Ok, so I answer to myself. I created 2 template and 1 controller.
You need tu put the controller in
[galaxy_install_dir]/lib/galaxy/webapps/galaxy/controllers/userskeys.py
Contains the user interface in the Universe class
import glob
import logging
import os
import socket
import string
Hi everyone,
Thank you very much for your help.
I want to download the complete directory of galaxy data through rsync -avzP
rsync://datacache.g2.bx.psu.edu/indexes/phiX.But It can't work.
And then I try to via http://dan.g2.bx.psu.edu/ by
http://datacache.g2.bx.psu.edu/ ,I get 502 Bad Gateway.
Hi Greg - the issue is that when the wrapper processes the Macs output,
it attempts to turn the 2nd column of every non-comment line (the
start field) into an integer (as an aside, it then also subtracts 1
from this value).
Unfortunately the line starting chr start end ... isn't commented,
Hello,
our Galaxy server is running low on disk space, so I asked all users to
(permanently) delete old histories and datasets. One specific user alone
managed to reduce his space usage by 2 TB. That's at least what the Galaxy
server says. Afterwards I additionally ran the following scripts:
Hmm, I don't see a patch for your changes to the wrapper script. Can you please
bundle up and send along your tool definition + wrapper script changes and I'll
add it to the card?
Thanks,
J.
On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote:
Hi Jeremy - that's awesome, thanks!
One thing:
Hi Sarah
May be the histories and/or datasets are shared with users who did not
delete them?
Also, have you looked at the log files? What is written in the log files
for the purge_datasets.sh step? Do you have lines like:
Removing disk, file ***/database/files/008/dataset_8271.dat
and
Hi Brad,
I think the method that Thon deBoer is using here is probably the best way to
do it:
http://dev.list.galaxyproject.org/Setting-up-a-proxy-with-authentication-while-waiving-this-for-API-calls-td4658497.html
--nate
On Feb 27, 2013, at 5:34 PM, Langhorst, Brad wrote:
I need to
Hi Hans,
thanks for your help. I didn't realize the sh scripts came with their own
options. I just misunderstood that in the documentation. It seems to have
worked though, the log file says:
# 2013-02-28 11:56:20 - Handling stuff older than 1 days
...
Purged 10097 datasets
Freed disk space:
Ok, sorry for having bothered you again with my stupidness... I actually have a
test instance of galaxy on the same server with the database directory
hard-linked. After I deleted that one the space was free *d'oh*.
- Original Message -
From: Sarah Diehl di...@ie-freiburg.mpg.de
To:
On Feb 28, 2013, at 7:37 AM, Arnau Bria wrote:
Hi all,
my name is Arnau Bria and I work at CRG, in BCN.
I'm a sysadmin and I'm helping one user to install/configure galaxy and
to run jobs in our SGE cluster. I think this is the correct list for
asking SGE/MySQL questions, if not, let me
Hi all,
Is this the correct forum to post blend4j issues ? Apologies if this is not the
case.
I was trying to run a custom workflow via blend4j, according to
https://github.com/jmchilton/blend4j
In my hands, the call to workflowDetails.getInputs() returns an empty Map. I
believe the
Attached to the card, thanks Peter.
J.
On Feb 28, 2013, at 11:14 AM, Peter Briggs wrote:
Hi Jeremy
No problem - zip file with the two patches is attached, please let me know if
there's a problem.
Best wishes
Peter
On 28/02/13 15:07, Jeremy Goecks wrote:
Hmm, I don't see a patch for
This is not a blend4j issue, it is more of a Galaxy API issue. I think
it is essentially a known problem that you cannot specify runtime
parameters for workflow, only data inputs. Here the relevant piece of
Galaxy code:
inputs = {}
for step in latest_workflow.steps:
if
-Original Message-
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Thursday, February 28, 2013 11:27 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] blend4j
This is not a blend4j issue, it is more of a Galaxy API issue.
Hi,I have some problems with the cleanup scripts...I seem to have a dataset_instance that is "None" and if it tries to delete that you obviously get an error. (See below..I added the print statement, but the line is the same)...I wonder how I could get a dataset with a None definition and how can
Hi all;
There are some upcoming coding events and conferences of interest to open source
biology programmers:
- BOSC/Broad Interoperability Hackathon -- This is a two day coding session at
the Broad Institute in Cambridge, MA on April 7-8 focused on improving tool
interoperability.
Hi -
I was only trying to upload a new gzipped-tarfile with new files to a
repository that I own on the sandbox toolshed server, and get the following
error:
Server ErrorURL:
http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d
Module
Hello all,
The March 2013 Galaxy Update is now
availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03.
See http://wiki.galaxyproject.org/GalaxyUpdates/2013_03. *Highlights
include:*
-
*GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_03#GCC2013 early
registration
Hi guys,
I was given the following error when upgrading the database from 109 to 110:
0109_add_repository_dependency_tables DEBUG 2013-03-01 15:14:15,554
Creating repository_repository_dependency_association table failed:
(OperationalError) (1059, Identifier name
Still waiting on a reply! Any suggestion is appreciated.
On Tue, Feb 26, 2013 at 1:55 PM, Mahtab Mirmomeni
m.mirmom...@student.unimelb.edu.au wrote:
Hi all,
I have installed Deseq (by vipints) from the main galaxy toolshed and have
followed the make instructions but I'm still not unable
Hi,
I have tried to follow instructions provided with this installation
a) Run ./setup_deseq-hts.sh and setup paths and configuration options for
DESeq-hts.
I successfully ran the setup scrip but is there other path and conf that
need to be done apart from those done by this script ?
b) Inside
Hi Philipe
Look into the bin/deseq_config.sh and see if the path to octave and
samtools have been set correctly.
I'm having problem running DESeq too. I go past this point by I get
get_reads.mex
error: path/shed_tools/
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