.org/Tool%20Shed
There were also some good overview talks at GCC2013,
http://wiki.galaxyproject.org/Events/GCC2013
If your work would be better as an enhancement to an
existing Tool Shed repository, then you could try to
contact the author - th
Hi Bjoern,
I can see man years of effort being spent on solving this problem within
Galaxy. I was going to title this email "Danger, Will Robinson", but I didn't
want to be disrespectful. I think the path being embarked upon, tool
dependency packaging, tool versioning, reproducibility, and lo
Hi,
I've reported the jobs running out of order issue before.
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014777.html
We use mysql database. It seems rather random, but it might be only jobs taking
multiple inputs. I'll check that if it happens.
I've not found a solution yet.
Geer
On Tue, Sep 17, 2013 at 4:16 PM, Matthew Paul wrote:
> Hey guys,
>
> I have been working witha local Galaxy for a couple of months now on a
> cluster. I have created a few tools and would like to know if you would like
> to include them in the central repository (or how I go about suggesting so).
Hey guys,
I have been working witha local Galaxy for a couple of months now on a
cluster. I have created a few tools and would like to know if you would
like to include them in the central repository (or how I go about
suggesting so).
I created a statisticss computer for de novo assembly builds.
Sqlite is absolutely not intended for production use. With multiple users or
complex components you will definitely see database locked. Use Postgres.
On Sep 16, 2013, at 9:48 PM, Nikhil Joshi wrote:
> I am not using CloudMan, but we do use a sqlite database. It seems to have
> that behavior
Hi,
Galaxy provides the option for users to change their login email. However, if
they do, they loose access to their ftp folder. Is there an option to allow
galaxy to rename these folders?
Best,
Geert
___
Please keep all replies on th
Hi John,
> On Tue, Sep 17, 2013 at 3:03 AM, Bjoern Gruening
> wrote:
> > Hi all,
> >
> > that is now implemented in:
> >
> > https://bitbucket.org/galaxy/galaxy-central/pull-request/219/implementation-of-the-a-r_environment-to/diff
> >
> > Any comments are much appreciated.
>
> Fantastic work, I
Heya, Michael
I'm currently working in this area as well now - so no worries if your
schedule doesn't permit.
The card is here: https://trello.com/c/c2AzV3Xf
Any feedback is appreciated.
On Mon, Sep 16, 2013 at 11:42 AM, Michael E. Cotterell <
mepcotter...@gmail.com> wrote:
> Over next couple
Hi,
I'm enjoying a lot using Bioblend to develop CLI toolbox to interact
with Galaxy API. I recently hit an issue regarding how to deal with
inputs after running a workflow.
bioblend.galaxy.workflows.run_workflow()[1] has an argument
import_inputs_to_history. From the documentation:
"import_input
On Tue, Sep 17, 2013 at 3:03 AM, Bjoern Gruening
wrote:
> Hi all,
>
> that is now implemented in:
>
> https://bitbucket.org/galaxy/galaxy-central/pull-request/219/implementation-of-the-a-r_environment-to/diff
>
> Any comments are much appreciated.
Fantastic work, I like this a lot.
> Is it still
On Tue, Sep 17, 2013 at 7:43 AM, Bjoern Gruening
wrote:
> Hi,
>
> oh I see. Great! I would vote to include them in the main samtools
> package and extend the help text a little bit, so that the search will
> find it.
Seconded, this would be helpful for some stuff I have been working on as well.
Hi,
oh I see. Great! I would vote to include them in the main samtools
package and extend the help text a little bit, so that the search will
find it.
If you like you can add it to:
https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_samtools_0_1_19
I have grant
On 9/17/13 7:08 AM, Bjoern Gruening wrote:
Hi JJ,
I've had occasion to use some of the samtools misc utilities in galaxy
tools.
Should those also be copied to the $INSTALL_DIR/bin when
package_samtools is installed?
Sorry, I do not get the question :(
Are you asking to enhance the existing sam
Hi JJ,
> I've had occasion to use some of the samtools misc utilities in galaxy
> tools.
> Should those also be copied to the $INSTALL_DIR/bin when
> package_samtools is installed?
Sorry, I do not get the question :(
Are you asking to enhance the existing samtools definition?
> Thanks,
>
> J
I've had occasion to use some of the samtools misc utilities in galaxy tools.
Should those also be copied to the $INSTALL_DIR/bin when package_samtools is
installed?
Thanks,
JJ
--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
___
On Tue, Sep 17, 2013 at 11:14 AM, Richard Kuo wrote:
> Hello,
>
> It looks like the default wrapper that comes with Galaxy for Tophat2 and
> Bowtie2 does not include options for selecting how many threads/cores to
> use. Is there an easy way to get this feature in the wrappers or do I simply
> nee
Hello,
It looks like the default wrapper that comes with Galaxy for Tophat2 and
Bowtie2 does not include options for selecting how many threads/cores to
use. Is there an easy way to get this feature in the wrappers or do I
simply need to add it to the wrapper code? I
Alternatively, does anyone kn
On Tue, Sep 17, 2013 at 10:05 AM, Bjoern Gruening
wrote:
> Hi,
>
> I want to start a discussion about the storage of tarballs to guarantee
> the availability to some degree. Currently, I store most of my tarballs
> in my github account, if I do not trust the official ftp/http server.
> Anyone has
Hello all,
Bjoern and I were talking about doing some work on more
datatype definitions, but this raises the question about how
to handle dependencies.
First of all, complex datatypes in Galaxy are defined using
Python code, so any Python dependency must be available
to the main Galaxy process (u
Hi,
I want to start a discussion about the storage of tarballs to guarantee
the availability to some degree. Currently, I store most of my tarballs
in my github account, if I do not trust the official ftp/http server.
Anyone has the same problems/concerns? Is there an official
guideline/recommenda
Hey Galaxy,
I am trying to use CuffDIff with replicate analysis on a local instance. I
saw that Jeremy Goecks had a solution to this problem:
http://user.list.galaxyproject.org/Cuffdiff-changes-tt4655893.html#a4655901.
Could I see/use this source code please? I can't really wait until the next
upd
Hi Nikhil,
do you use the CloudMan?http://wiki.galaxyproject.org/CloudMan
I have such a behaviour when I used the sqlite database and not
postgresql.
Cheers,
Bjoern
> Hi all,
>
>
> So we use Galaxy to teach our bioinformatics courses and we have an
> install of Galaxy in the Amazon cl
Dave,
The space isn't there in my actual XML file. I must have accidentally
put the space there while constructing the email.
The URL that fails with the 404 error is actually correct (as stated in
my first post). This means that it successfully obtained the URL from
the XML file. So I suspect th
Hi James,
thanks for your thoughts on abstraction of common tasks.
For most of these things we have now patches in bitbucket.
> Similar recipes could be:
>
> autoconf: default to configure; make; make install, allow providing
> configuration options
https://bitbucket.org/galaxy/galaxy-central/p
I did an extra test. Started with a clean 'galaxy-dist'. This time
both repositories fail with the same error. I guess before something
was cached for the repository with version 0.1.4.
I used biopython repository as a guide to write my tool dependency definition:
http://testtoolshed.g2.bx.psu.edu
Hi Carlos,
> On Mon, Sep 16, 2013 at 4:19 PM, Peter Cock wrote:
> > On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
> > wrote:
> >> I did an extra test. Started with a clean 'galaxy-dist'. This time
> >> both repositories fail with the same error. I guess before something
> >> was cached for the
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