Dear all,
I was wondering if there is a place within the Galaxy content (a config, an
xml file)
that gives me some handles on how to address attributes of data input.
For example, I can get the 'file_name' of data input, by addressing this
attr
as 'input.file_name', and for example, the original
I realise now this question was also posted to the dev list, which is
probably a better place to discuss it.
-- Forwarded message --
From: Peter
Date: Thu, Feb 3, 2011 at 11:05 AM
Subject: Re: [galaxy-user] listing attributes of data input
To: Freddy de Bree
Cc: galaxy-u...@lists
Hi all,
I'm currently working with some 454 data where the sample was
amplified with selective primers, and therefore the reads need a
little processing to remove the primer sequences before assembly
or mapping (something that sff_extract cleverly spots and warns
the user about when doing an SFF t
Looks like Galaxy is OK with LSF queue that submits to Debian etch
nodes; it seg. faults with jobs running on Debian lenny. The server
itself is running on a lenny node. Investigating further...
Marina
On 02/02/2011 16:43, Marina Gourtovaia wrote:
Hello
I've set up Galaxy to use LSF. My firs
On Thu, Feb 3, 2011 at 11:54 AM, Peter Cock wrote:
> Hi all,
>
> I'm currently working with some 454 data where the sample was
> amplified with selective primers, and therefore the reads need a
> little processing to remove the primer sequences before assembly
> or mapping (something that sff_extr
I asked a similar question in this thread
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-January/004183.html, I
agree it would be nice to have a wiki page showing all the attributes
available to tool elements.
On Thu, Feb 3, 2011 at 12:06 PM, Peter wrote:
> I realise now this question was als
In my earlier email about Barcode/adapter/primer trimming/filtering of
sequences/reads I wrote:
> ...
>
> Currently I have used three separate scripts, with three separate
> XML files - one for each supported file type (FASTA, FASTQ, SFF).
> They all have the same interface, so could be done as a s
To be more precise I made the following change in
scripts/scramble/build/py2.4-linux-x86_64-ucs2/pbs_python/scramble.py
# version string in 2.9.4 setup.py is wrong
print "scramble(): Patching setup.py"
if not os.path.exists( 'setup.py.orig' ):
shutil.copyfile( 'setup.py', 'setup.py.orig' )
Hi,
Sorry I tried to search for this and couldn't find an example to this basic
question where can I find an example on how to populate a tool select
menu with database data?
best,
Leandro
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Hi Nate,
If there are problems with this method please do let us know so we can
look in to it.
Your thoughts about using the FTP upload as you describe should work
fine. Unfortunately it is not written so generically, so you'll need to
set an FTP server name in the appropriate option in the co
Hi all,
In brainstorming here about how to organise the tools menu in our
local Galaxy, we considered an automatically populated list of the
user's frequently or recently used tools. Unlike a favourites system,
this doesn't require explicit action from the user.
That brought us to another thought
Hi Peter,
On Feb 3, 2011, at 10:55 AM, Peter Cock wrote:
> Hi all,
>
> In brainstorming here about how to organise the tools menu in our
> local Galaxy, we considered an automatically populated list of the
> user's frequently or recently used tools. Unlike a favourites system,
> this doesn't req
Stephen Taylor wrote:
> Hi Nate,
>
> >If there are problems with this method please do let us know so we can
> >look in to it.
> >
> >Your thoughts about using the FTP upload as you describe should work
> >fine. Unfortunately it is not written so generically, so you'll need to
> >set an FTP serve
What type of data are you trying to add? For NGS references, see
https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup. Let us know
if that isn't enough info.
Ah, thanks Kelly. I had not come across this page. Following these
instructions, I was able to get a genome to show up in th
On Thu, Feb 3, 2011 at 4:10 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> On Feb 3, 2011, at 10:55 AM, Peter Cock wrote:
>
>> Hi all,
>>
>> In brainstorming here about how to organise the tools menu in our
>> local Galaxy, we considered an automatically populated list of the
>> user's frequently or r
They run under a separate Galaxy webapp which you configure using the
reports_wsgi.ini in the Galaxy install directory ( copy reports_wsgi.ini.sample
and make appropriate changes for your local app ). This is where you'll set a
port, and connect to the same database your Galaxy instance uses.
On Thu, Feb 3, 2011 at 4:38 PM, Greg Von Kuster wrote:
> They run under a separate Galaxy webapp ...
Why? It seems to me it would be easier to have it under the admin pages
of the main Galaxy webapp.
> ... which you configure using the
> reports_wsgi.ini in the Galaxy install directory ( copy
>
Hi,
There are two things: first, the Bowtie for Illumina and Bowtie for
SOLiD wrappers use different data tables (bowtie_indexes as opposed to
bowtie_indexes_color), which refer to different loc files
(bowtie_indexes.loc and bowtie_indexes_color.loc, respectively).
Secondly, although this
On Feb 3, 2011, at 11:58 AM, Peter Cock wrote:
> On Thu, Feb 3, 2011 at 4:38 PM, Greg Von Kuster wrote:
>> They run under a separate Galaxy webapp ...
>
> Why? It seems to me it would be easier to have it under the admin pages
> of the main Galaxy webapp.
Running as a separate web application
Hello everybody,
i'm sorry for posting again. I didn't have any answer during the
christmas holiday, so i take another (and last) chance :)
I'm running a fresh galaxy-dist installation (changeset
4640:8729d2e29b02) on a Centos 5.5 distribution. I'm using LDAP
authentication through Apache.
Here
Hi Nate,
If there are problems with this method please do let us know so we can
look in to it.
Your thoughts about using the FTP upload as you describe should work
fine. Unfortunately it is not written so generically, so you'll need to
set an FTP server name in the appropriate option in the c
Hello Jean-Baptiste,
Running the latest revision in the distribution, (4895:ad933d160a7c), I have
followed your steps precisely and do not see the behavior you state. Making
sure that the user foobar is not an admin user, the only upload options I see
are 'Upload files', 'Upload a directory of
There are two things: first, the Bowtie for Illumina and Bowtie for SOLiD
wrappers use different data tables (bowtie_indexes as opposed to
bowtie_indexes_color), which refer to different loc files (bowtie_indexes.loc
and bowtie_indexes_color.loc, respectively). Secondly, although this won't
Ah
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