>>>>>> hg19.len.
>>>>>>
>>>>>> Can you point me to a link for how to do this? I imagine I am missing
>>>>>> something obvious.
>>>>>>
>>>>>> Best,
>>>>>> Aaron
>>&g
__
> 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
quot;, "QC
> METRICS...") on the main site.
>
> Is this possible somehow?
>
> Best,
> Aaron
>
> On Nov 23, 2011, at 9:51 AM, Greg Von Kuster wrote:
>
>>> Here is my current repo including just one tool:
>>>
>>> http://testtoolshed.
ntdebug = True
> use_interactive = True
> use_heartbeat = False
>
>
>
>
>
> On 27/12/11 20:15, Greg Von Kuster wrote:
>> If the following config setting is set to True in universe_wsgi.ini, then
>> the event messages will be logged to the message column of the Event
e, HausslerLab, CBSE, UCSC
> (650) 743-4141
> http://soe.ucsc.edu/~ted
>
>
> ___
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> in your mail client. To manage your subscriptions to this
> and o
read (there are others as well if you search the mailing list
archives with various search strings):
http://galaxy-users-list-archive.2308625.n4.nabble.com/restart-server-td4131372.html
>
> Thanks!
> Ted
>
> On Dec 28, 2011, at 5:30 AM, Greg Von Kuster wrote:
>
>> Hello
in create
>>>engine._run_visitor(visitorcallable, self, *args, **kwargs)
>>> File
>>> "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/eggs/SQLAlchemy-0.5.6_d
>>> ev_r6498-py2.6.egg/sqlalch
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> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
Greg Von Kus
to be changed to this - note the elimination of relative imports:
import logging
import os,os.path,re
import galaxy.datatypes.data
from galaxy.datatypes.data import Text
from galaxy import util
from galaxy.datatypes.metadata import MetadataElement
Thanks very much for helping out with this, and pl
ANGE 3
---
You can optionally choose to remove your suite_config.xml file from your
repository as it is no longer used in any way.
Thanks!
Greg Von Kuster
On Oct 18, 2011, at 11:03 AM, Jim Johnson wrote:
> Greg,
>
> The mothur_toolsuite in the ToolShed contains a file w
mplementation
> file should be?
>
> Thanks,
>
> JJ
>
> On 1/5/12 1:38 PM, Greg Von Kuster wrote:
>>
>> Hello Jim,
>>
>> I've implemented support for proprietary datatypes that use class modules
>> included in tool shed repositori
Of course, this assume that there is not more than one datatypes class module
in your repository with the same name. This would definitely pose problems, so
care should be taken that it is not done.
On Jan 5, 2012, at 3:29 PM, Greg Von Kuster wrote:
> However, your datatype class mod
Yes, this is certainly important, but I think the hope is that proprietary data
types will not become so prevalent that name-spacing the extensions is
necessary.
On Jan 5, 2012, at 4:15 PM, Jim Johnson wrote:
>
> Big Question?
> When I started creating all those datatype classes for mothu
Of course, your approach of prepending the repository name would probably
eliminate any future issue in this regard. Whatever you feel is best... ;)
On Jan 5, 2012, at 4:49 PM, Greg Von Kuster wrote:
> Yes, this is certainly important, but I think the hope is that proprietary
> data
the file_ext fields include the toolshed name, e.g. should "otu"
> be named "mothur.otu" to avoid conflicts with other downloaded tools from the
> toolshed?
> Seems like this would be the time to establish rules/practices for such
> concerns.
>
> JJ
>
&
Hello Thon,
In case you don't get an answer from the community, you can send your question
to the repository owner by selecting the option from the "Repository Options"
pop-up menu in the upper right corner when viewing the repository in the tool
shed.
<>
Greg Von Kus
our subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx.psu.edu/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
___
Please keep all replies on the list by using "reply all
of course that most users who want to search for
> new galaxy tools will not be logged in (because they probably have no
> account) and thus cannot contact the owner ... and will not even know that
> there exists such an option.
>
>
> Cheers,
> Marcel
>
> On 1/12/12 5:55
I've corrected this problem in change set 6510:3d9f0ce7bb61, which is running
on both the Galaxy main and test tool sheds. Thanks for reporting this issue.
Greg Von Kuster
On Jan 11, 2012, at 5:10 PM, Anthonius deBoer wrote:
> Im trying to install a tool from the toolshed that showed
brary%20Files
For details about Galaxy Data Libraries in general, see our wiki here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries
Greg Von Kuster
On Jan 16, 2012, at 6:35 PM, Joshua Gross wrote:
> Hello all--
>
> We have set up a local version of Galaxy on our own server
puting Applications
> Institute for Genomic Biology
> University of Illinois at Urbana-Champaign
>
>
> ___
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> in your mail client. To manage your subscriptions to this
> and other
> Leandro
> _______
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> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
> http://lists.bx
current at revision
6626:d8af2f7b1f35.
For clarification what value have you set for the tool_path config setting in
your shed_tool_conf.xml file?
After you update your Galaxy instance, try installing the tool again and let me
know if you encounter issues.
Thanks very much!
Greg Von Kuster
laxy central. Thanks in advance.
>
> Kind regards,
> Anne.
>
>
> On 27 Jan 2012, at 13:03, Greg Von Kuster wrote:
>
>> Hello Anne,
>>
>> I apologize for the delay in responding to you on this. The first issue I
>> see is that the revision of your loca
omfortable in updating to the latest from central, just use
hg pull -u
>
> Before migrating and updating I will manually remove the installed tool shed
> repository from disk as you advised.
>
> Kind regards,
> Anne.
>
>
> On 27 Jan 2012, at 14:57, Greg Von Kuste
ool shed should not cause you problems.
Let me know how this goes.
Greg Von Kuster
On Jan 27, 2012, at 2:27 PM, Anne Pajon wrote:
> Hi Greg,
>
> Thanks for your answer. I've upgraded my Galaxy instance to 56bdee21dc78 from
> Galaxy central repository.
>
> I tried again
; and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscription
.py',
> line 660 in write
> File
> '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py',
> line 695 in _write
> File
> '/opt/local/home/webapp/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py
e a
> shed_tool_conf.xml updated:
>
> Let me know when you commit your next change set, so I will be able to test.
> Thanks a lot for your help.
> Anne.
>
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
___
Please keep all replies
ease 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/
Greg Von Kuster
Galaxy Development Team
g...@bx.psu.edu
can test this out. I will get fixes for issues (if any exist) as fast as
possible. My hope is that this will be the last major feature introduced until
we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 3, 2012, at 10:20 AM, Bossers,
alaxy tool sheds
can test this out. I will get fixes for issues (if any exist) as fast as
possible. My hope is that this will be the last major feature introduced until
we get everything stabilized a bit more between the tool shed and Galaxy.
Thanks!
Greg Von Kuster
On Feb 2, 2012, at 8:
Hello Ira,
I will fix the sniff problem with proprietary data types included in tool sheds
- I should be able to have this fixed within the next day or two. With regard
to the upload tool respecting these sniffers, I've already designed this tool
as well as the metadata setting components to d
hat section. :-(
> Actually the complete section is again invisible.
>
> Van: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
> Verzonden: maandag 6 februari 2012 8:45
> Aan: 'Greg Von Kuster'; Ira Cooke
> CC: g
rt the repository tool when it’s an empty
> section.
> Sorry for being unclear.
> Alex
>
> Van: Greg Von Kuster [mailto:g...@bx.psu.edu]
> Verzonden: maandag 6 februari 2012 12:57
> Aan: Bossers, Alex
> CC: Ira Cooke; galaxy-dev@lists.bx.psu.edu Dev
> Onderwerp: Re: [galaxy
Hello Ira,
I believe proprietary datatype sniffers included in tool shed repositories are
loading as expected - at least I cannot reproduce the behavior you are seeing.
The datatypes_conf.xml file included in the latest revision of the gmap
repository on the main Galaxy tool shed looks like th
Hello Thon,
Attempting to run the migration script twice to the same version always poses
problems. Can you downgrade successfully as follows?
sh manage_db.sh downgrade 90
If so, downgrade, then upgrade again and send the paster log from the clean
upgrade if you see a problem. Also:
What dat
nux-x86_64-ucs2.egg/simplejson/decoder.py",
> line 420, in raw_decode
> simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1
> column 0 (char 0)
>
>
> On Feb 06, 2012, at 02:08 PM, Anthonius deBoer wrote:
>
>> Hi Greg,
>>
>&g
:08 PM, Anthonius deBoer wrote:
> Oh, and whatever you did in the little patch, it worked...At least I have a
> working version of galaxy again and the database seems to be all intact..
>
> Thanks!
>
> Thon
>
> On Feb 06, 2012, at 03:52 PM, Greg Von Kuster wrote:
>
&g
pending
> sniffer for datatype galaxy.datatypes.gmap:IntervalAnnotation to sniff_order:
> No module named gmap
> galaxy.datatypes.registry WARNING 2012-02-07 14:25:38,609 Error appending
> sniffer for datatype galaxy.datatypes.gmap:SpliceSiteAnnotation to
> sniff_order: No module named gmap
> galaxy.datatype
Hi Alex,
If your migration scripts through 90 executed cleanly, then your
tool_shed_repository.uninstalled column should exist as that column is created
in the 0090 script. What was the log of your db migration upgrades that
occurred when your database was migrated from version 85 to 90?
Than
is empty though:
>
> galaxydev=> select * from tool_shed_repository;
> id | create_time | update_time | tool_shed | name | description | owner |
> changeset_revision | deleted | metadata | includes_datatypes |
> update_available | installed_changeset_revision | uninstalled | dist_to_shed
> +-+-
I don't seem to see revision 271ccd09bc23 there...Is
>> this issue fixed in galaxy central or only in the main installation?
>>
>> Thanks
>>
>> Thon
>>
>> On Feb 07, 2012, at 08:11 AM, Greg Von Kuster wrote:
>>
>>> Hi Thon,
>>&g
class hierarchy. I believe this option
> makes sense since a subclass of a datatype should always override its parent
> .. and I think it would also avoid the potential for conflicts with galaxy's
> defaults.
>
> What do you think? Is that a system that would work?
>
>
Thanks Ira, I'll have this fixed tomorrow and let you know. Sorry for these
glitches, we'll get these things ironed out rapidly. Thanks for helping!
On Feb 7, 2012, at 7:40 PM, Ira Cooke wrote:
> Dear Greg,
>
> In the latest version of the galaxy-central code there seems to be a bug
> preve
This is fixed in change set revision 6691:c9bdeba75bd1 on our central repo.
Thanks very much for reporting this.
Greg
On Feb 7, 2012, at 7:40 PM, Ira Cooke wrote:
> Dear Greg,
>
> In the latest version of the galaxy-central code there seems to be a bug
> preventing me from updating my tools
s parent
> .. and I think it would also avoid the potential for conflicts with galaxy's
> defaults.
>
> What do you think? Is that a system that would work?
>
> Cheers
> ira
>
>
>
>
> On 08/02/2012, at 3:25 AM, Greg Von Kuster wrote:
>
>> H
To clarify, proprietary datatypes currently being loaded will be ignored if
they conflict with a proprietary datatypes that was already loaded. Only
datatypes defined in the datatypes_conf.xml file will take precedence, and
override conflicts.
On Feb 8, 2012, at 11:34 AM, Greg Von Kuster
be appended to
the sniff order, not placed in the same position as the replaced sniffer. This
makes things cleaner and more easily understood.
On Feb 8, 2012, at 11:37 AM, Greg Von Kuster wrote:
> To clarify, proprietary datatypes currently being loaded will be ignored if
> they conflic
Hi Thon,
I've been working on fixes which I believe may be related to this. When
uploading a file, the proprietary datatypes / sniffers (datatypes included in
installed tool shed repositories) are not correctly handled by the upload
process. Also, when running jobs, if setting metadata extern
On Feb 9, 2012, at 9:04 PM, Greg Von Kuster wrote:
> Hi Thon,
>
> I've been working on fixes which I believe may be related to this. When
> uploading a file, the proprietary datatypes / sniffers (datatypes included in
> installed tool shed repositories) are not correctly h
loser look, but if your tool is
functional when installed from the tool shed to a local Galaxy instance, all
should be ok.
Thanks for your contribution!
Greg Von Kuster
On Feb 14, 2012, at 1:49 PM, Carlos Borroto wrote:
> Hi,
>
> I'm currently developing my first Galaxy tool. I&
extension). They were originally
in the datatypes.conf.xml.sample file for datatype indexers\, but datatype
indexers have been eliminated from the Galaxy framework because datatype
converters do the same thing.
Greg Von Kuster
On Feb 17, 2012, at 3:25 AM, Wetzels, Yves [JRDBE Extern] wrot
Hello Frank, see my inline comments.
On Feb 20, 2012, at 6:56 AM, Frank Sørensen wrote:
> Hi Guys,
>
> Sorry if this is a stupid question, but in order to find out which external
> reference files (.loc - list files etc.) we need for our newly installed
> Galaxy server, and to get an overview
ctory, but I am not able to tell
you why (I assume you haven't moved any directories).
Sorry for not being of any help here.
Greg Von Kuster
On Feb 21, 2012, at 2:55 AM, Frank Sørensen wrote:
> Hi Greg,
>
> Den 20-02-2012 15:06, Greg Von Kuster skrev:
>> Hello Fran
ry for the inconvenience.
Greg Von Kuster
On Feb 21, 2012, at 4:19 PM, Luobin Yang wrote:
> Hi, Greg,
>
> I am a bioinformatics research scientist at Idaho State University and we're
> planning to use the Sample Tracking System for our ION Torrent PGM sequencer.
> However, I en
Hi David,
I cannot reproduce this behavior from my local Galaxy instance, but clicking
'2', '3', '4' or 'Show All" does take a second or more to display the response.
Can you provide more information about the environment you have or what you
are doin
sonation = True
> allow_user_dataset_purge = True
> new_user_dataset_access_role_default_private = True
> enable_quotas = True
> retry_job_output_collection = 10
> output_size_limit = 10737418240
> start_job_runners = drmaa
>
> On Feb 22, 2012, at 4:07 PM, Greg Von Kuster wrote:
>
>&g
Lisa,
In case you aren't aware, you can set your user preferences for your account in
the tool shed to receive an email message when a new repository's first upload
occurs. This would keep you from having to check the tool shed. Go to User ->
Preferences -> Manage your email alerts and you'll
try:
os.unlink( proprietary_datatypes_config )
except:
pass
return converter_path, display_path
Sorry for the inconvenience - I'll get this fix out as soon as I possibly can.
Let me know if you bump into any problems with this.
Greg Von Kuster
On Feb 24, 2012, at
!
Greg Von Kuster
On Feb 24, 2012, at 4:17 PM, JIE CHEN wrote:
> Hello everyone,
>
> I'm a new to Galaxy and the tool sheds. Right now i am learning it by reading
> the tutorial and have a problem:
>
> when i try to start my local tool shed by typing the command "%sh
&g
then there may be a bug in that process. What do
your paster logs show?
Also, your data attachments have been lost in the mail thread - did only Peter
get them?
Greg Von Kuster
On Feb 25, 2012, at 5:20 AM, Peter Cock wrote:
> On Sat, Feb 25, 2012 at 9:40 AM, Yingwei HU wrote:
>> Dear P
and questions in your message.
Thanks!
Greg Von Kuster
On Feb 15, 2012, at 2:24 PM, Carlos Borroto wrote:
> Hi Greg,
>
> Thanks for your answer. Would be great to get the tool to preview
> correctly but is not a big deal.
>
> I'm having a few more problems. I'm getting
ot be reasonable, so perhaps I spoke
too soon. If you have questions about how to add support for new datatypes,
see our wiki at http://wiki.g2.bx.psu.edu/Admin/Datatypes.
Thanks!
Greg Von Kuster
On Feb 29, 2012, at 11:59 AM, Carlos Borroto wrote:
> Hi Greg,
>
> Thanks for looking and resolv
to, I'm
> guessing I would have to do what is explained here:
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Including_proprietary_data_types_that_use_class_modules_contained_in_your_repository
>
> Thanks,
> Carlos
>
> On Wed, Feb 29, 2012 at 12:14 PM, Greg Von Kuster wrote:
>> Hi Car
not sure how many in the community that have this
environment are using the tool shed.
Greg Von Kuster
On Mar 2, 2012, at 3:14 PM, Zachary Charlop-Powers wrote:
> Hello Galaxy Team/Users,
>
> Thanks again for your great work. A few months back I setup a local Galaxy
> server beh
cause doing do prevents
reproducibility. I'm looking for feedback from the community on this one -
does eliminating this repository affect anyone?
Thanks for the new contributions tot he tool shed!
Greg Von Kuster
On Mar 6, 2012, at 1:47 AM, Edward Kirton wrote:
> i created a new toolshe
Hi Lisa,
It looks like you are current with the tip from the galaxy-dist repository.
What are you attempting to do, what exactly is the error you are seeing, and
what is shown in your paster log?
Thanks,
Greg Von Kuster
On Mar 6, 2012, at 9:08 PM, Lisa wrote:
>>
> Hi Greg,
&g
not, change your ~/.hg/hgrc file
so that the default path pulls from our galaxy-central repository, something
like this.
[paths]
default = https://@bitbucket.org/galaxy/galaxy-central
Sorry for the inconvenience,
Greg Von Kuster
On Mar 7, 2012, at 1:13 PM, Liusong Yang wrote:
> Hi G
ssing from the repository. The fix I've committed
handles the problem caused by the missing entry in the tool shed.
Thanks very much for reporting this.
Greg Von Kuster
Metadata was defined for some items in revision '9266d807ca85'. Correct the
following problems if nec
ffice. however you folks how you want to handle it is fine.
>
> On Tue, Mar 6, 2012 at 3:38 AM, Greg Von Kuster wrote:
> Hi Ed,
>
> Do you want the hmmscan repository itself deleted? It's been downloaded /
> cloned 86 times, although it is never been automatically instal
Hi Michal,
Looks like you're running with a postgres database - can you get into your
database and execute the following sql command and send me the result?
select * from migrate_tools;
Thanks!
Greg Von Kuster
On Mar 14, 2012, at 12:04 PM, Michal Stuglik wrote:
>
> Dear gal
- all is good!
If you see the same problem you reported below, try running this sql statement
in your psotgres database:
INSERT INTO migrate_tools VALUES ('GalaxyTools',
'lib/galaxy/tool_shed/migrate', 1);
Now start your Galaxy server.
Let me know how this turns out.
Greg
Hi Daniel,
What does your tool shed paster log say when you get the 404 error trying to
install? You can see the paster log by running the following from your Galaxy
installation directory when your tool shed is running.
tail -f community_webapp.log
Greg Von Kuster
On Mar 16, 2012, at 4:34
ecko/20100101
> Firefox/10.0.2"
>
> Nothing that helps me much.
> I have has some problems with permissions in the tmp dir, but I
> reconfigured it and it still does not work.
>
> Daniel
>
> On 03/16/2012 11:04 AM, Greg Von Kuster wrote:
>> Hi Daniel,
>>
>&
>>
>>
>> On Tue, Mar 13, 2012 at 3:34 PM, Xuebing Wu wrote:
>>>
>>> I see. It's a set of tools we have on our local galaxy server. So it's
>>> pretty heterogeneous, including interval manipulation, meta-gene
>>> analysis, sequen
r the value of the tool shed will be
significantly diminished over time. Filtering out files that actually are not
tools from a list of invalid tools could become a bit messy.
Thanks,
Greg Von Kuster
Repository Actions
Metadata was defined for some items in revision '66f8262e1686
hat's what I think you're
attempt here), so your list of refresh_on_change values will be attributes of
those history items.
Greg Von Kuster
On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote:
>>
>> Here's one example:
>>
>>
>>> label="
enables you to have complete
control over your own environment. Some changes in the .sample file may not
make sense to change in your own environment.
Greg Von Kuster
On Mar 22, 2012, at 6:39 AM, Praveen Raj Somarajan wrote:
> Hello Dev team,
>
> I normally use "hg incoming&quo
plugin code file(s)
> are? Then I can make a copy and make the change you mentioned.
Look in ~/lib/galaxy/jobs/deferred
Greg Von Kuster
>
> Sorry for needing this help,
> Leandro
>
>
___
Please keep all replies on t
new addition which I
> can incorporate manually, but I don't know which are other
> additions/modifications in such files which might me useful for me.
>
> Raj.
>
> From: Greg Von Kuster [mailto:g...@bx.psu.edu]
> Sent: Thursday, March 22, 2012 4:18 PM
Dear Greg,
>
> On Wed, Mar 21, 2012 at 3:20 PM, Greg Von Kuster wrote:
>> Leandro,
>>
>> For refresh_on_change to work you need a set of optional selections and a
>> set of refresh_on_change values, so in your example, the type should
>> probably be a sel
Hi Daniel,
>>
>> On Mar 22, 2012, at 11:21 AM, Daniel Sobral wrote:
>>
>>> Hi Greg,
>>>
>>> This is the output I get in the toolshed log:
>>> "
>>> Firefox/10.0.2"
>>> 172.22.50.249 - - [22/Mar/2012:15:11:50 +0100] "GET
>>> /toolshed/repository/install_repository_revision?repository_id=190cd60
to come from my toolshed. I'm running the galaxy and the
> toolshed under the same galaxy clone, but I think this is the intended
> usage, no?
Yes, this is fine to do, but you should not be using the same database.
>
> Thanks for the help,
> Daniel
>
>
> O
You'll need to configure your Python 2.6 to include mercurial. You can do
something like
easy_install -U mercurial
but there are other approaches as well.
On Mar 23, 2012, at 10:33 AM, Joachim Jacob wrote:
> Hi all,
>
>
> In order to ease sharing the developed Galaxy tools in our group, w
our Galaxy install dir.
Greg Von Kuster
On Mar 23, 2012, at 9:52 AM, Leandro Hermida wrote:
> Dear all,
>
> I followed the directions in
> https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer to set up the
> Galaxy AMQP listener service so that the sample tracking system can
> tra
Hi Leandro,
The directory should not have been created upon Galaxy server start-up. This
issue has been resolved in change set 6892:6b8535e5b030 in our central
repository. Thanks for reporting this.
Greg Von Kuster
On Mar 26, 2012, at 5:57 AM, Leandro Hermida wrote:
> Dear all,
>
&
We have a buildbot set up that runs our functional tests against various
platforms / environments. The .sample file used by the buildbot tests
everything. The tool_conf.xml.main contains a subset of everything that is
tested.
On Mar 27, 2012, at 11:48 AM, Anne Pajon wrote:
> Hi Nate,
>
> Th
Hi Leandro,
This issue should be fixed in change set 6911:9f5750e19c1e, which is currently
available in our central repository. You're separate reported issues are being
corrected as well and we'll let you know when fixes are available. thanks very
much for reporting this.
Greg
Hello Leandro,
This issue should be corrected in change set 6912:7273e1405094, which is
available in our central repository. Thanks very much for reporting this.
Greg Von Kuster
On Mar 28, 2012, at 11:23 AM, Leandro Hermida wrote:
> Dear Galaxy Dev,
>
> On the viewed transferred
We know what the problem is and it is being fixed. We'll have the fix
available shortly and let everyone know.
Thanks for reporting this!
Greg Von Kuster
On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote:
>
> Hi Leandro,
>
> I am also experiencing the same problem with t
Hello Ira,
I've added the category to the main tool shed. Thanks for the request and your
upcoming contributions!
Greg Von Kuster
On Mar 29, 2012, at 5:33 PM, Ira Cooke wrote:
> Dear list,
>
> I would like to add a suite of proteomics tools to the toolshed but there is
ad
> later on today.
>
> We're working on some better documentation ... to get it all working takes
> some extra setup steps on the part of the user.
>
> Ira
>
>
> On 30/03/2012, at 9:49 AM, Greg Von Kuster wrote:
>
>> Hello Ira,
>>
>> I&#
ntral) if you want it now.
Thanks very much for reporting this problem, and we apologize for the
inconvenience it caused.
Greg Von Kuster
On Mar 29, 2012, at 1:49 PM, TerAvest, Emily wrote:
>
> Hi Leandro,
>
> I am also experiencing the same problem with the latest version of
your hgweb.config match those you
have on disk?
Greg Von Kuster
On Apr 2, 2012, at 8:38 AM, Joachim Jacob wrote:
> Hi all,
>
> On a local Toolshed freshly installed, I got these errors when browsing my
> repository.
>
> Perhaps a bug?
>
>
> Cheers,
> Joachim
>
;
>
> If it is most likely a configuration error, I will check my settings, and let
> you know my progress.
>
> But one note: I do not have a hgweb.config file. Where is it supposed to
> reside? I cannot find this info on the toolshed wiki.
>
>
> Joachim
>
>
g your repositories on disk (if you in fact have
any), you can delete them, and create the hgeweb.config file with just the
[paths] setting and no entries. This will result in a new, pristine tool shed
environment.
Greg Von Kuster
On Apr 2, 2012, at 10:38 AM, Joachim Jacob wrote:
> I am s
the
> error from below.
>
> Did I do something wrong, or are my steps from above not correct? Thanks for
> the help!
>
>
> Kind regards,
> Joachim
>
>
> On 04/02/2012 05:00 PM, Greg Von Kuster wrote:
>> This is the problem - it's unclear how your l
On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
>
> Have you seen the README file that comes with the
> Blast2GO wrapper? Perhaps the 'install from toolshed'
> could be tweaked to make this kind of documentation
> more visible...
>
If you are installing a single repository that contains a file
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote:
> On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster wrote:
>>
>> On Mar 24, 2012, at 7:30 AM, Peter Cock wrote:
>>>
>>> Have you seen the README file that comes with the
>>> Blast2GO wrapper? Perhaps the &#
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