On Thu, Apr 14, 2011 at 2:08 PM, Leandro Hermida
soft...@leandrohermida.com wrote:
Hi,
I have a tool with a code file=my_script.py/ tag and in that code file
I'm trying to get the tool dirpath where that script and the tool XML
exist. I've tried:
I could narrow it down even further. As soon as I set anything to To be
set at runtime the download fails.
On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a
screenshot of a really simple workflow whose download fails. I
Thanks Sarah. I was having trouble reproducing because I hadn't set a runtime
parameter. I've fixed the bug in galaxy-central changeset 5387:835656900dd0 ;
after making this change, I was able to successfully export and import
workflows with runtime parameters.
Best,
J.
On Apr 14, 2011, at
I assume when you dropped the old database and recreated the new, empty
database, you made sure the database connection string in universe_wsgi.ini was
correctly set. if so, when you started up Galaxy, it would have created all of
the required tables in the new database, and they would all be
I used this step by step :
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
to set up galaxy with apache proxy.
I added these lines to httpd.conf file :
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*)
On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote:
Here is the result I got from the debug statements:
galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ###
history: None
This is the problem - when you registered normally, a history would have been
automatically
Hello,
I'm working on a simple python script that auto-magically creates all
indexes, and pre-processing necessary to add a genome to galaxy. I was
wondering if anyone had a script to download all the genomes that are
presented to you in the default genome drop down box?
Also I'm not to
Dear Sir
I try to use Bowtie mapping in galaxy , I import my Illumina
s_1_sequence.txt , then I try to use the convert
my userName is my email
21: FASTQ Groomer on data 9
An error occurred running this job: /There was an error reading your
input file. Your input file is likely
Hi all,
I just wanted to mention (to avoid duplicate work) that I have a working
Galaxy wrapper for NLStradamus v1.6, a tool for prediction of nuclear
localization signals (NLSs) from a protein FASTA file. The wrapper
does a little reformatting of the output to get a clean tabular file for use
in
The thing is, we use LDAP logging so we can't even access the website
without logging in.
Moreover, when I logged in, I arrived on the data analysis page where the
automatic unnamed history was obviously created in the history panel.
I forgot to mention we have issues creating and deleting
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 this behavior.
On Apr 14, 2011, at
I'm working on a module that involves calling a workflow multiple times over a
set of data.
The workflow has a variable that I use for renaming output files.
I see, using the workflow_execute.py example how to pass in file names, but I
don't see how to pass in a value for this variable.
When
James;
I'm working on a simple python script that auto-magically creates
all indexes, and pre-processing necessary to add a genome to galaxy.
I was wondering if anyone had a script to download all the genomes
that are presented to you in the default genome drop down box?
Really great you are
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