[galaxy-dev] Using a Galaxy image on a local system

2011-04-28 Thread Clare Sloggett
Hi all, I would like to set up Galaxy locally. At the moment, I'm just trying to use it on my desktop (a Mac, OSX 10.6.7), but later we will want a local server to play with. Rather than install galaxy and then install all the tools it can use (and deal with OSX issues for some of them), it

Re: [galaxy-dev] Using a Galaxy image on a local system

2011-05-05 Thread Clare Sloggett
Good luck, Enis On Thu, Apr 28, 2011 at 3:16 AM, Clare Sloggett s...@unimelb.edu.auwrote: Hi all, I would like to set up Galaxy locally. At the moment, I'm just trying to use it on my desktop (a Mac, OSX 10.6.7), but later we will want a local server to play with. Rather than install

[galaxy-dev] Configuration of a local install - mi-deploy ?

2011-11-09 Thread Clare Sloggett
Hi all, Most of our playing around with Galaxy has been in getting it working on our local cloud, but now for the first time I'm configuring a non-cloud local install of galaxy-dist (set up as per http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server) So I have some naive

Re: [galaxy-dev] Configuration of a local install - mi-deploy ?

2011-11-10 Thread Clare Sloggett
, 2011 at 9:14 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Clare, On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote: Hi all, Most of our playing around with Galaxy has been in getting it working on our local cloud, but now for the first time I'm configuring a non-cloud local install

[galaxy-dev] installing multiple versions of a tool / path configuration

2011-11-15 Thread Clare Sloggett
Hi all, I am a little confused as to the right way to configure my installed NGS tools. From the documentation I've found and from looking at the xml/python wrappers, it looks to me like the NGS tool wrappers simply call the tools and assume they will be in the galaxy account's PATH. For

Re: [galaxy-dev] installing multiple versions of a tool / path configuration

2011-11-15 Thread Clare Sloggett
Great! Thanks James, this is exactly what I need. On Wed, Nov 16, 2011 at 2:20 PM, James Taylor ja...@jamestaylor.org wrote: On Nov 15, 2011, at 9:59 PM, Clare Sloggett wrote: If this is the case, what is the best way to install and maintain two versions of the same tool? I can write code

Re: [galaxy-dev] installing multiple versions of a tool / path configuration

2011-11-15 Thread Clare Sloggett
%20Setup to save time for people like me who had tools installed in a non-standard place. Thanks again! Clare On Wed, Nov 16, 2011 at 3:01 PM, Clare Sloggett s...@unimelb.edu.au wrote: Great! Thanks James, this is exactly what I need. On Wed, Nov 16, 2011 at 2:20 PM, James Taylor ja

[galaxy-dev] Missing requirements in xml wrappers in galaxy-dist?

2011-11-16 Thread Clare Sloggett
or would it be better just to raise an issue? Thanks, Clare On Wed, Nov 16, 2011 at 4:33 PM, Clare Sloggett s...@unimelb.edu.au wrote: Looks like it's working! The problem I had run into, in hindsight, was a) I hadn't set tool_dependency_dir as I didn't know about it b) if I had set it, I

Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop

2011-11-20 Thread Clare Sloggett
Hi Jeremy, Enis, That makes sense. I know I can configure how many threads BWA uses in its wrapper, with bwa -t. But, is there somewhere that I need to tell Galaxy the corresponding information, ie that this command-line task will make use of up to 4 cores? Or, does this imply that there is

[galaxy-dev] Removing nodes from a CloudMan instance

2011-11-30 Thread Clare Sloggett
Hi galaxy-devs, Quick question: when using the cloud console on CloudMan, it's possible to add different types of nodes (large, micro, etc) to the virtual cluster using the 'Add Nodes' option at the top. I can also remove a given number of nodes using the 'Remove Nodes' option at the top.

Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop

2011-11-30 Thread Clare Sloggett
is being run (BWA), but if analyses are being run that use multiple tools, jobs will get spread over the cluster to balance the overal load a bit better than by simply looking at the number of slots. Enis On Mon, Nov 21, 2011 at 4:34 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi Jeremy

Re: [galaxy-dev] [galaxy-user] Using Galaxy Cloudman for a workshop

2011-12-01 Thread Clare Sloggett
/2011-10-19--03-14 You simply paste that string into new cluster box you mentioned. Enis On Thu, Dec 1, 2011 at 6:31 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi Enis, Jeremy, and all, Thanks so much for all your help. I have another question which I suspect is just me missing something

Re: [galaxy-dev] Removing nodes from a CloudMan instance

2011-12-04 Thread Clare Sloggett
look into how to implement this option. Enis On Thu, Dec 1, 2011 at 6:20 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi galaxy-devs, Quick question: when using the cloud console on CloudMan, it's possible to add different types of nodes (large, micro, etc) to the virtual cluster using

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-05-09 Thread Clare Sloggett
in your mail client.  To manage your subscriptions to this and other Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/ -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne

[galaxy-dev] Citations for tools

2012-06-18 Thread Clare Sloggett
. Any thoughts? Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357          M: 0414 854

Re: [galaxy-dev] Citations for tools

2012-06-21 Thread Clare Sloggett
is all that's needed? Clare On 18 June 2012 19:50, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, Jun 18, 2012 at 10:29 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi all, I'd like to suggest, or request, a feature - I think that posting to galaxy-dev is the right place to start

[galaxy-dev] egg distribution error when running galaxy-central

2012-07-31 Thread Clare Sloggett
pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto=2.1,!=2.4')) Fetch failed. Any idea what is causing this? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life

Re: [galaxy-dev] egg distribution error when running galaxy-central

2012-07-31 Thread Clare Sloggett
On 1 August 2012 15:28, Clare Sloggett s...@unimelb.edu.au wrote: I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. oops, of course I mean 'so want to run galaxy

Re: [galaxy-dev] egg distribution error when running galaxy-central

2012-08-14 Thread Clare Sloggett
more info here pkg_resources.VersionConflict: (ssh 1.7.14 (/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg), Requirement.parse('pycrypto=2.1,!=2.4')) Fetch failed. Any idea what is causing this? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life

Re: [galaxy-dev] egg distribution error when running galaxy-central

2012-08-20 Thread Clare Sloggett
on galaxy. Works fine after that for me. Cheers Tomithy On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi Scott, Thanks very much for this! virtualenv is ok I think: clare$ echo $PATH /Users/clare/galaxy/galaxy_central_env/bin: . which is where I

Re: [galaxy-dev] egg distribution error when running galaxy-central

2012-08-23 Thread Clare Sloggett
the problem. I think it might be due to an erroneous version of the egg hosted on galaxy. Works fine after that for me. Cheers Tomithy On Wed, Aug 15, 2012 at 10:55 AM, Clare Sloggett s...@unimelb.edu.au wrote: Hi Scott, Thanks very much for this! virtualenv is ok I think: clare$ echo

[galaxy-dev] Using the tools API

2012-08-23 Thread Clare Sloggett
reference genome field is not. The type of the reference genome field also presumably depends on which value is supplied for the referenceGenomeSource conditional. Is there currently a way to specify (or see) these missing fields? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician

Re: [galaxy-dev] Using the tools API

2012-08-23 Thread Clare Sloggett
supported. As always, community contributions are welcome and encouraged. Best, J. On Aug 23, 2012, at 4:10 AM, Clare Sloggett wrote: Hi guys, The Tools API is currently working for me from galaxy-central, but I'm not sure how to correctly run a tool. Are there any example scripts

Re: [galaxy-dev] patch contribution (was Re: So I think I fixed a bug.)

2012-08-28 Thread Clare Sloggett
/ -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

[galaxy-dev] Pull request, and missing step connections

2012-08-28 Thread Clare Sloggett
Dataset is connected to? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357

Re: [galaxy-dev] Using the tools API

2012-08-28 Thread Clare Sloggett
. -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

[galaxy-dev] How to remove a broken toolshed install

2012-10-15 Thread Clare Sloggett
) Module elementtree.ElementTree:859 in parse Module elementtree.ElementTree:576 in parse TypeError: coercing to Unicode: need string or buffer, NoneType found Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation

Re: [galaxy-dev] How to remove a broken toolshed install

2012-10-17 Thread Clare Sloggett
, status='Uninstalled', error_message=Null where name = 'bcftools_view'; Thanks very much! Yes it's postgres. I'll let you know if I succeed. Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University

Re: [galaxy-dev] How to remove a broken toolshed install

2012-10-29 Thread Clare Sloggett
. Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759

[galaxy-dev] Illumina adaptor sequences in tools - copyright?

2012-10-29 Thread Clare Sloggett
with this? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854

[galaxy-dev] Displayed versions of tools in Galaxy

2012-12-11 Thread Clare Sloggett
exported Workflow was built with, and I'm not sure how to do it without confusing them. Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street

Re: [galaxy-dev] BioBlend: Problem Running Example file

2013-03-17 Thread Clare Sloggett
Oops sorry, meant to keep the list cc'd - resending. On 18 March 2013 16:18, Clare Sloggett s...@unimelb.edu.au wrote: Hi Rob, Were you using a very old version of the library and examples or was it quite recent? In any case, try grabbing the script from https://github.com/afgane/bioblend

[galaxy-dev] two versions of show datasets API call?

2013-03-18 Thread Clare Sloggett
. Is it necessary for it to be this way, or are they just there for historical reasons? If it would be desirable to either only have one show-dataset REST method or to make the behaviour of the two identical, should I add a Trello card for this? Thanks, Clare -- Clare Sloggett Research Fellow

[galaxy-dev] Troubleshooting file uploads (to Data Library)

2013-08-21 Thread Clare Sloggett
one of very few users of this instance (quite likely the only user right this moment). I don't think the server is busy, so I'm not sure why the files uploads don't seem to be proceeding. How can I investigate further? Thanks, Clare -- Clare Sloggett Research Fellow / Bioinformatician Life

Re: [galaxy-dev] Troubleshooting file uploads (to Data Library)

2013-08-21 Thread Clare Sloggett
Sorry, missed some information: there are a handful of files, 35MB (gzipped) each. The issue occurs even if I only try to upload one of them though. The server is a 16-core machine. On 21 August 2013 17:08, Clare Sloggett s...@unimelb.edu.au wrote: Hi, I am having trouble uploading files

Re: [galaxy-dev] Troubleshooting file uploads (to Data Library)

2013-08-21 Thread Clare Sloggett
: Hi Clare a few points to start: - do you define the 'File Format'? (don't use 'Auto-detect' for big files) - and similar to a recent question on the list: check your proxy settings Regards, Hans-Rudof On 08/21/2013 09:09 AM, Clare Sloggett wrote: Sorry, missed some