On Tue, May 31, 2011 at 11:26 AM, Peter Cock wrote:
> Hi all,
>
> As I mentioned on Twitter, at the end of last week I wrapped Blast2GO
> for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See
> http://blast2go.org/
>
> Currently current code is on bitbucket under my tools branch,
>
Hi,
I want to convert my database from sqlite to postgres. I am able to do it as
far as schema is concerned, but I want to preserve the data as well. When I
changed the database to postgres, all my history got lost. Is there any way
I can preserve the data in sqlite database while converting to po
Hi all,
I have a couple of minor suggestions for improving the website
http://galaxy.psu.edu/gcc2011/Home.html
First, please fill in a meaningful HTML titles since that will be used
as the default caption in a bookmark, tab or window title.
Second, please add a link to the presentation slides an
Hi Harendra
I am not aware of anybody who made this kind of transition without
running into all kind of problems. I suggest the following workaround:
- set up a new, independent Galaxy server using PostgreSQL.
- transfer the histories you want to keep to the new server using the
'Export to F
Matthew Conte wrote:
> Hi Nate,
>
> I was able to finally track down the login issue. It had to do with the
> following setting in my universe_wsgi.ini:
> *
> *
> *cookie_path = /galaxy*
>
> Removing this out fixed the problem and I should be fine leaving it out out
> since I don't need to run m
Harendra chawla wrote:
> Hi Nate,
>
> I have used the local.py logic for submission of my jobs, for a grid based
> architecture. But local.py does not have the recover() function so I was
> trying to use the concept of recover() from other modules. My job submission
> also uses the drmaa api's, so
After following the instructions in the wiki for setting up scaling/load
balancing, I was testing out submitting a job and got this error when trying to
pull data from USCS Main:
Traceback (most recent call last):
File "/usr/local/galaxy-dist/tools/data_source/data_source.py", line 6, in
f
On Wed, Oct 6, 2010 at 11:16 AM, Peter wrote:
> On Tue, Sep 28, 2010 at 12:04 PM, Peter wrote:
>> Hi all,
>>
>> I'm wondering if there is any established way to share parameter
>> definitions between tool wrapper XML files?
>>
>> For example, I am currently working on NCBI BLAST+ wrappers, and th
Louise-Amélie Schmitt wrote:
> Hello everyone
>
> I have an issue when trying to import new datasets or when putting a
> dataset into a history. I saw Edward Kirton had the same problem but he
> got no answer:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html
>
> Here is the err
Greg Von Kuster wrote:
> Hello Louise,
>
> I've CC'd Nate on this as he may be able to help - although no guarantees.
> I'm not expert enough in this area to know where to look for the cause.
> Perhaps someone in the community can help as well.
>
> It is likely that LDAP is playing a role in
Lewis, Brian Andrew wrote:
> After following the instructions in the wiki for setting up scaling/load
> balancing, I was testing out submitting a job and got this error when trying
> to pull data from USCS Main:
>
> Traceback (most recent call last):
> File "/usr/local/galaxy-dist/tools/data_s
Patch Imported in 5618:b9fdb88da530.
Thanks!
Dan
On Mar 16, 2011, at 11:50 AM, Jim Johnson wrote:
> Request is issue#494
> https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch
>
> I'm finding that some qiime metagenomics applications build HTML r
John Eppley wrote:
>
> I had an error upgrading my galaxy instance. I got the following exception
> while migrating the db (during step 64->65):
>
> sqlalchemy.exc.ProgrammingError: (ProgrammingError) (1064, "You have an error
> in your SQL syntax; check the manual that corresponds to your MySQ
Nate -
I checked and I still have a copy of universe_wsgi.ini within my galaxy-dist
directory. I did also make a change in
/usr/local/galaxy-dist/lib/galaxy/eggs/__init__.py according to the post here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002637.html
~ Brian
-Original
On Thu, 2 Jun 2011 11:48:55 -0400, Nate Coraor wrote:
> Greg Von Kuster wrote:
>> Hello Louise,
>>
>> I've CC'd Nate on this as he may be able to help - although no
>> guarantees. I'm not expert enough in this area to know where to look
for
>> the cause. Perhaps someone in the community can hel
Hi all,
Something I've not needed to do until now is define a new file format
in Galaxy. I understand the basic principle and defining a subclass in
Python... however, how does this work with new tools on the Tool Shed?
In particular, if an output format is likely to be used by more than
one tool,
Lewis, Brian Andrew wrote:
> Nate -
>
> I checked and I still have a copy of universe_wsgi.ini within my galaxy-dist
> directory. I did also make a change in
> /usr/local/galaxy-dist/lib/galaxy/eggs/__init__.py according to the post
> here: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May
Okay, yeah, when I changed it back to the original code it worked.
~ Brian
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Thursday, June 02, 2011 12:47 PM
To: Lewis, Brian Andrew
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error: unable to read Galaxy conf
Peter Cock wrote:
> Hi all,
>
> Something I've not needed to do until now is define a new file format
> in Galaxy. I understand the basic principle and defining a subclass in
> Python... however, how does this work with new tools on the Tool Shed?
> In particular, if an output format is likely to
For some odd reason, when I try to import data using the URL
http://localhost:8081 or http://localhost:8081/galaxy none of my jobs will even
show up. However if I go to http://127.0.0.1 or http://127.0.0.1/galaxy the
jobs run fine. Here's a snip from my httpd.conf file:
RewriteEngine on
Rewri
On Jun 2, 2011, at 1:29 PM, Nate Coraor wrote:
> Peter Cock wrote:
>> Hi all,
>>
>> Something I've not needed to do until now is define a new file format
>> in Galaxy. I understand the basic principle and defining a subclass in
>> Python... however, how does this work with new tools on the Tool
I am not sure if this is the right place to post this message, I want to
download TSS fro a list of around 1000 human genes. Is this something I can
do in Galaxy?
Thanks.
___
Please keep all replies on the list by using "reply all"
in your mai
Hi Marco,
Thanks for all of the details, they make a big difference when
troubleshooting. Sorry for the delay in response.
Can you ensure that you don't have any of the pbs_* options set in
universe_wsgi.ini? I noticed that there are stagein/stageouts
set on the job.
You may also need to set $
(moved to galaxy-dev)
Nate Coraor wrote, On 06/02/2011 01:31 PM:
> Peter Cock wrote:
>> On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor wrote:
>>>
>>> pbs.py then knows to translate '8' to
>>> '-l nodes=1:ppn=8'.
>>>
>>> Your tool can access that value a bunch, like $__resources__.cores.
>>>
>>> The
Assaf Gordon wrote:
> (moved to galaxy-dev)
>
> Nate Coraor wrote, On 06/02/2011 01:31 PM:
> > Peter Cock wrote:
> >> On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor wrote:
> >>>
> >>> pbs.py then knows to translate '8' to
> >>> '-l nodes=1:ppn=8'.
> >>>
> >>> Your tool can access that value a bunch,
Shantanu Pavgi wrote:
>
> On May 12, 2011, at 3:43 PM, Nate Coraor wrote:
>
> > Shantanu Pavgi wrote:
> >>
> >> I need some help in configuring galaxy with SGE scheduler using unified
> >> method. The galaxy is running on a system distinct from SGE scheduler
> >> install. The cluster nodes can
SHAUN WEBB wrote:
>
> Hi,
>
> I have a tool that takes a zipped archive as input, finds all the
> sequence files (~90 of them), separates them by barcode, does a
> little extra processing and outputs a single fasta file. I would
> like this to run on Galaxy in a workflow with a few other tools.
>
On Thu, Jun 2, 2011 at 6:29 PM, Nate Coraor wrote:
> Peter Cock wrote:
>> Hi all,
>>
>> Something I've not needed to do until now is define a new file format
>> in Galaxy. I understand the basic principle and defining a subclass in
>> Python... however, how does this work with new tools on the Too
George, David wrote:
> Hi,
>
>
>
> I'm a Galaxy and Python newbie and I'm working on project that desires
> to upload files from a directory to the Galaxy server. We'd like to
> physically copy the files rather than maintain references to them.
>
>
>
> I'm starting by following the example
scott.cou...@monash.edu wrote:
> Hi,
>
> I'm a newbie when it comes to this kind of thing, so I was wondering whether
> you can tell me the most appropriate place to ask questions about making some
> modifications to your nglims extension for galaxy? Should they be posted to
> the normal galaxy
Louise-Amélie Schmitt wrote:
> On Thu, 2 Jun 2011 11:48:55 -0400, Nate Coraor wrote:
> > Greg Von Kuster wrote:
> >> Hello Louise,
> >>
> >> I've CC'd Nate on this as he may be able to help - although no
> >> guarantees. I'm not expert enough in this area to know where to look
> for
> >> the cau
Just FYI,
With the recent version of cufflinks (at least 1.0.2), the developers added a
'feature' of automatic version check.
While the idea is nice, the implications are not:
cufflinks,cuffcompare and cuffdiff will connect to host
"cufflinks.cbcb.umd.edu" every time you run them.
I'm sure the
If you haven't already registered for BOSC, now is your chance--after
June 3, prices will go up!
Registration for BOSC is through the ISMB main conference website:
http://www.iscb.org/ismbeccb2011-registration#sigs . Since BOSC is a
two-day SIG, the price is 2x the one-day SIG price listed on the
shashi shekhar wrote:
> Hi All,
>
> I am using standalone system for galaxy and am doing some modification
> in galaxy .i need the all output file names in local.py .How can i get all
> the output file names in local.py file.
>From the job wrapper object in local.py, job_wrapper.get_output_f
Lewis, Brian Andrew wrote:
> For some odd reason, when I try to import data using the URL
> http://localhost:8081 or http://localhost:8081/galaxy none of my jobs will
> even show up. However if I go to http://127.0.0.1 or http://127.0.0.1/galaxy
> the jobs run fine. Here's a snip from my httpd
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