On Fri, Feb 15, 2013 at 6:10 PM, Nicola Soranzo wrote:
>Peter wrote:
>>
>> It seems to have confused the bitbucket page a little, but I have
>> checked in your initial wrapper to my development repository (I
>> use the tools branch):
>> https://bitbucket.org/peterjc/galaxy-central/commits/2284d485
Il giorno lun, 11/02/2013 alle 13.19 +, Peter Cock ha scritto:
> On Fri, Feb 8, 2013 at 4:30 PM, Nicola Soranzo wrote:
> > Il giorno mer, 06/02/2013 alle 20.01 +0100, Nicola Soranzo ha scritto:
> >> Hi Peter,
> >> I added these file formats mostly as placeholders for a future
> >> implementati
On Fri, Feb 15, 2013 at 11:08 AM, Dannon Baker wrote:
> Well, (un)fortunately this file works for me in both firefox and
> chrome on the current galaxy-dist. Just to confirm -- when you click
> the eye, it doesn't download the file either, right -- nothing at all
> happens?
>
> In chrome, could y
On Fri, Feb 15, 2013 at 4:57 PM, Greg Von Kuster wrote:
>
> On Feb 15, 2013, at 11:45 AM, Peter Cock wrote:
>> Actually for the example I am working on, the motif.py script would be
>> the tool executable, called from motif.xml like this:
>>
>> motif.py $fasta_file $tabular_file
>>
>> i.e. A compl
On Feb 15, 2013, at 11:45 AM, Peter Cock wrote:
> On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster wrote:
>
> Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
> say motif.dat) which is used by a script (say motif.py) via a normal
> Galaxy tool XML file (
Thank you Greg,
I will contact the owner of that software and see if we can get it installed.
Regards
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, February 15, 2013 10:13 AM
To: Hakeem Almabrazi
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Install NGSRich in local galaxy
Hello Hakee
On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster wrote:
Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
say motif.dat) which is used by a script (say motif.py) via a normal
Galaxy tool XML file (say motif.xml).
Perhaps I can just put my data
Hi Peter,
On Feb 15, 2013, at 11:14 AM, Peter Cock wrote:
> On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster wrote:
>>>
>>> Hi guys,
>>>
>>> Reading the rest of the thread from December, Greg's new code did
>>> get checked in and should be working (I've not tried this yet).
>>>
>>> However, I
On Feb 15, 2013, at 11:12 AM, Rodolfo Aramayo wrote:
> Hi,
>
> I hope this is the right place to ask,
>
> I am trying to rsync from:
>
> rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/
>
> and I am getting the error:
>
> @ERROR: chroot failed
> rsync error: error starting client-server p
On Feb 15, 2013, at 11:13 AM, greg wrote:
> Thanks! One followup, see below.
>
> -Greg
>
> On Fri, Feb 15, 2013 at 11:01 AM, Nate Coraor wrote:
>> On Feb 15, 2013, at 10:45 AM, greg wrote:
>>
>>
>> Migrate:
>>
>> % sh manage_db.sh upgrade
>>
>> Pay attention to whatever the first revision
On Fri, Feb 15, 2013 at 4:05 PM, Greg Von Kuster wrote:
>>
>> Hi guys,
>>
>> Reading the rest of the thread from December, Greg's new code did
>> get checked in and should be working (I've not tried this yet).
>>
>> However, I can't help feeling that defining the two environment variables
>> David
Hi,
I hope this is the right place to ask,
I am trying to rsync from:
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/
and I am getting the error:
@ERROR: chroot failed
rsync error: error starting client-server protocol (code 5) at main.c(1534)
[Receiver=3.0.9
I know I can rsync to any ot
Thanks! One followup, see below.
-Greg
On Fri, Feb 15, 2013 at 11:01 AM, Nate Coraor wrote:
> On Feb 15, 2013, at 10:45 AM, greg wrote:
>
>
> Migrate:
>
> % sh manage_db.sh upgrade
>
> Pay attention to whatever the first revision you are migrating from is.
> Probably 109 if you were at the 1/
Hello Hakeem,
When searching the tool shed from Galaxy, only repositories that are
automatically installable into Galaxy will be located. Repositories are
considered "installable" if they contain valid Galaxy utilities (tools,
proprietary datatypes, repository dependency definitions, tool depe
Well, (un)fortunately this file works for me in both firefox and
chrome on the current galaxy-dist. Just to confirm -- when you click
the eye, it doesn't download the file either, right -- nothing at all
happens?
In chrome, could you open the console (Tools -> Javascript Console or
Ctrl+Shift+J)
Hello Peter, please see my response at the end.
On Feb 15, 2013, at 6:47 AM, Peter Cock wrote:
>>> 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
On Feb 15, 2013, at 10:45 AM, greg wrote:
> Hi guys,
>
> I'm trying to do my first update on my local galaxy install (it's been
> a few months at least since I installed)
>
> I'm trying to follow the instructions here to update the code:
> http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_yo
It's really hard to say what's going on with those issues without more
information about the particular version of galaxy (which
unfortunately we'd get from `hg tip`, which won't work on your bio
linux install) or proxy configuration, if any. I'm also not sure what
the appropriate bio linux update
Hi guys,
I'm trying to do my first update on my local galaxy install (it's been
a few months at least since I installed)
I'm trying to follow the instructions here to update the code:
http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date
My first question is how do I roll ba
Thank you Greg,
That what I tried to do initially but I could not find this tool the tool shed
repository. Here is what I did, as an admin I went to Search and browse shed
tool->Galaxy main tool shed
Then I searched for "ngsrich" I could not find it. Then I looked under static
category I stil
Ok, I created a ~/.hgrc file and add this:
[trusted]
users=galaxy
It seems to have fixed it.
-Greg
On Fri, Feb 15, 2013 at 9:50 AM, greg wrote:
> Thanks.
>
> I'm trying to follow the instructions here to update the code:
> http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_d
Hi,
Enclosed is a dataset that I am not able to see anymore.
I don't see any error in the log (but maybe I missed it !).
To answer to Carlos, I have the problem with Firefox and Chrome.
Cheers,
Mathieu
- Mail original -
> De: "Dannon Baker"
> À: "Mathieu Bahin"
> Cc: galaxy-dev@lists.
I still haven't heard back from the Bio-Linux guys regarding how to update
Galaxy within Bio-Linux...
In the meantime, I tried to play with the "Manage data libraries", in order
to import large datasets. I modified the "library_import_dir" line in the
universe_wsgi.ini. The first thing I can say i
Thanks.
I'm trying to follow the instructions here to update the code:
http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date
But I'm getting this error:
>hg incoming
Not trusting file /misc/local/galaxy/galaxy-dist/.hg/hgrc from
untrusted user galaxy, group scicomp
Not trust
Hello Greg,
What version of Galaxy are you running - it is likely older than the December
20, 2012 Galaxy release. You'll have to upgrade to at least that release to
use the main Galaxy tool shed.
Greg Von Kuster
On Feb 15, 2013, at 9:43 AM, greg wrote:
> Hi guys,
>
> I'm getting an error w
Hi guys,
I'm getting an error when trying to install this from the toolshed?
Let me know what I should do?
Thanks,
Greg
Error - : too many values to unpack
URL:
http://galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=67abe7fe2882a54c&changes
You likely want the newest version (3)
On Feb 15, 2013 9:37 AM, "greg" wrote:
> Thanks! So one question, when I go to install it from the toolshed I
> see two choices for a revision to select:
>
> 3:cdd9791c0afa
> 0:c1eeccec29d1
>
> Which would I choose and why?
>
> Thanks,
>
> Greg
>
> On Fri,
Thanks! So one question, when I go to install it from the toolshed I
see two choices for a revision to select:
3:cdd9791c0afa
0:c1eeccec29d1
Which would I choose and why?
Thanks,
Greg
On Fri, Feb 15, 2013 at 9:30 AM, James Taylor wrote:
> The wrapper you are using is for MACS 1.3, there is a
The wrapper you are using is for MACS 1.3, there is a wrapper that is
compatible with 1.4 in the toolshed.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Fri, Feb 15, 2013 at 9:26 AM, greg wrote:
> Hi guys,
>
> I'm trying to run MACS in my local galaxy install (see screen
Hi guys,
I'm trying to run MACS in my local galaxy install (see screenshot:
http://snag.gy/5QGUH.jpg)
And I'm getting this error:
Usage: macs <-t tfile> [-n name] [-g genomesize] [options]
Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks
macs: error: no such opti
Jeremy,
But the tophat2 is running successfully in the command line. So, I guess
it's related to Galaxy. Why am I getting this error in Galaxy? Is it
because I don't have latest Galaxy? Is it file permission issue? I am using
Tophat V2.0.7 and latest Bowtie2 version.
On Fri, Feb 15, 2013 at 8:02
This is not a known bug. For questions related to Tophat errors, you might try
the Tophat mailing list:
tophat.cuffli...@gmail.com
Good luck,
J.
On Feb 15, 2013, at 6:02 AM, Sachit Adhikari wrote:
> Galaxy is working fine in command line whereas in Galaxy at last i got this
> error:
>
>
> [
Now try running the test data in Galaxy to see if you get the same results. You
should probably try running from the history first and then try adding the test
data as a built-in genome via the bowtie2_indexes.loc table
Best,
J.
On Feb 15, 2013, at 12:18 AM, Sachit Adhikari wrote:
> Hi Jeremy,
Stefano,
Sounds like it's most likely that the security groups aren't configured
correctly. What I'd recommend would be to launch your instance using
http://usegalaxy.org/cloudlaunch which does all of those configuration steps
for you automatically.
-Dannon
On Feb 14, 2013, at 8:28 PM, stef
>> 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
>> $GALAXY_HOME, then uploaded it the test toolshed, then installed it
>> automatically. Nei
-- Forwarded message --
From: Sachit Adhikari
Date: Fri, Feb 15, 2013 at 11:02 AM
Subject: Error while writing data in tophat2
To: galaxy-dev@lists.bx.psu.edu
Galaxy is working fine in command line whereas in Galaxy at last i got this
error:
[2013-02-15 01:39:12] Reporting outp
Hi Stefano,
Can you try out what we put together:
https://github.com/modENCODE-DCC/Galaxy
Thanks,
Q
On Thu, Feb 14, 2013 at 8:28 PM, stefano cardinale
wrote:
> Hi, I am having a problem with running galaxy on the Amazon cloud. I have
> tried this several times over the past few days, I foll
Galaxy is working fine in command line whereas in Galaxy at last i got this
error:
[2013-02-15 01:39:12] Reporting output tracks
[FAILED]
Error running /usr/local/bin/tophat_reports --min-anchor 8
--splice-mismatches 0 --min-report-intron 50 --max-report-intron
50 --min-isoform-fract
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