It looks like the Cheetah syntax only is parsed within the command
tags so I figured out a way to do it... but it seems hackish. I
basically changed the string values of truevalue and falsevalue within the
parameter to be an English sentence that would become the label for the
output. I.e.,
On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB swe...@staffmail.ed.ac.uk
wrote:
I meant to say label=${input} or label=${input.value}.
Nikhil, did you try as Shaun and others have suggested? Any available
string parameter can be used in a label as far as I can tell.
This is a common idiom -
Jack Zhu wrote:
Hi all,
I have problems with updating my local instance of Galaxy.
Specifically I can not migrate the database schema from 80 to 81:
Hi Jack,
Thanks for reporting this issue. It has been fixed in changeset
5951:62d51750d7df.
--nate
--
$$ sh manage_db.sh
Hi All,
I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the
great work.
I have a question regarding contribution of software to galaxy. We developed
a ChIP-seq peak calling algorithm and software (R package) and hope to
contribute it to galaxy. I have read the wiki and prior
Hi All,
I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the
great work.
I have a question regarding contribution of software to galaxy. We developed
a ChIP-seq peak calling algorithm and software (R package) and hope to
contribute it to galaxy. I have read the wiki and prior
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it working
with EPD python?
I've never worked with EPD and since it's not free it's unlikely we can
do much debugging on it here. It would appear that they bundle a
version of pkg_resources which changes the
It is free for academic use. I'll try what you suggested below - thanks!
On Mon, Aug 29, 2011 at 7:59 AM, Nate Coraor n...@bx.psu.edu wrote:
Paul Tanger wrote:
Yes it works with the default python install. Any way I can get it
working
with EPD python?
I've never worked with EPD and
sys path is:
['/Users/paultanger/galaxy-dist/scripts',
'/Users/paultanger/python/scripts',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
Louise-Amélie Schmitt wrote:
Hi,
I ran into a little something that is a bit annoying for debug when
trying to upload files through the API with
library_upload_from_import_dir.py. When the specified folder is
wrong, python tries to process the error tuple like a dict, so the
original error
Le 29/08/2011 15:52, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone,
These questions are a bit silly but I'm really ignorant when it
comes to security. Sorry about that.
Why use API keys instead of user names? Is it to to prevent anyone
from figuring out who is behind an
Hello everybody,
I would like to suggest including mycoplasma genomes (preferably all
genomes in one file) as reference genomes. It would enable fast
checking if cells used for deep-seq experiments were not contaminated.
Best,
Lukasz
___
Paul Tanger wrote:
sys path is:
['/Users/paultanger/galaxy-dist/scripts',
'/Users/paultanger/python/scripts',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python26.zip',
'/Library/Frameworks/Python.framework/Versions/6.1/lib/python2.6',
Getting somewhere, but it looks like it can't find numpy 1.6?
error returned is:
pkg_resources is: module 'pkg_resources' from
'/Users/paultanger/galaxy-dist/lib/pkg_resources.py'
Some eggs are out of date, attempting to fetch...
pkg_resources is: module 'pkg_resources' from
Paul Tanger wrote:
Getting somewhere, but it looks like it can't find numpy 1.6?
error returned is:
pkg_resources is: module 'pkg_resources' from
'/Users/paultanger/galaxy-dist/lib/pkg_resources.py'
Some eggs are out of date, attempting to fetch...
pkg_resources is: module
Louise-Amélie Schmitt wrote:
Le 29/08/2011 15:52, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone,
These questions are a bit silly but I'm really ignorant when it
comes to security. Sorry about that.
Why use API keys instead of user names? Is it to to prevent anyone
That worked, for everything but pysam. I also tried to install it directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try
building it by hand with:
python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
pkg_resources is: module 'pkg_resources'
Dear Nate,
Thank you very much.
Best regards,
Crystal
Date: Mon, 29 Aug 2011 10:04:21 -0400
From: n...@bx.psu.edu
To: crysta...@live.com.my
CC: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy Test disk quota
Crystal Goh wrote:
Dear Nate,
Thanks.
I used
Paul Tanger wrote:
That worked, for everything but pysam. I also tried to install it directly:
pysam 0.4.2 couldn't be downloaded automatically. You can try
building it by hand with:
python scripts/scramble.py -e pysam
Some eggs are out of date, attempting to fetch...
I don't know if I did this correctly, but the output from
python get_platforms.py
is:
macosx-10.5-i386-ucs2
On Mon, Aug 29, 2011 at 12:13 PM, Nate Coraor n...@bx.psu.edu wrote:
Paul Tanger wrote:
That worked, for everything but pysam. I also tried to install it
directly:
pysam 0.4.2
Paul Tanger wrote:
I don't know if I did this correctly, but the output from
python get_platforms.py
is:
macosx-10.5-i386-ucs2
Okay, it looks like EPD python is only compiled for one platform. To
use this, you'll need to scramble your own versions of the eggs which
use C code. Could you try
Hello all
The Galaxy Project is growing and has open positions in both the Penn State
and Emory groups (http://wiki.g2.bx.psu.edu/News/Galaxy%20is%20Hiring).
*Penn State: System administrators/analysts*
The Nekrutenko Lab http://www.bx.psu.edu/%7Eanton/ at the Huck Institutes
of Life Sciences
Hi Ross,
Yes, I did try that... but what I want is string parameter that changes
based on whether or not you've checked a checkbox (or a way to change the
label of the output based on whether or not the checkbox was checked). So
my idea below did work, but it seems like a hack. Which is why I
Most times I need a user supplied label substring. I'm not sure how
else to conditionally set a string to a predetermined value other than
with boolean true/false strings or select parameter values.
One even more ugly option is to use a (strictly speaking now
deprecated) post job exec hook to
Hi Nate,
Thanks for the fix. Everything is working great now.
Jack
On 29 August 2011 09:33, Nate Coraor n...@bx.psu.edu wrote:
Jack Zhu wrote:
Hi all,
I have problems with updating my local instance of Galaxy.
Specifically I can not migrate the database schema from 80 to 81:
Hi Jack,
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