lShedToolFeatures#Automatic_third-party_tool_dependency_installation_and_compilation_with_installed_repositories
> How to secure R and bowtie2? Just by requirements?
Can you clarify this question?
> And their licenses?
See http://wiki.galaxyproject.org/ToolShedReadmeFiles
>
> Thanks
> Alex
>
> Van: Greg Von Kuster [mailto:g...@b
rrent definitions. I will
continue to update the tool shed wiki page as these definition tag sets evolve.
Thanks very much for your message and your contributions.
Greg Von Kuster
On Jan 30, 2013, at 10:49 AM, Jean-Frédéric Berthelot wrote:
> Hi list,
>
> When working to get a tool wrapper
ional
supporting content to be included in the repository (e.g., a
tool_data_table_conf.xml.sample file. etc)
If you could provide more details about what types of utilities you are
building, I can steer you to the wiki pages that provide information about
those specific utilities.
Thanks!
Gre
tes for citing a
specific repository revision, etc) but this should be a good start and it will
be in the next Galaxy release currently scheduled for next week.
Thanks very much for your contribution on this and please let me know if you
encounter any issues or have any additional suggestions.
Gre
Hi Peter,
Thanks for the update and your contributions. Would you like me to continue
with the work you've started, or would you like to continue yourself? I'll try
to fit this in this week if you want to hand it off to me. Please let me know.
Thanks!
Greg Von Kuster
On Jan 31
, but that's why it slipped by me until now.
Thanks for alerting me to this issue!
Greg Von Kuster
On Jan 31, 2013, at 9:40 AM, Peter Cock wrote:
> The following cryptic error is not helpful:
>
> $ sh run_community.sh
> Command 'serve' not known (you may need to run
Hi Peter,
The default sqlite database connection string has been uncommented in change
set 8707:5e60f2efceaf.
Thanks!
Greg Von Kuster
On Jan 31, 2013, at 9:48 AM, Peter Cock wrote:
> On Thu, Jan 31, 2013 at 2:40 PM, Peter Cock wrote:
>
> I noticed that the community_wsgi.ini.sa
Thanks Peter- I'll make sure to update the tool shed wiki accordingly as soon
as possible.
Greg Von Kuster
On Jan 31, 2013, at 9:48 AM, Peter Cock wrote:
> On Thu, Jan 31, 2013 at 2:40 PM, Peter Cock wrote:
>> Hi all,
>>
>> I was hoping to make some enhancements
believe the plan is to soon make the
development view public.
https://trello.com/card/change-the-references-to-community-in-the-galaxy-code-to-be-tool-shed-or-some-related-string-since-galaxy-tool-shed-replaced-the-original-galaxy-community-space/506338ce32ae458f6d15e4b3/186
Greg Von Kuster
O
Yes, the tool shed used to be named the Galaxy Community Space.
On Jan 29, 2013, at 11:14 AM, Peter Cock wrote:
> On Tue, Jan 29, 2013 at 4:04 PM, Peter Cock wrote:
>>
>> I was wondering about taking a look at this to see how hard it would
>> be - but my first query is where is the ToolShed s
ake a look.
Greg Von Kuster
On Jan 29, 2013, at 11:04 AM, Peter Cock wrote:
> On Mon, Jan 28, 2013 at 7:56 PM, Greg Von Kuster wrote:
>> I've opened a Trello card, but it's in the Galaxy development project, so
>> not sure if you can see it or not. Here's the link to t
We have only edited configuration files and .loc files
> for various tools.
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
> From: Greg Von Kuster [g...@bx.psu.edu]
> Sent: Tuesday, January 29, 201
cialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
> From: Greg Von Kuster [g...@bx.psu.edu]
> Sent: Tuesday, January 29, 2013 9:52 AM
> To: Waldron, Michael H
> Cc: galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-dev] Error trying to add tools
Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
> From: Greg Von Kuster [g...@bx.psu.edu]
> Sent: Tuesday, January 29, 2013 9:12 AM
> To: Waldron, Michael H
> Cc: galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-
re_for_install
description, repository_clone_url, changeset_revision, ctx_rev,
repository_owner, tool_dependencies = repo_info_tuple
However, that line no longer exists in the revision to which you've updated,
and line 1201 of the admin_toolshed.py file is now:
status = kwd.get( 'status', '
the development code
may include new features that are not available on the main tool shed since it
tracks Galaxy dist.
What is the result of typing the following in your Galaxy installation
directory?
hg heads
Thanks,
Greg Von Kuster
On Jan 29, 2013, at 8:38 AM, Waldron, Michael H wrote
Hello Carlos,
On Jan 28, 2013, at 5:13 PM, Carlos Borroto wrote:
> Hi,
>
> I'm trying to get lastz to show a locally cached reference. As I'm
> used to do I went ahead and copy tool-data/lastz_seqs.loc.sample(still
> included with galaxy-dist) to tool-data/lastz_seqs.loc and added my
> local ref
lem, and if not, we'll
figure out next steps if possible.
Thanks,
Greg Von Kuster
On Jan 24, 2013, at 4:36 PM, Kyle Ellrott wrote:
> I'm willing to put in the coding time, but I'd need some pointers on the best
> way to go about making the changes.
>
> Kyle
>
&g
2:28 PM, Peter Cock wrote:
> On Mon, Jan 28, 2013 at 6:49 PM, Greg Von Kuster wrote:
>> Hi Peter,
>>
>> Thanks for your request, having citable tool shed URLs is definitely
>> important. I've got this on my list (which is maxed out as usual).
>> I will
Hi Peter,
Thanks for your request, having citable tool shed URLs is definitely important.
I've got this on my list (which is maxed out as usual). I will look into this
in a timely manner and keep you posted appropriately.
Greg Von Kuster
On Jan 28, 2013, at 8:41 AM, Peter Cock
n the main Galaxy tool shed 2 Galaxy releases from now.
Thanks very much for reporting this!
Greg Von Kuster
On Jan 25, 2013, at 10:21 AM, Johannes Röhr wrote:
> Recently, I updated the Flexbar tool definition in the Galaxy Tool Shed
> repository flexbar to work with a new version o
alaxy instance will
not be a result of this particular issue however.
Greg Von Kuster
On Jan 19, 2013, at 3:25 PM, Anthonius deBoer wrote:
> Hi,
>
> I am seeing this in the log files when I start up...
> It seems to identify a name error in the file update_manager.py
>
> I am no
Hi Mark,
What version of Galaxy are you running, and what does your tool shed paster log
show?
Greg Von Kuster
On Jan 15, 2013, at 5:49 PM, wrote:
> Having followed the directions in “HostingALocalToolShed” I ran
> run_community.sh with the default configurations in community_wsgi.in
/Config/Tool%20Dependencies
tool_dependency_dir = ../tool_dependencies
Greg Von Kuster
On Jan 8, 2013, at 10:45 AM, Joachim Jacob wrote:
> Hi all,
>
>
> Updating our Galaxy: the migration of some tools to the toolshed (let's take
> picard as an example) and installing them ba
Hi Ted,
This looks like a good solution to me. I'll add your contributions to the
Galaxy code base as soon as I get a chance.
Thanks for all of your efforts on this!
Greg Von Kuster
On Jan 7, 2013, at 3:22 PM, Ted Goldstein wrote:
> Hi Greg and James,
> This has become a plumb
url_args=url_args,
allow_multiple=False,
async_compatible=False ) ]
return self.valid_repository_grid( trans, **kwd )
Sorry if I misunderstood you
Hello Thon,
Thanks for reporting this. This issue was corrected 2 weeks ago, but
unfortunately just missed the cutoff for the last Galaxy release. It will be
available in the next release currently planned for next week.
Greg Von Kuster
On Jan 3, 2013, at 6:18 PM, Anthonius deBoer wrote
version of Homer did you install before you uninstalled it and pulled the
new Galaxy revision?
What is displayed in your Galaxy paster log?
What is the result of executing the following sql manually in your Galaxy
database environment?
SELECT * FROM tool_shed_repository where name = 'ho
le optimal response to questions and issues.
Greg Von Kuster
On Dec 22, 2012, at 10:45 AM, Quang Trinh wrote:
> Hi Greg,
> Quick question: I am running off Amazon EC2 and when I do the
> upgrade, I get the following error:
>
> Not trusting file /mnt/galaxyTools/galaxy-central/.hg/h
n Galaxy and the tool shed
>will be backward compatible to this December 20 release, so new tool shed
>features introduced in the future will function for any Galaxy instance
>running the December 20 release or newer.
Greg Von Kuster
On Dec 22, 2012, at 9:53 AM, Quang Trinh wrote:
with the Galaxy
release currently scheduled for this week, the communication layer between
Galaxy and the tool shed will be backward compatible (to this week's release)
going forward.
Greg Von Kuster
On Dec 16, 2012, at 11:52 PM, Kyle Ellrott wrote:
> Is anybody else getting 404 error
ython 2.5. What's your
environment?
Greg Von Kuster
On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote:
> Since I've had issues with workflow and the toolshed in the past, I have
> changed my workflow so that my only interaction with the toolshed is either
> via uploadi
se of the problem.
Greg Von Kuster
On Dec 10, 2012, at 1:45 PM, Lance Parsons wrote:
> I recently updated the htseq-count tool in the Galaxy toolshed to version
> 0.3. This version has some functional changes and thus the tool version was
> incremented. I installed this new version
ncies.
http://wiki.galaxyproject.org/ToolShedToolFeatures
Greg Von Kuster
On Dec 12, 2012, at 7:01 PM, Franco Caramia wrote:
> Dave,
>
> Thanks for that, will pull the latest version and give it a go..
>
> Is there any documentation on these tags and flags??? (tool depende
en I'll have to take a look and see if I can
reproduce this. I'm swamped right now, but I'll get to this as soon as
possible.
Greg Von Kuster
On Dec 11, 2012, at 1:17 AM, Franco Caramia wrote:
> Hi Greg, list
>
> When installing a tool dependency, and the Installation
release.
Greg Von Kuster
On Dec 11, 2012, at 6:03 AM, Adam Carr (NBI) wrote:
> Hi,
>
> I have been using the tool shed recently and come across a problem.
>
> When a searching for valid tools within the Public Tool Shed, it seems that
> if the search should return nothing fo
/wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
> Would it make sense to stop including tool
> links on the left panel that aren't bundled with Galaxy, and then let
> the toolshed add them in?)
>
Not sure what you mean here.
> -Greg
>
> On Mon, Dec 10, 2012 at 11:16
tions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
Greg Von Kuster
___
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/
7; where tool_shed_repository_id
= ;
Step 4:
Manually edit the shed_tool_conf.xml file to remove the entry for the contra
repository
This should be all you need to do. Let me know if you bump into additional
issues.
Greg Von Kuster
On Dec 6, 2012, at 2:08 AM, Franco Caramia wrote:
>
ok, I'll wait on the additional information I requested.
On Dec 5, 2012, at 6:56 AM, Adam Carr (NBI) wrote:
> Hi Greg,
>
> Thank you for helping me out here.
> I’m running on the galaxy-dist branch, changeset 8285:f364d992270c.
>
> Many Thanks,
> Adam.
>
>
pt an upload being:
> Module galaxy.util.shed_util:336 in check_tool_input_params
> >> if options.tool_data_table or options.missing_tool_data_table_name:
> AttributeError: 'str' object has no attribute 'tool_data_table'
I'll need all of the answers above along w
If you have not yet updated your Galaxy instance to the revision from the
galaxy-dist repository in bitbucket, then that is most likely the cause of the
behavior you are seeing.
Greg Von Kuster
On Dec 5, 2012, at 12:52 AM, Franco Caramia wrote:
>
>
> Hi Greg,
>
> I have n
It's likely that you are tracking galaxy-central in your local Galaxy instance,
but using the main Galaxy tool shed. If this is the case, you can use only the
test Galaxy tool shed. You have to be tracking galaxy-dist in your local
Galaxy instance to use the main Galaxy tool shed.
Gre
Hi Adam,
I believe this is related to the invalid xml definition in your repository's
tool_data_table_conf.xml.sample file which I discussed in a previous reply.
Greg Von Kuster
On Dec 4, 2012, at 8:08 AM, Adam Carr (NBI) wrote:
> Hi,
>
> I hadn't caught this as I pos
tool_dependencies file
> Then the following steps:
>
> Installing the tool from toolshed: Success
> Installing tool dependencies: Failed
> Deleting tool: Success
> Re-installing tool: Failed
>
>
> Thanks,
>
> Franco
>
>
>
>
> On 4/12/12 12:
Hi Ido,
On Dec 4, 2012, at 10:26 AM, Ido Tamir wrote:
> Hi,
> how do I get tools from one local toolshed (or the main galaxy toolshed)
> into another tool-shed? Is it possible to clone the content of a complete
> tool-shed - all repositories
> at once into another tool-shed?
Not at the current
path
Thanks,
Greg Von Kuster
On Dec 3, 2012, at 6:40 PM, Franco Caramia wrote:
> Hi list,
>
> Trying to upload, delete, update files from a repository I own in the
> toolshed I keep getting Server Error..
>
> This is the repo:
> http://fcara...@to
vior first thing tomorrow with the
dist revision to ensure there are no problems using your steps below. If we
discover any issues we'll let you know.
Thanks for the additional information.
Greg Von Kuster
On Dec 3, 2012, at 9:21 PM, Franco Caramia wrote:
> Hi Greg,
>
> Our
e 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:
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
http://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 K
, 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
Hi Anne,
We've never seen this error before and we are not able to reproduce it, so not
sure we can help. Have you made any changes to your Galaxy code base or to
your Galaxy environment?
Greg Von Kuster
On Nov 15, 2012, at 9:15 AM, Anne Pajon wrote:
> Hi,
>
> I'm h
the id from the tag.
toolshed.g2.bx.psu.edu
picard
devteam
e0232cbac965
toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0
1.56.0
Greg Von Kuster
On Nov 15, 2012, at 9:10 AM, Andreas
++
> | mothur_toolsuite |
> | protk |
> | roche454_toolsuite |
> | toolfactory|
> ++
> 4 rows in set (0.00 sec)
>
>
> The mothur entries in 'shed_tool_conf.xml' file and the mothur repository are
>
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
executed 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,
>
SocketServer.py", line 694, in
> finish
> self.wfile.flush()
> File "/local/python/2.7-bis/lib/python2.7/socket.py", line 301, in flush
> self._sock.sendall(view[write_offset:write_offset+buffer_size])
> error: [Errno 32] Broken pipe
>
> Cheers,
> Mathieu
in the "Debug at" address will provide a
stack 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"
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,
>
_table_conf.xml file and not have
them munged 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
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.
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
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 too
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.
>
> W
n 2.6+, 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 bism
.
# 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
snpindex.xml
tool-data/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
.
Thanks again,
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
Hi John,
Thanks very much for your continued contributions. I've applied your patches
described below to change set revision 8012:5fc775a03f0b, which will be
available in the Galaxy release currently scheduled for about 2 weeks from now.
Greg Von Kuster
On Oct 22, 2012, at 12:55 AM,
ToolFeatures#Finding_dependencies_included_in_an_installed_repository_at_tool_execution_time
Thanks very much for contributing - I'll take a look at this patch and
integrate part or all of it into the next release if appropriate.
Greg Von Kuster
On Oct 15, 2012, at 1:15 PM, Björn Grüning wrote:
> Hi,
>
> i&
f you're running an older version of Galaxy, you'll need to update 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
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
l contacts.
Thanks very much,
Greg Von Kuster
Begin forwarded message:
> From: "Oliver Berkowitz"
> Date: October 14, 2012 11:47:13 PM EDT
> To:
> Subject: Galaxy data upload
>
> Dear Greg,
>
> not sure if you are the right person to contact…
>
> I hav
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
> wrote:
>>
>> Thanks for the quick turnaround. On the contrary, your examples are very
>> helpful. I'll try your approach. I haven't upgraded Galaxy in
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
ine on this is, but we'll 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 an
Hi Derrick,
Yes, this approach will work fine.
Greg Von Kuster
On Oct 8, 2012, at 11:44 PM, Derrick Lin wrote:
> 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?
>
> Der
Greg Von Kuster
On Oct 8, 2012, at 8:49 PM, Derrick Lin wrote:
> 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 migrati
1.2.3
1.2.3
toolshed.g2.bx.psu.edu
bwa_wrappers
devteam
ffa8aaa14f7c
toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_color_wrapper/1.0.2
1.0.2
Greg Von Kuster
On Oct 8, 2012,
Hello David,
What version of Galaxy are you running?
Please send me your community_wsgi.ini file so I can take a look at how you
have things configured.
Thanks,
Greg Von Kuster
On Oct 5, 2012, at 9:51 AM, David Hoover wrote:
> I'm trying to host a local toolshed, and I've hit
t unwanted 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
) and just pushing
changes from TOOL_DEV_LOCAL_DIR 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
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
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 neede
bx.psu.edu/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
tory in the tool shed.
The name of the tool shed repository itself can 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
pying conditions. There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
I'm running version 2.2.3, so I'll upgrade to version 2.3.1 to see if the newer
version breaks my environment.
>
> Let me know if I can help track things down any fu
l, but so far no
>> luck. I've created a few spurious revisions in the attempt, and I think now
>> I may just try bumping the version (already did to no avail, toolshed still
>> thinks it's the same) and uploading a tar file. That seems to more reliably
>> p
s. I 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 f
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 wrote:
>> Hi Peter,
>>
>> On Sep 20, 2012, at 5:53 AM, Peter Cock wrote:
>>
>>> Hi all,
>>>
>>> I'd like to ch
section of the tool shed wiki should clarify this:
http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_repositories_installed_in_a_local_Galaxy_instance
Greg Von Kuster
>
> Regards,
> Kevin.
>
>
> ___
> Please keep all replies on the list by using "reply a
version of an
installed tool (if one exists), you need to install a new (different) changeset
revision from the tool shed 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 anyt
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,
>
>
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
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 Ta
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 lat
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
p 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
#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
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