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
certain it has 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 fart
l the next 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
grade 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
>
I responded to your original email, which I should have done initially. Sorry
for the back-and-forth on this.
On Aug 27, 2012, at 10:16 AM, Hans-Rudolf Hotz wrote:
> Hi Greg
>
> Thank you very much for your e-mail
>
> Unfortunately, we still see this behavior in
&g
Hi Hans,
Sorry, I missed your information about your using the latest dist release in my
original response. See my inline comments.
On Aug 21, 2012, at 11:18 AM, Hans-Rudolf Hotz wrote:
> HI
>
>
> We have been struggling with this problem since we updated to
> "changeset:6799:40f1816d6857"
A possible work-aound is to add the following entry into your local
tool_data_table_conf.xml file located in your Galaxy installation directory.
line_type, value, path
Let us know if this still does not correct the problem.
Greg Von Kuster
On Aug 27, 2012, at 10:07
pes_conf.xml file as they used to be.
Greg
On Aug 27, 2012, at 9:39 AM, Peter Cock wrote:
>
> That is helpful Greg - thank you - although I worry the learning
> curve for developing Galaxy tools is getting steeper.
>
> You've implied 'simple' proprietary datatypes w
mmonly used
> files are also setup on our system as shared libraries
> within Galaxy.
It seems weird to ask them to upload something that's already in their
home directory and available to the cluster jobs otherwise.
I wonder if there's a way they can copy files to the Galaxy data
d
datatypes_conf.xml files in a
configuration 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 Ga
n the next 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
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
reset 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
On Fri, Aug 24, 2012 at 9:56 AM, Peter Cock wrote:
> On Fri, Aug 24, 2012 at 1:25 PM, mailing list
> aka Greg wrote:
>> Thanks Assaf.
>>
>> Would anyone know about my question 1? If I install a local version
>> of Galaxy and connect it to our cluster, where is e
o the datatypes_conf.xml file
installed with the emboss_datatypes tool shed repository (or any other
repository that includes this file). SO display_in_upload will now function
correctly for the installed proprietary datatypes.
Thanks for reporting this issue, and sorry for the inconvenience.
Gre
are not quite right. I'll continue to keep a close watch on this
area and provide fixes as necessary.
Please don't hesitate to contact me if you come across anything that is
questionable.
Thanks!
Greg Von Kuster
On Jul 30, 2012, at 11:32 AM, Greg Von Kuster wrote:
> Hi Pet
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
> hav
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,
> Bjoer
gs is necessary.
update tool_shed_repository set status = 'New' where status = 'Cloning';
It was great to talk with you at the conference as well!
Greg
On Aug 3, 2012, at 8:36 PM, Nikhil Joshi wrote:
> Hi Greg,
>
> So I looked at the the URL from the log file and
n 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
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
> Kind regards,
>
> Joachim Jacob, PhD
>
> 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
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
the
first place.
Thanks again!
Greg
On Aug 1, 2012, at 7:03 AM, SHAUN WEBB wrote:
> Quoting Greg Von Kuster on Wed, 1 Aug 2012 06:23:11 -0400:
>
>> I cannot reproduce this behavior, so can you let me know the steps you use
>> to do so? I need the page on which you are a
Hi Shaun,
On Aug 1, 2012, at 6:13 AM, SHAUN WEBB wrote:
>
>>>
>>> c) The toolshed interface allows me to change the name of my tool. If I do
>>> this, then go to my Galaxy admin ui and try to get updates for my tool then
>>> it fails. Does it make sense to change a tools name after it is crea
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 ver
h the WoLF 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 - Eukaryo
com and exits with an error if fred is
not one of the privileged id's. I'm trusting that the standard security in
Galaxy will be enough to prevent any determined workaround to make it run
(and indeed view the code).
However it would be better if non-privilged users couldn't even s
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
>
>
u.edu/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.
> N
es on the issue.
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, wrote:
> I found the guid for the tool and tried the usual method of configuri
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 si
d? I'm not sure if this works, but just wanted to make sure you
were 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 dow
determine the cause.
Thanks!
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
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
ld 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, 201
will able 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 dis
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 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. B
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.
I
2, at 4:09 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 1
not that good at SQL to begin with, but maybe a script that would sync
> stuff would be an idea...
>
> Thanks
>
> On Jul 11, 2012, at 12:29 PM, Greg Von Kuster wrote:
>
>> Hi Thon,
>>
>> What revision of Galaxy are you running? Have you made multiple attempts
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:
>
>
ce 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 downloade
change the value of the path to track galaxy central:
[paths]
default = https://,your user na...@bitbucket.org/galaxy/galaxy-central
When you pull and update, you'll get the latest from galaxy central.
On Jul 10, 2012, at 6:13 PM, Peter van Heusden wrote:
> Hi Greg
>
> Is there any
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:
>
>
data into Galaxy's file store. See the
following wiki page for details.
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
For all the details about Galaxy data libraries, see:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries
Greg Von Kuster
On Jul 10, 2012, a
ually ok because 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:
ing for tool_path in your shed_tool_conf.xml file - is it
the default of ../shed_tools ?
3. What changeset revision of the mothur tool suite were you trying to install
- is the the tip of 5c77423823cb in the main tool shed?
Thanks!
Greg Von Kuster
On Jul 2, 2012, at 10:57 AM, Hollander, Mat
le I added works for me... did i just screw up
> my installation by doing that?
>
>
>
>
> Brad
> On Jun 28, 2012, at 3:05 PM, Greg Von Kuster wrote:
>
>> Hi Brad,
>>
>> Are you running the tip from Galaxy central repository? That is required
>&
Hi Brad,
Are you running the tip from Galaxy central repository? That is required for
using the main galaxy tool shed.
Greg Von Kuster
On Jun 28, 2012, at 2:16 PM, Langhorst, Brad wrote:
> I found the problem with my blocked cookies, now I encounter a new error.
>
> File
> &
Hi Brad,
It looks like you have some rewrite rules defined (apache?) that are messing up
your routes. Where does Noneadmin_toolshed come from?
Greg Von Kuster
On Jun 28, 2012, at 1:24 PM, Langhorst, Brad wrote:
> When i try to install a tool from the main toolshed i see this error
&g
this tend to crop up every so often.
Thanks again,
Greg Von Kuster
On Jun 20, 2012, at 11:41 AM, Birgit Crain wrote:
> I have to refine that statement about the error message I'm getting now:
> On upload I get the same error message
>>>> Metadata was defined for som
Hi Robert,
This section of the tool shed wiki should provide the information you need.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel
Greg Von Kuster
On Jun 21, 2012, at 5:33 PM, Robert Chase wrote:
> Hello,
>
> We are trying to perfect so
got in the main toolshed. I went back to the test toolshed and
> uploaded the same tar ball there, none of the tools loaded properly.
> Hope this helps.
>
> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
> Genomics, Inc.
> (650) 428
Thanks Anne, I'll make sure this fix makes it into my next commit to Galaxy
central.
Greg
On Jun 20, 2012, at 11:42 AM, Anne Pajon wrote:
> Dear,
>
> I've been running unit tests on the latest galaxy-central 7294:663e03e40c86
> that have me this error
Hi Birgit,
Did you upload the same tarball you sent me previously, or was it a different
tarball. If different, can you send it to me?
Thanks
On Jun 18, 2012, at 8:18 PM, Birgit Crain wrote:
> Hi Greg
>
> I just created a repository on the main toolshed and upload a tar ball. I g
erent from mine.
Thanks for reporting this problem!
Greg Von Kuster
> On 06/15/2012 02:58 PM, Greg Von Kuster wrote:
>>
>> Hi Matthias,
>>
>> There is really nothing to configure in your Galaxy environment in order to
>> use the public Galaxy tool sheds.
dated after 6 months of development, your
repository has some issues. What are the results of the following commands?
hg diff
hg status
hg verify
hg summary
On Jun 15, 2012, at 7:55 AM, Hollander, Mattias de wrote:
> Hi Greg,
>
> I guess something went wrong while update, because I
I don't believe so as it would require users to have unrestricted access to the
system in a way that could result in problems.
On Jun 14, 2012, at 10:46 PM, Ciara Ledero wrote:
> Can non-admin users also utilize the option using filepaths?
>
861460482541/galaxy-cloudman-2011-03-22
is Python 2.6.5. Current local Mac is 2.6.1.
Sorry about somewhat dim questions. I'm starting a big Python learning
binge and want to set up a local Galaxy on Mac, an AWS Galaxy, and a
learning environment
in the most useful way.
Thanks.
--
Greg Ed
ch user will be able to upload files to a data library that are
contained in their respective directory.
Make sure the stop / restart your Galaxy server whenever you make changes to
universe_wsgi.ini.
Greg Von Kuster
On Jun 14, 2012, at 10:11 PM, Ciara Ledero wrote:
> Hi all,
>
> I was
Hello Birgit,
This issue has been resolved in changeset 7272:b761471d7590, which is currently
available from our Galaxy central repository. Both the Galaxy test and Galaxy
main tool sheds are running this latest changeset revision.
Thanks very much for reporting this problem!
Greg Von Kuster
d?
Thanks,
Greg Von Kuster
On Jun 13, 2012, at 6:13 PM, Birgit Crain wrote:
> Hi Greg
>
> Thanks for the tip. The .file items appear when I tar the directory on my
> Mac, so I work around that issue and tar the directory on a UNIX server. Thus
> said I happily did the same wi
mine.
Thanks,
Greg Von Kuster
On Jun 13, 2012, at 11:38 AM, Hollander, Mattias de wrote:
> Hi,
>
> I just updated my local Galaxy installation to the latest version. I am
> trying out the feature to add tools directly from the toolshed, but this
> is not working. It result
Hi Birgit,
I don't see any problem with your xml definition below. Are you sure the
problem is not with another file in the tarball? If you can send me the
tarball, I'll take a look.
Greg Von Kuster
On Jun 12, 2012, at 4:09 PM, Birgit Crain wrote:
> Hi
>
> I'm d
Hello Ciara,
See the following Galaxy wiki page for details about configuring this option.
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
Greg Von Kuster
On Jun 11, 2012, at 2:54 AM, Ciara Ledero wrote:
> Hi all,
>
> I was checking out how to upload la
Hi John,
I feel this is an important topic and that others in the community are
undoubtedly benefitting from it, so I'm glad you started this discussion.
On Jun 9, 2012, at 12:36 AM, John Chilton wrote:
> We don't pull down from bitbucket directly to our production
> environment, we pull galaxy
Hi John,
On Jun 8, 2012, at 1:22 PM, John Chilton wrote:
> Hello Greg,
>
> Thanks for the prompt and detailed response (though it did make me
> sad). I think deploying tested, static components and configurations
> to production environments and having production environments not
Hi Bjoren,
What revision are you seeing this in? I don't think this issues exists in
Galaxy central's tip, but let me know.
Thanks!
Greg
On Jun 8, 2012, at 10:44 AM, Björn Grüning wrote:
> Hi Greg,
>
> thanks! I can confirm that it is working now. I can upload new
>
Hi John,
On Jun 7, 2012, at 11:55 PM, John Chilton wrote:
> I have read through the documentation a couple times, but I still have
> a few questions about the recent tool shed enhancements.
>
> At MSI we have a testing environment and a production environment and
> I want to make sure the tool v
rror. I had followed up with Greg
> on this issue off-list as I didn't want to share all the hg output here on
> the list.
>
> The galaxy had downloaded Mercurial egg however it's directory wasn't defined
> in the PYTHONPATH environment variable. However, it was includ
Hello Shantanu,
What is the result of typing the following in your Galaxy installation
directory?
hg heads
Als, the result of the following:
hg status
And finally, the results of the following:
hg diff
Thanks!
Greg Von Kuster
On Jun 1, 2012, at 5:12 PM, Shantanu Pavgi wrote:
>
>
dling this approach, but things may change slightly before I call it
finished.
I look forward to your response on this. Thanks very much for your interest!
Greg Von Kuster
On Jun 1, 2012, at 12:06 PM, Sebastian J Schultheiss wrote:
> Dear Greg,
>
> according to the Tool Shed wik
ivate=False,
override=True ):
What is the result of typing the following in your Galaxy install directory?
hg heads
What about the following:
hg status
And then finally:
hg diff
Thanks,
Greg Von Kuster
On Jun 1, 2012, at 12:06 PM, Luobin Yang wrote:
> Hi,
>
> After I update gala
Hello Bjoern,
This should be resolved in change set 7211:16a93eb6eaf6, which is available
from our central repository. Thanks for reporting this, and please let me know
if you encounter additional issues.
Greg Von Kuster
On May 26, 2012, at 10:51 AM, Björn Grüning wrote:
> Hi,
>
On May 28, 2012, at 2:03 PM, Wanmei wrote:
> Thank you again, Greg.
>
> Thank you for the link too (however the image in the link is not accessible
> anymore). In your example, 4366992 is an auto generated number appended when
> a user uploads a data file into the Galaxy insta
On May 28, 2012, at 8:34 AM, Wanmei wrote:
> Thank you Greg.
>
> > This job keeps information about the tool that was used, including the
> > version. The results of the job running is the analysis consisting of one
> > or more additional datasets.
> [Wanmei]
some later point. The
resulting dataset is not versioned in the way you describe, but information is
kept about the analysis process that produced the resulting dataset.
Greg Von Kuster
>
>
> Thanks,
> Wanmei
>
>
> ___
running by typing the
following in your Galaxy installation directory.
%hg heads
I believe this behavior will be resolved if you update to the latest code, but
let me know if you continue to bump into problems.
Thanks,
Greg Von Kuster
On May 26, 2012, at 10:51 AM, Björn Grüning wrote:
>
Hi Peter,
The tool shed should be functional now. Thanks for reporting this!
Greg
On May 25, 2012, at 6:08 AM, Peter Cock wrote:
> Hi,
>
> Could someone take a look at the Tool Shed server please?
> I'm getting this for http://toolshed.g2.bx.psu.edu/
>
> 502 Ba
Hello Sarah,
This section of the Galaxy tool shed wiki should provide the information you
need. Let me know if you bump into any additional questions.
http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel
Thanks!
Greg Von Kuster
On May 24, 2012, at 8:15 AM
#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
Greg Von Kuster
On May 18, 2012, at 1:33 PM, Xu, Jianpeng wrote:
> Hi,
> I have installed the local galaxy. Right now I am interested in incorporating
> some new tools into our local galaxy. I am interested in some tools in the
> galaxy
, we don't want to impact that.
Not a very insightful comment ! I used to be indecisive but now I'm not so
sure ...
Greg Edwards
On Thu, May 10, 2012 at 3:20 PM, Clare Sloggett wrote:
> Hi all,
>
> I'm at one of the places Ross mentions (VLSCI), with Enis - among
>
Hi Vipin,
I believe I've fixed the problem that you encountered - the tool shed has been
updated with the fix. Thanks for reporting this! If you see additional
problems, please let me know - I assume I discovered the correct exception in
the log.
Thanks!
Greg Von Kuster
On May 9,
h the repository was
installed. This enhancement is available in change set 7145:ea9f3c25a415 in
our central repository. Thanks for reporting this problem!
Greg Von Kuster
On May 3, 2012, at 6:49 AM, Ira Cooke wrote:
> Hi Dan and Greg,
>
> Thanks for your answers on this. So far I h
Hi Ira,
You'll need to include an entry for the display application in a
datatype_conf.xml file in the tool shed repository- this will result in the
display application being properly installed with the repository and made
functional in the local Galaxy instance. For details about this, see th
Ann,
I'm interested. I'm running a Galaxy instance on AWS Cloud, using the
standard Galaxy Cloudman. Based in Sydney, Aus and also users at SDU,
Odense, Denmark. My timezone for a conf call would be UTC +10 as for some
others here.
Greg Edwards
On Sat, Apr 28, 2012 at 4:45 AM,
alaxy/galaxy-central
Greg Von Kuster
On Apr 30, 2012, at 2:46 PM, Shantanu Pavgi wrote:
>
> I am getting following "ValueError: too many values to unpack" from Python
> while trying to install a tool from toll_shed repository.
>
> {{{
>
> URL:
&g
king down what is different in yours.
Thanks!
Greg Von Kuster
On Apr 26, 2012, at 2:27 PM, Ira Cooke wrote:
> Hi Greg,
>
> I seem to run into the problem regardless of the revision of Galaxy I use ...
> it was happening infrequently until recently ... but now it happens every
>
ngs figured out. By the way, from your description, I assume you
are not running an Apache front-end on either your Galaxy instance or your tool
shed - is this correct?
Thanks!
Greg Von Kuster
On Apr 26, 2012, at 3:41 AM, Ira Cooke wrote:
> Dear List,
>
> I'm trying to c
Hi hans,
On Apr 24, 2012, at 10:49 AM, Hans-Rudolf Hotz wrote:
> Hi Greg
>
>
> I was hoping to avoid thisI will let you know the outcome.
This really shouldn't be a problem, the migration scripts for 91, 92 simply
create new tables with 91 generating new data to insert,
hould backup your database before
attempting this)?
$sh manage_db.sh downgrade 90
After this,
$sh manage_db.sh upgrade
Greg Von Kuster
On Apr 24, 2012, at 10:09 AM, Hans-Rudolf Hotz wrote:
> Hi everybody
>
> I usually don't like people sending the same e-mail several times, so I
&
e run is finished.
I'll work on implementing this enhancement, but I want to understand how you're
lab will use it. Any additional information you can provide will be helpful.
Thanks!
Greg
Add samples to sequencing request "one"
NameState Data LibraryFolder H
actually looks like this in your config file:
database_connection = postgres:///galaxy_db?user=ubuntu&host=/var/run/postgresql
Greg Von Kuster
On Apr 23, 2012, at 2:03 PM, zhengqiu cai wrote:
> Hi All,
>
> I want to use postgresql instead of sqlite, and below is how I did the
ntral repository, updating will
hopefully solve the problems you were seeing.
Thanks!
Greg Von Kuster
On Apr 20, 2012, at 7:39 AM, Paul-Michael Agapow wrote:
> Thanks Greg,
>
> It's a puzzling one alright. Looking forward to testing the new version, if
> only because I'v
in order to use any features
that interact between Galaxy and the tool shed. I believe a new release to the
dist repository is scheduled for some time in the next week or so, so you can
wait for it if you want.
Sorry for the inconvenience!
Greg Von Kuster
On Apr 23, 2012, at 5:53 AM, Peter
east it will
eliminate one of the variables.
Greg Von Kuster
On Apr 19, 2012, at 5:02 AM, Paul-Michael Agapow wrote:
> [For those who came in late - I've installed a local toolshed, which allows
> me to create repositories, but every time I attempt to upload files, it
> errors
On Apr 19, 2012, at 10:37 AM, Lance Parsons wrote:
> and also see about changing the tool id.
I would recommend NOT doing this - see the separate thread for this message
that describes ow this works in the tool shed.
> Sorry for the conflict, that was an oversight on my part, though it wou
On Apr 19, 2012, at 10:04 AM, Peter Cock wrote:
> On Thu, Apr 19, 2012 at 2:32 PM, Greg Von Kuster wrote:
>> The tool shed forces unique repository names per user account, allowing for
>> uniqueness with that combination. All tools uploaded into a tool shed
>> repository
The tool shed forces unique repository names per user account, allowing for
uniqueness with that combination. All tools uploaded into a tool shed
repository are assigned a unique id called a guid, which is unique for all
tools across all possible tool sheds. These guids follow a named spacing
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