On Mon, Oct 8, 2012 at 8:26 AM, Joel Rosenberg wrote:
> So I'm trying to install the recently migrated ncbi_blast_plus tool from the
> Tool Shed to my local galaxy instance running in EC2 and am getting errors at
> the installation step.
>
> After clicking "Install to local Galaxy" I immediately
Hi Bjorn,
I saw that printed message but I decided not to append install_dependencies
flag to the command because we have had BWA binary in the galaxy running
environment.
I don't think the use of install_dependencies is compulsory?
Derrick
On Mon, Oct 8, 2012 at 5:14 PM, Björn Grüning <
bjoern
Hi Derrick!
> I saw that printed message but I decided not to
> append install_dependencies flag to the command because we have had
> BWA binary in the galaxy running environment.
> I don't think the use of install_dependencies is compulsory?
Sorry, im not sure if it is compulsory. But i would
Jim Johnson and I have been discussing that approach to handling
fractionated proteomics samples as well (composite datatypes, not the
specifics of the interface for parallelizing).
My perspective has been that Galaxy should be augmented with better
native mechanisms for grouping objects in histor
Hi guys,
I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via
the migration script. However, I couldn't find any entry has been added
in migrated_tools_conf.xml (thus the BWA tools are not display in the tool
panel).
I check in the admin "Installed tool shed repositories" sec
Hi Derrick,
I am not able to reproduce this behavior, so it's difficult to tell what
problem may have occurred that resulted in the entries for the bwa tools to not
be added to you migrated_tools_conf.xml file. Choosing to install or not
install tool dependences makes no difference in whether
On Sun, Oct 7, 2012 at 3:02 PM, Shane Sturrock wrote:
> using xemacs, just the terminal based one. And typing a raw
> tab involves a tedious control sequence... there probably is an
> easier way, but I don't edit these loc files very often.
>
>
> Just hit 'Tab' in vi.
Somehow I don't think this w
Hello everyone,
We are working with Next Generation Sequencing tools on Legionella
pneumophila.
When trying to use NGS Tools such as Bowtie or BWA on the Main instance of
Galaxy, L. pneumophila genomes are not available, although they are listed
in the Data Libraries, at
http://wiki.g2.bx.psu.edu/
(Apologies if this is in duplicate, Peter Cock may have forwarded it on after I
posted it to the user list)
So I'm trying to install the recently migrated ncbi_blast_plus tool from the
Tool Shed to my local galaxy instance running in EC2 and am getting errors at
the installation step.
After
Looks great, committed in -central changeset 02fe49c3d251
Best,
J.
On Oct 6, 2012, at 6:31 PM, Björn Grüning wrote:
> Hi all,
>
> if we try to wrap a single script-tool, for example bismark [1], it has
> its own version number and should be included in .
> I would like to ship bismark with the
Hello,
I've been learning about the tool shed, as precipitated by the decision to move
the blast tool out of the standard distribution.
(I'm having a problem doing so as documented here:
http://dev.list.galaxyproject.org/Cannot-install-ncbi-blast-plus-or-other-tools-from-Tool-Shed-HTTP-500-err
This looks fantastic Brad and we should be able to integrate it soon. I have a
couple questions, though, and I've noted them in the request's comments section.
Best,
J.
On Oct 4, 2012, at 3:44 PM, Brad Chapman wrote:
>
> Hi all;
> I've been thinking about ways to upload into user histories via
Jeremy;
Brilliant, thanks for looking at this. I explained the intent of that
code more in the comments and happy to answer any other questions.
While you're looking at the API, would you also be willing to consider
this pull request:
https://bitbucket.org/galaxy/galaxy-central/pull-request/77/p
Hi Greg,
I did another test on a fresh installed galaxy Oct 5 release, I simply
cloned from the galaxy-dist, start the server once so everything's
populated, then here was how I ran the migration script and output:
pwbcad@gamma00:galaxy-dist$ sh ./scripts/migrate_tools/0005_tools.sh
No handlers c
Velveth wrapper passes the location of the database/files/xxx/dataset_yyy_files
to the velveth as an argument. Same paths are put into the output html file.
This method can't work anymore when jobs are submitted under real user names as
a real user doesn't have write permissions outside of the e
Can I actually just skip executing the migration script, and just install
BWA from the tool shed like I did for other shed tools?? Should be fine I
guess?
Derrick
On Tue, Oct 9, 2012 at 11:49 AM, Derrick Lin wrote:
> Hi Greg,
>
> I did another test on a fresh installed galaxy Oct 5 release, I s
> I explained the intent of that
> code more in the comments and happy to answer any other questions.
Everything makes sense; I've accepted the pull request.
> While you're looking at the API, would you also be willing to consider
> this pull request:
>
> https://bitbucket.org/galaxy/galaxy-cent
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