are the precise steps you took to produce
the behavior?
Keep in mind that the Galaxy test tool shed tracks the galaxy-central
repository on bitbucket while the Galaxy main tool shed tracks the galaxy-dist
repository on bitbucket.
Greg Von Kuster
On Dec 2, 2012, at 11:36 PM, Franco Caramia wrote:
URL
Hello Fab,
What version of Galaxy are you running? Did you install it from the
galaxy-dist repo on bitbucket? Am I understaning correctly that you are using
a symbolic link to point your installation directory to
/var/lib/galaxy-server/shed_tools? If so, why not just set the config setting
://wiki.galaxyproject.org/GalaxyToolPanel
Greg Von Kuster
On Nov 16, 2012, at 2:52 AM, Andreas Kuntzagk wrote:
Thanks, that helps in this case.
But I might also need the ids for other toolshed tools to adjust the job
runner settings.
Andreas
On 15.11.2012 15:23, Greg Von Kuster wrote:
Hi Andreas
/repository_name
repository_ownerdevteam/repository_owner
installed_changeset_revisione0232cbac965/installed_changeset_revision
idtoolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0/id
version1.56.0/version
/tool
Greg Von Kuster
this, try
%sh run.sh
which will start up your Galaxy server. Then you can run any of the tool
migrations you want by getting the commands from the Admin menu link.
Let me know if this works.
Greg Von Kuster
On Nov 15, 2012, at 11:39 AM, Anne Pajon wrote:
Hi Greg,
No change at all, how can I
|
| roche454_toolsuite |
| toolfactory|
++
4 rows in set (0.00 sec)
The mothur entries in 'shed_tool_conf.xml' file and the mothur repository are
still existing.
Cheers,
Mathieu Bahin
De: Greg Von Kuster g...@bx.psu.edu
À: Mathieu Bahin mathieu.ba
trace of the exception thrown due to the problem. What is this this
complete stack trace?
Thanks,
Greg Von Kuster
On Nov 12, 2012, at 4:56 AM, Mathieu Bahin wrote:
And here is the paster...
De: Mathieu Bahin mathieu.ba...@irisa.fr
À: Greg Von Kuster g...@bx.psu.edu
Cc: galaxy
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
Cheers,
Mathieu
De: Mathieu Bahin mathieu.ba...@irisa.fr
À: Greg Von Kuster g...@bx.psu.edu
Cc: galaxy-...@bx.psu.edu
Envoyé: Lundi 12 Novembre 2012 15:54:35
Objet: Re: [galaxy-dev] Bug report
in the Galaxy instance in case
this is what you're looking for.
http://wiki.galaxyproject.org/ToolShedToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time
Greg Von Kuster
On Nov 12, 2012, at 1:51 AM, Kevin Y wrote:
Hi dev list,
What is the simplest xml I can
Hi Peter,
I've tweaked the template for this email in change set 8211:3024a86c0d0d, which
is currently running on the test tool shed. It'll be moved to the main tool
shed 2 Galaxy releases from now - I'm not quite sure of the date of that
release.
Thanks for requesting this fix.
Greg Von
by the tool shed's installation process. This is the same approach
used for the tool_conf.xml file, where the Galaxy tool shed repository
installation process uses the shed_tool_conf.xml file.
Thanks Derrick,
Greg Von Kuster
Cheers,
D
On Fri, Nov 9, 2012 at 2:10 AM, Greg Von Kuster g
Hello Mathieu,
What version of Galaxy are you running? Also, I cannot read the stack trace
from your pasted image, so can you send a text version of the complete stack
trace from your paster log?
Thanks,
Greg Von Kuster
On Nov 9, 2012, at 11:26 AM, Mathieu Bahin wrote:
Hi,
I am using
they may have caused.
Greg Von Kuster
On Nov 7, 2012, at 8:19 PM, Derrick Lin wrote:
It's actually in related to a new galaxy shed tool we developed called
meme-chip, we uploaded it to the main Tool Shed site.
We provided tool_data_table_conf.xml.sample and xxx.loc.sample along
Greg Von Kuster
On Nov 7, 2012, at 6:29 PM, Philipe Moncuquet wrote:
Hi developers,
We have our own instance running and under continuoius development.
I installed velvetg and velveth from the toolshed (revision 0:4afe13ac23b6)
and manually installed binaries for velvet_1.2.08.
When I try
On Oct 29, 2012, at 9:23 PM, Todd Oakley wrote:
I changed the name of this thread, to go in a related by new direction:
I wonder if the Galaxy developers and community have any opinions on what is
the best way to organize tools into repositories. We've developed a large
number of tools
in
repositories in the tool shed. These repositories in the main Galaxy tool
shed provide some good examples: htseqcount, emboss_5, freebayes, picard
Greg Von Kuster
On Oct 26, 2012, at 1:49 AM, Franco Caramia wrote:
Hi Greg,
Sorry to ask you something unrelated.
Where can I find
+, so I made
some changes to support Python 2.5+.
Please let me know if you have additional questions regarding this.
Thanks very much for your contributions!
Greg Von Kuster
On Oct 15, 2012, at 1:15 PM, Björn Grüning wrote:
Hi,
i'm writing a galaxy wrapper for bismark and trim-galore. Both
,
Greg Von Kuster
On Oct 22, 2012, at 7:03 AM, Peter Cock wrote:
FAO the Galaxy dev team,
I've tested a patch (at end of email) which issues a warning if loading
a loc file with inconsistent numbers of tabs. In the case of blastdb_p.loc
this would result in showing the warning three times
/datatypes_conf.xml
tool-data/gmap_indices.loc.sample
You can contact the repository owner via the Contact repository owner option
in the Repository Actions pop-up menu when viewing the repository.
Greg Von Kuster
On Oct 24, 2012, at 12:27 PM, Carlos Borroto wrote:
Hi,
I get a HTTPError: HTTP
.
# Enabling remote user disables regular logins. For more information, see:
# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
use_remote_user = True
Thanks!
Greg Von Kuster
On Oct 24, 2012, at 1:53 PM, David Hoover wrote:
One more question. Is there any hope of having external authentication
to the
October 5 release in order to have these features.
The news brief release information is:
upgrade: $ hg pull -u -r b5bda7a5c345
Let me know if this is not what you're looking for.
Thanks,
Greg Von Kuster
This worked fine for fixing failed installs. But, this
time, I thought (wrongly
of it into the next release if appropriate.
Greg Von Kuster
On Oct 15, 2012, at 1:15 PM, Björn Grüning wrote:
Hi,
i'm writing a galaxy wrapper for bismark and trim-galore. Both are plain
perl scripts, that wraps around other dependencies (e.g. Bowtie). The
idea was to include the perl-scripts directly
Hello Clare,
On Oct 16, 2012, at 1:02 AM, Clare Sloggett wrote:
Hi all,
I managed to break a toolshed-installed tool by fiddling with the
files under shed_tools.
As you've discovered, this is not a good thing to try. Always use the Galaxy
interface features to perform tasks like this.
of
the tool shed wiki:
http://wiki.g2.bx.psu.edu/ToolShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
Sorry for the confusion the Admin wiki you were using caused.
Greg Von Kuster
On Oct 10, 2012, at 12:07 AM, Derrick Lin wrote
My comments inline...
On Oct 10, 2012, at 4:39 PM, John Chilton wrote:
Comments inline.
On Wed, Oct 10, 2012 at 2:35 PM, Mark Johnson mjohn...@ncbi.nlm.nih.gov
wrote:
Thanks for the quick turnaround. On the contrary, your examples are very
helpful. I'll try your approach. I haven't
communicate information to the
community when things are worked out.
Thanks,
Greg Von Kuster
On Oct 9, 2012, at 8:01 AM, Lukasse, Pieter wrote:
Hi Greg,
I noticed I don’t have access to
https://bitbucket.org/galaxy/galaxy-central/issues anymore. I logged some
cases there before and I
idtoolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2/id
version1.0.2/version
/tool
/section
Greg Von Kuster
On Oct 8, 2012, at 1:55 AM, Derrick LIN wrote:
Hi guys,
I have updated the galaxy to Oct 5 dist, and BWA has been reinstalled via
items from your
tarball like .hg subdirectories.
You could also choose to not use a source code revision system in your
TOOL_DEV_LOCAL_DIR if that is more appropriate.
Greg Von Kuster
On Sep 27, 2012, at 5:02 PM, Greg Von Kuster wrote:
Hi Lance,
On Sep 27, 2012, at 4:37 PM, Lance Parsons
be changed only until the first
clone occurs. Once a clone occurs, the cloned repository path includes the
name of the repository, so if it was subsequently changed in the tool shed,
those that cloned it previously could not get updates to their local clones.
Greg Von Kuster
Thanks,
Joachim
/RepositoryRevisions
Greg Von kuster
On Sep 27, 2012, at 9:42 AM, Joachim Jacob wrote:
Hi Greg,
Indeed, I mean the tool config wrapper, named razers3_wrapper.xml, when I
mention 'tool config'.
This xml is the alpha version, and is loaded correctly in my development
Galaxy. So I pushed
Hello Peter,
My recent change set 7753:c28c5f906c6b added the ability to view a tool shed
repository's README file from the pop-up menu on pages in the tool shed
repository as well as in the Galaxy Admin UUI for installed repositories.
Since many of these README files are rather large, I
Hi Peter,
I've handled this request in change set revision 7761:9972ac6ee91d, which will
be included in the next Galaxy release scheduled for about 10 days from now.
Thanks!
Greg Von Kuster
On Aug 28, 2012, at 9:48 AM, Peter Cock wrote:
P.S. It would be nice to automatically line wrap
to the tool shed repository.
So, the path is something like:
TOOL_DEV_LOCAL_DIR pushes new changes to your tool shed repository, and others
in the Galaxy community clone from your tool shed repository, including updates
you committed over time
Greg Von Kuster
I've added some comments inline
.
Let me know if I can help track things down any further, etc. Thanks.
Lance
Greg Von Kuster wrote:
Hi Lance,
On Sep 21, 2012, at 6:04 PM, Lance Parsons wrote:
OK, I was able to get a new version installed. It seems there are two
issues:
1) New revisions with the same version
. That seems to more reliably
parse metadata. Will let you know what, if anything, works. Thanks.
Lance
Greg Von Kuster wrote:
Hello Lance,
I've just committed a fix for getting updates to installed tool shed
repositories in change set 7713:23107188eab8, which is currently available
Hi Peter, see below...
On Sep 20, 2012, at 9:43 AM, Peter Cock wrote:
On Thu, Sep 20, 2012 at 2:16 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Sep 20, 2012, at 5:53 AM, Peter Cock wrote:
Hi all,
I'd like to check (before I try this), if is this expected to work
hope this is what you
intended, but if not, let me know and I'll help with what's needed.
Contents:
fastq_groomer_parallel
README
fastq_groomer_parallel.py
fastq_groomer_parallel.xml
Thanks,
Greg Von Kuster
On Sep 18, 2012, at 7:44 PM, kevyin wrote:
Hi Greg,
Thanks for the toolshed links I'll
Hi Jim,
thanks very much for catching this and providing the fix (I've been away from
email for a few days, so am just getting caught up). I've committed this in
change set 7705:ba64c2178fbe.
Greg Von Kuster
On Sep 17, 2012, at 5:13 PM, Jim Johnson wrote:
Greg,
I think templates/admin
repository.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_repositories_installed_in_a_local_Galaxy_instance
Let me know if there is anything I can do to help sort this out.
Lance
Greg Von Kuster wrote:
Hi Lance,
What is the changeset revision that you installed
Von Kuster
Regards,
Kevin.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu
Hi paul,
We'll need enough information from your paster log to determine the problem.
If your server threw an exception, you may also have a stack trace in your
browser window and we'll need that infomration as well.
Thanks,
Greg Von Kuster
On Sep 13, 2012, at 10:38 PM, Paul Tanger wrote
Paul,
Glad to hear things are working. The next install should go more easily now
that you've done the first one, which is always the hardest.
Let us know if you bump into any issues in the future.
Greg Von Kuster
On Sep 14, 2012, at 2:11 PM, Paul Tanger wrote:
ok, I forgot to set
that is created to set the value of the
R_SCRIPT_PATH environment variable.
Let me know if you bump into any issues in getting this working for your tools.
Thanks!
Greg Von Kuster
On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
Are there any environment variables that are honored by toolshed
week. You'll have to pull
from the Galaxy central repo if you want to use the fix before the next release.
Sorry for the inconvenience on this,
Greg Von Kuster
On Sep 10, 2012, at 4:30 PM, Birgit Crain wrote:
I downloaded the latest galaxy-dist this morning and I used the test toolshed
for the inconvenience.
Greg Von Kuster
On Sep 12, 2012, at 6:16 PM, David Hoover wrote:
I've created a repository in the test toolshed and tried uploading gzipped
tarballs with all files required. I have several tool config files (.xml)
wrapping a single python script with some tool-data dependencies
#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
Greg Von Kuster
On Sep 13, 2012, at 4:46 PM, Paul Tanger wrote:
Hi,
I'm trying to enable all the emboss tools on a local galaxy install.
I found this tidbit (below) which I thought might help, but when I
look at the tool_conf.xml, I
and contributions!
Greg Von Kuster
On Sep 10, 2012, at 2:45 PM, Björn Grüning wrote:
Hi Greg,
what did you think about the attached patch?
In my setup i have 'deployment folder' where i symlink all different
wrapper under a new logical structure for toolshed deployment. That
directory gets tarred
Hi Paul,
You have to be running the latest Galaxy dist release from
https://bitbucket.org/galaxy/galaxy-dist in your local Galaxy instance. Your
repository tip should be e6444e7a1685.
Greg Von Kuster
On Sep 13, 2012, at 5:24 PM, Paul Tanger wrote:
Hmm, ok this tool shed is all new to me
Hi Paul,
You should be able to get things working using the same sql command in the
email below. This process will be a new UI feature in the next Galaxy release.
Greg Von Kuster
On Sep 13, 2012, at 6:15 PM, Paul Tanger wrote:
Thanks for your help with this. So I updated to the latest
manual, but the next release of Galaxy (coming in
about 10 days) will provide the ability to do this via a Galaxy Admin UI
feature.
Greg Von Kuster
On Sep 11, 2012, at 11:48 PM, Oleksandr Moskalenko wrote:
Hi Greg,
What's the best way to completely clean up a borked repository on disk
...
/command
I'm close to having this working, so if you are interested in testing before
the next Galaxy dist release, let me know and I'll tell you when the Galaxy
central repository has the new feature.
Thanks!
Greg Von Kuster
On Sep 12, 2012, at 1:00 PM, David Hoover wrote:
Are there any
Hi David,
Can you send me your tarball?
Thanks,
Greg Von Kuster
On Sep 12, 2012, at 6:16 PM, David Hoover wrote:
I've created a repository in the test toolshed and tried uploading gzipped
tarballs with all files required. I have several tool config files (.xml)
wrapping a single python
Kuster
On Sep 12, 2012, at 1:47 PM, David Hoover wrote:
On the topic of toolshed tools, is there any documented guidance about how to
create a tool for the toolshed? There is some syntactical help on the wiki,
but no comprehensive guide.
On Sep 12, 2012, at 1:41 PM, Greg Von Kuster
. Did you install 4 and are trying to get
updates?
I've tried several things but am not able to reproduce this behavior, so it's
difficult to determine what may be causing the problem
Greg Von Kuster
On Sep 12, 2012, at 3:08 PM, Lance Parsons wrote:
I've updated my development system now
Hi Bjorn,
The main Galaxy tool shed is tracking the Galaxy-dist repository. Per requests
from the Galaxy community, it no longer tracks Galaxy-central.
Greg Von Kuster
On Sep 10, 2012, at 12:25 PM, Björn Grüning wrote:
Hi,
the toolshed is not starting with the latest galaxy-central
this information in your initial
emails in the future.
The main Galaxy tool shed now track the Galaxy dist repository on bitbucket.
Thanks,
Greg Von Kuster
On Sep 10, 2012, at 3:44 PM, Birgit Crain wrote:
Hi
I got a problem with the tool_data_table.xml and tool-data/*.loc files when
testing
components are fairly immature, so adding
enhancements for new tools like yours is very valuable.
Thanks for your help on this,
Greg Von Kuster
Any thoughts on how to address these issues would be appreciated.
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis
Galaxy release is
currently scheduled for Friday. so this problem will be fixed in the tool shed
at that time.
Sorry for the hassle on this,
Greg Von Kuster
On Sep 6, 2012, at 5:59 AM, Brad Chapman wrote:
Hi all;
I've been working on updating the bam_to_bigwig tool in the Toolshed
Hi Paul,
In case you are not aware of it, the Galaxy tool shed wiki explains the tool
shed: http://wiki.g2.bx.psu.edu/Tool%20Shed
On Sep 4, 2012, at 6:25 AM, Paul-Michael Agapow wrote:
I've inherited a galaxy setup from someone (details: a contractor set it up
but left it unfinished so
Hi Lance,
Thanks for reporting these issues - the tool dependencies component is fairly
new, so you may have uncovered some problems that need correction. I'll take a
look at these. make corrections if necessary, and get back to you when all is
functional.
Thanks!
Greg Von Kuster
On Sep 4
Von Kuster
On Aug 31, 2012, at 3:59 PM, Lance Parsons wrote:
Thanks for the explanation. That makes sense. I went ahead and installed the
new version along with dependencies in my development environments and all
went well. Then in production, the installation seems to have failed and I'm
dependencies
tool_dependency_dir = ../tool_dependencies
Greg Von Kuster
On Aug 29, 2012, at 9:34 AM, Philip Mabon wrote:
I upgrade Galaxy to changeset 2531e085f262 and attempt to install freebayes
from the admin panel.
It installed the freebaye xml tool and appears in the tool panel
to compile
samtools. If you find out what is missing from your environment you'll have to
install it. Then uninstall the samtools dependency using the Galaxy UI and
attempt to install it again.
Greg Von Kuster
On Aug 29, 2012, at 10:08 AM, Philip Mabon wrote:
Looks like I forgot to reset
if you do not need the freebayes tool
in your local instance immediately.
Sorry for the inconvenience I'm sure this is causing.
Greg Von Kuster
On Aug 27, 2012, at 4:18 PM, Philip Mabon wrote:
I already had that entry to the tool_data_table_conf.xml but still getting
the same error
release to the
galaxy-dist repository.
Greg Von Kuster
On Aug 22, 2012, at 9:19 AM, Peter Cock wrote:
Hi all,
This is an idea I mentioned to Dannon (off list during discussion
about moving the NCBI BLAST+ wrappers to the Tool Shed), and
he seemed positive about it.
Currently the left hand
something to
do with the server configuration (not a Galaxy issue).
Greg Von Kuster
On Aug 22, 2012, at 3:18 PM, Dan Sullivan wrote:
I apologize for spamming this list, the screenshot that I specified as
attached was supplied in a hyperlink farther down in the mail (not as an
attachment
Hello Hans,
I've committed a fix for this issue in changeset 7560:738b703f725c, which will
be included in the next Galaxy release. Thanks for reporting this!
Greg Von Kuster
On Aug 28, 2012, at 5:40 AM, Hans-Rudolf Hotz wrote:
Hi Greg
Thank you for your help. Although
the metadata on all repositories
using the Reset selected metadata option on the tool shed's Admin menu. Let
us know if this does not work.
Greg Von Kuster
On Aug 27, 2012, at 6:22 AM, Joachim Jacob wrote:
Hi all,
I want to change the location of the toolshed database. First I copied all
entry (tool or tool section) were
appended to the end of the section or panel rather than inserted into the
desired location. This is probably the cause of the behavior you are seeing.
This issue was corrected in the next Galaxy release after the March release.
Greg Von Kuster
On Aug 21, 2012
couple of weeks. I
have the implementation worked out in my head, and I don't think it will take
too long to finish once I can get started. I'll keep you and the community
informed as progress is made.
Greg Von Kuster
On Aug 23, 2012, at 9:12 AM, Peter Cock wrote:
Dear all,
Is there any way
entry.
Sorry for the long-winded answer - hopefully the context is helpful.
Greg Von Kuster
On Aug 23, 2012, at 10:11 AM, Peter Cock wrote:
Dear all,
Until recently I'd not needed to define new datatypes while
developing tools for Galaxy - instead using (and sometimes
modifying) existing
20, 2012 release).
All screen shots in my original e-mail (21-Aug) were made with a server
running the July release.
Regards, Hans-Rudolf
On 08/27/2012 02:18 PM, Greg Von Kuster wrote:
Hello Hans-Rudolph,
If I remember correctly, the release in March did not properly handle
That is the workaround I currently use.
Marc
This may result in a merge at some point if the contents of the
datatypes_conf.xml file changes in the emboss_datatypes repository in the
main tool shed and you pull the updates to your
local repository.
Greg Von Kuster
Hi Björn
Hi Edward,
On Aug 10, 2012, at 8:26 PM, Edward Turk wrote:
Hello,
I have a local instance, I am the only user, and I would like to use a tool
that is in the galaxy tool shed but not in my local instance.
After reading the toolshed wiki (http://wiki.g2.bx.psu.edu/Tool%20Shed) I
have a
Thanks for the help Bjorn, I've applied your patch in 1eab72ce0a48.
Greg Von Kuster
On Aug 9, 2012, at 4:11 AM, Björn Grüning wrote:
Hi,
galaxy-central does not start because of commit 9f790bc90769. The
attached patch should fix it.
Salve,
Bjoern
--
Björn Grüning
Albert-Ludwigs
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 08/02/2012 03:37 PM, Greg Von Kuster wrote:
allow_user_creation = False
___
Please keep
Hello Nikhil,
On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote:
Hi all,
We just upgraded our local galaxy to the latest version and now I am
trying to get automatic tool installation to work properly. I changed
the universe_wsgi.ini file to enable the toolshed xml file,
Regarding this, do
in the emboss_datatypes repository in the main
tool shed and you pull the updates to your local repository.
Greg Von Kuster
On Aug 3, 2012, at 10:51 AM, Marc Logghe wrote:
Hi Björn,
I think the issue is that the genbank datatype is coming in via the tool shed
and is not taken into account by the upload
view
return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith'
Any help is highly appreciated! BTW, it was really nice to get to
talk to you at the conference. :)
- Nik.
On Fri, Aug 3, 2012 at 3:49 AM, Greg Von Kuster g...@bx.psu.edu wrote
Hi Joachim,
Yes, add the following to the [app:main] section of your community_wsgi.ini
file.
allow_user_creation = False
On Aug 2, 2012, at 4:51 AM, Joachim Jacob wrote:
Hi,
Can I disable the account creation by users in our Galaxy tool shed?
Joachim
--
Joachim Jacob, PhD
Hi Shaun,
On Jul 31, 2012, at 9:37 AM, SHAUN WEBB wrote:
Hi, I have been trying out the latest version of Galaxy and a newly installed
local toolshed and I have a few questions/suggestions/bug reports:
1. Tool Versioning:
a) As I understand from the wiki, when I create a new version
PSORT tool is not being displayed as part
of what will get installed, it should still be installed along with the tools
that are being displayed.
Greg Von Kuster
On Jul 30, 2012, at 10:37 AM, Peter Cock wrote:
Why is this missing?:
* WoLF PSORT - Eukaryote protein subcellular localization
Both of these tables were introduced in the most recent Galaxy release.
On Jul 25, 2012, at 10:32 PM, Derrick Lin wrote:
ar..
Just saw the news brief, will that be possible that these two tables are
added as part of the Tool Shed and Admin Genome Indexing update??
Regards,
D
On Thu,
/DevNewsBriefs/2012_07_20
Greg Von Kuster
On Jul 22, 2012, at 3:48 PM, Pete Schmitt wrote:
I'm trying to install deseq_and_sam2counts from the main toolshed using the
admin interface in galaxy.
I get the following error:
The resource could not be found.
No action for /admin_toolshed
is included in the News Brief for the current Galaxy release
- see http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_07_20.
Greg Von Kuster
On Jul 15, 2012, at 7:19 PM, Ira Cooke wrote:
Hi Greg,
Thanks very much for the clarification. I'll just use a local toolshed for
now since there are not many
.
https://bitbucket.org/galaxy/galaxy-central/issue/779/fix-job-runner-to-handle-tools-installed
Thanks for reporting this, and sorry for the inconvenience.
Greg Von Kuster
On Jul 21, 2012, at 8:29 AM, hoove...@helix.nih.gov wrote:
I found the guid for the tool and tried the usual method
!
Greg Von Kuster
On Jul 20, 2012, at 8:51 AM, Jon Manning wrote:
Hi all,
I'm new to Galaxy- so hello, and excuse me while I get to grips with all the
conventions!
I've successfully got my local Galaxy (galaxy-central) install set up and
working correctly, as well as a local toolshed
using the correct id value. If it still doesn't work, let us know and
we'll get a fix asap.
Thanks!
Greg Von Kuster
On Jul 20, 2012, at 5:16 PM, David Hoover wrote:
Is there a way to configure a tool downloaded from the toolshed depot to use
a job runner other than the local runner
Hello Sabbirjoy,
In order to use the public Galaxy tool sheds you need to be running the tip
from Galaxy central. This will change as of the next Galaxy release, which I
believe is scheduled soon. After the next release, the tool sheds will follow
the Galaxy dist repository.
Greg Von Kuster
be available soon. I am not able to
fully test this fix though, so if you can let me know if problems still exist
when you get a chance to test it, I'll look further into the problem after the
GCC. Sorry for the inconvenience this has caused.
Thanks ver much!
Greg Von Kuster
On Jul 12, 2012, at 1:07
to begin tracking Galaxy dist.
Ultimately that will happen, it's just a matter of when.
I will, in fact, try to have the tool sheds track dist at this upcoming
release, but I cannot guarantee that fixes won't be necessary within the 8 to
10 week time frame between dist updates.
Greg Von
on this, but my schedule over the
next few weeks is very hectic. If you'll be at either ISMB or the GCC, we can
certainly get together to look at this.
Greg Von Kuster
On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote:
Hi, Greg,
I've still got issues after I downloaded the latest version from the dist
to the Galaxy code base in your
environment? Any additional information that you can send will help track down
the problem in your environment.
Thanks!
Greg Von Kuster
On Jul 11, 2012, at 2:46 PM, Anthonius deBoer wrote:
I'm getting this error when I try to run the tool migration:
sh ./scripts
...
Thanks
On Jul 11, 2012, at 12:29 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Thon,
What revision of Galaxy are you running? Have you made multiple attempts at
the migration? Are you running a postgres database? How many records do you
have in your tool_dependency table in your
PM, Anthonius deBoer wrote:
If I drop the following two tables, would those be reconstructed again
correctly if I had the XML files in order?
tool_version_association
and
tool_version
Thanks
Thon
On Jul 11, 2012, at 12:29 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Thon
How did you try to remove the tool? Do you mean that you used the Galaxy Admin
UI to Uninstall the repository? The datatypes are defined in a file named
datatypes_conf.xml in the installed gmap repository. Assuming you can
uninstall this repository, doing so will eliminate this problem.
Hi John,
On Jul 11, 2012, at 4:53 PM, John Chilton wrote:
On Wed, Jul 11, 2012 at 3:25 PM, Greg Von Kuster g...@bx.psu.edu wrote:
The way the tool shed components are architected do not result in this
syncing issues. You do not have to use the tool shed at all. Based on
your statements
the Galaxy central repository.
Greg Von Kuster
On Jul 10, 2012, at 5:45 PM, Peter van Heusden wrote:
I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed
using the Admin interface to Galaxy. Unfortunately, each time I do this
I get an error page with the message:
No action
from galaxy-dist to galaxy-central, or is a
re-installation necessary?
On 07/10/2012 11:56 PM, Greg Von Kuster wrote:
Hello Peter,
To use the public Galaxy tool sheds, your local Galaxy instance must be
running the tip from Galaxy central, not Galaxy dist. You need to be
running at least
the steps I
was referring to in my previous email are not necessary, but you should still
update your Galaxy to the tip asap.
Thanks Matthias!
Greg Von Kuster
On Jul 3, 2012, at 5:23 AM, Hollander, Mattias de wrote:
Hi Greg,
1. changeset: 7284:87be4c8d7f7f
2. toolbox tool_path=./shed_tools
3
301 - 400 of 648 matches
Mail list logo
