Hey there
Using the new upload tool my data uploads but never appears in the
history. All I can see in paster.log when I do an upload is:
10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] POST /tool_runner/index
HTTP/1.0 200 - https://phillipl.sanbi.ac.za/root; Mozilla/5.0 (X11;
Ubuntu; Linux x86_64;
Hi there
I updated a tool of mine recently, committed to the local toolshed, did
the update from within the Admin panel and then got this error:
Error - type 'exceptions.AttributeError': 'Tool' object has no
attribute 'citations'
A restart of Galaxy seemed to fix the problem, but since then
- cannot say if it is the only error though:
param format=graphml name=in_graph_filename type=data
label=Protein interaction graph
/inputs
-John
On Tue, Aug 12, 2014 at 2:00 PM, Peter van Heusden p...@sanbi.ac.za wrote:
1. Yes, its definitely a delete (checked the box).
2. The tool
I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed
using the Admin interface to Galaxy. Unfortunately, each time I do this
I get an error page with the message:
No action for /admin_toolshed/prepare_for_install
My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0.
Hi everyone
The Galaxy system as described in Belinda Giardine et al's 2005 Genome
Research paper (Galaxy: A platform for interactive large-scale genome
analysis) appears to be radically different from the current Galaxy, at
least in its technical specification. The paper mentions a C core spoken
on the Galaxy team that are
more familiar with the API and can provider better answers. I expect they'll
chime in soon to address your questions.
Best,
J.
On May 20, 2012, at 5:39 PM, Peter van Heusden wrote:
Hi Jeremy
I'm need this for something I'm implementing at the moment, and how I'm
Hi there
I've got a workflow that uses BioPerl's bp_genbank2gff3 to convert
Genbank to GFF3, then hands the GFF3 to Extract features to filter to
only genes, before moving on. The workflow JSON is at
http://pastebin.com/zHWsC6YT. Step 4 - the Genbank2GFF runs fine, and if
I view the output in the
Hi there
Because my Galaxy workflows tend to sprawl outside the viewable space in
my browser, I've written a script that, when given a workflow JSON file
as input, writes out a graphviz dot format graph of the workflow. By
default the graph treats datasets as nodes and analyses as edges (unlike
Hi Jeremy
I'm need this for something I'm implementing at the moment, and how I'm
thinking about it is making a tool that uses the API to call a workflow.
There are a few problems though, correct me if I'm wrong:
1) In order to make an input history item available to the called
workflow, the
Hi there
As I adapt Galaxy to the needs of the particular workflows I'm
implementing, I invariably end up tweaking the existing code,
especially the tool definitions and the datatypes config file. These
tweaks are often minor - e.g. adding an extra parameter to Ross Lazarus'
ClustalW's code,
Hi there
I'm trying to wrap Bioperl's bp_genbank2gff script. This script, by
default, produces an output file named the same as the basename of the
input file, with .gff added. So e.g.
bp_genbank2gff data.gbk
produces a file named data.gbk.gff.
I'm trying to use the from_work_dir attribute of
Hi there
Is there a way in Galaxy to use workflows as components in workflows?
I've got two datasets that start as Genbank files and are processed
(features extracted, translated to AA) by a small workflow, and then
BLASTed against one another. Ideally I'd like to modularise the initial
steps as
We have a small collaboration between institutions in the greater Cape
Town region (UCT, UWC, Stellenbosch) on this topic (the so-called
Pipelines group). If anyone in South Africa is interested in talking
about these topics, please get in touch because we could share expertise.
Peter
SANBI - UWC
Hi there
I've got nginx 1.0.5 in front of my Galaxy instance, and I'm trying to
get uploads to work as per 'Receiving files using nginx' instructions on
the Galaxy wiki.
I've added the relevant config to my nginx setup (pastebin
http://paste.ubuntu.com/961983/) and universe_wsgi.ini (pastebin
Hey there
The instructions on using REMOTE_USER with nginx are still a bit vague
in the wiki, so let me share how I got this working with nginx's
http_auth_pam module and our local Kerberos setup. Really simple actually:
First, I created a pam.d entry for nginx, as follows:
auth[success=1
Hi there
I recently wrote some code to run Galaxy jobs as a different user, and
was just merging my codebase (https://bitbucket.org/pvanheus/galaxy)
with galaxy-central when I noticed that code doing the same thing is now
part of galaxy-central. The code in galaxy-central is more
straightforward
On 30/11/2011 11:58, Peter Cock wrote:
On Wed, Nov 30, 2011 at 9:49 AM, Peter van Heusden wrote:
Yes, this went away with newer versions of BLAST (and BLAST+).
The 2.2.15 version is from 2006.
OK, that would explain why I didn't find the issue myself
during the development.
I've added test
Hi everyone
I've been using the twobit datatype as generated by faToTwoBit (part of
Jim Kent's BLAT package) and read by bx-python (bx.seq.twobit). So
here's a patch to add the twobit datatype to Galaxy.
Peter
# HG changeset patch
# User Peter van Heusden p...@sanbi.ac.za
# Date 1307966741
As discussed in the Workflows and APIs breakaway session, here is the
paper on Workflow patterns:
van der Aalst, ter Hofsted, Kiepuszewski and Barros, Distributed and
Parallel Databases, Volume 14, Number 1, 5-51: Workflow Patterns
PDF available at:
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