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-dat
next 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
Hi Lance,
I installed your htseq repository and all 3 tool dependencies installed fine on
my mac, so the xml definition works!
Greg Von Kuster
On Sep 11, 2012, at 5:50 PM, Lance Parsons wrote:
> Thanks Greg. I used you're updated version and added numpy as a separate
> dependency
o 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 installed
> tools? I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or
>
to 4. 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
-party_tool_dependency_installation_and_compilation_with_installed_repositories),
this is the first change to the way Galaxy tool configs should be written.
I'll get a wiki put together for this new enhancement as soon as possible. I'm
hoping to have it as part of the next Galaxy dist release when the feature is
released.
Greg
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)
> wra
$param1 $param2...
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 wro
from you shed_tool_conf.xml file.
This process is currently 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&#
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 f
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 galax
dditional help or bump into further problems. The
tool dependency installation 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 ap
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
This system level stuff is out of my area of expertise, so others may need to
chime in if you're still having issues.
Greg Von Kuster
On Sep 5, 2012, at 5:22 AM, Paul-Michael Agapow wrote:
> Thanks Greg,
>
>
next 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
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
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
e inconvenience on this.
Greg 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, th
component required 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:
> Look
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 th
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
>
t; "changeset:7404:ec29ce8e27a1" (July 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-Rudo
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
If you install the blast_datatypes repository into your Galaxy instance using
the tool shed installation process everything necessary is handled for you
automatically, but I understand you are not yet installing from the tool shed.
If you are not installing, you'll have to manually download th
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
types repository in the
>> main tool shed and you pull the updates to your
>> local repository.
>>
>> Greg Von Kuster
>
>
>
>>> Hi Björn,
>>> I think the issue is that the genbank datatype is coming in via the tool
>>> shed and is not taken
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
gt; Module posixpath:53 in isabs 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. :)
&g
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
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
way to migrate 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 G
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:
>
> [localhost] out:
> ===
ot
> the same error messages again as described in the email thread below.
>
> Regards
>
> Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
> Genomics, Inc.
> (650) 428-6023 office | (408) 605-3938 mobile
> bcr...@completegenomics.com
>
>
&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.
oolshed before I can install something form the
> public one?
>
> Thanks!
>
> Mattias
>
>
> On 06/13/2012 05:43 PM, Greg Von Kuster wrote:
>> Hello Mattias,
>>
>> Did you pull from the Galaxy central repo? The latest change set is
>> 7262:4fb
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?
>
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
what specific tools
included in the repository are loaded into your tool panel by having them
defined in your tool_conf.xml prior to the installation. This whole process is
associated only with tools that have moved from the Galaxy distribution to the
tool shed.
>
> Thanks again for
27;latest_ctx' referenced before
> assignment
>
> Removing and installing works fine.
> If you need more information to track that bug done, let me know.
>
> Cheers,
> Bjoern
>
>
>> Hello Bjoern,
>>
>> This should be resolved in change set 7211:16a
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
quot;, line
> 1816, in load_egg_for_url
>dialect = guess_dialect_for_url( url )
> File "/home/shantanu/tmp/galaxy-dist/lib/galaxy/model/mapping.py", line
> 1812, in guess_dialect_for_url
>return (url.split(':', 1))[0]
> AttributeError: 'bool
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,
>
write datasets that were
previously generated.
>
> Wanmei
>
>
> From: Greg Von Kuster
> To: Wanmei
> Cc: "galaxy-dev@lists.bx.psu.edu"
> Sent: Monday, May 28, 2012 9:26 AM
> Subject: Re: [galaxy-dev] Data file and Analysis Program versioning
>
>
Job#1 is the previous analysis with the corresponding
> tool/version/output dataset; Job#2 is the new analysis with the corresponding
> tool/version/output dataset. Is my understanding correct?
Yes!
>
>
> Thanks,
> Wanmei
>
> From: Greg Von Kuster
> To: Wanmei
> Cc:
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 Bad Gateway
> nginx/1.1.4
>
> Th
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
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
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