Re: [galaxy-dev] ASN.1 (text and binary) formats in Galaxy & Tool Shed

Clarity in this case, definitely needs the 1. On Feb 19, 2013, at 3:38 PM, Peter Cock wrote: > On Tue, Feb 19, 2013 at 6:45 PM, Nicola Soranzo wrote: >> Il giorno mar, 19/02/2013 alle 14.15 +, Peter Cock ha scritto: >>> On Tue, Feb 19, 2013 at 2:00 PM, James Taylor wrote: On Tue, Feb

[galaxy-dev] Submitting jobs as a real user without using chown, please

Hi, I am trying to setup my galaxy system to allow jobs to be submitted as the real user, since people want to keep an eye on their job on the cluster sometimes and they have no ideas which ones are theirs. I tried the approach on the wiki here: http://wiki.galaxyproject.org/Admin/Confi

Re: [galaxy-dev] Merge internal head to release_2012.02.08

Thanks guys, I will give it a try. Cheers, D On Wed, Feb 20, 2013 at 12:40 AM, Nate Coraor wrote: > Thanks Dannon. One more tip: If you commit your changes on the default > branch, you will need to merge them with stable, i.e. `hg update > release_2013.02.08` followed by `hg merge ` > > --n

Re: [galaxy-dev] deleting and free space

Thank Alfonso, Where is the Options menu though? I do not see anything called Options. Thank you -Original Message- From: Alfonso Garrido-Lecca [mailto:alfonso.garrido-le...@colorado.edu] Sent: Tuesday, February 19, 2013 2:54 PM To: Hakeem Almabrazi; Galaxy Dev Subject: Re: [galaxy-d

[galaxy-dev] Galaxy @ GMOD2013 & Biocuration 2013

Hello all, There are a couple of things going on with the GMOD Project that the Galaxy Community might be interested in. If you aren't familiar with GMOD, it is a federation of open-source projects and tools that enable visualizing, annotating, managing, and analyzing biolog

Re: [galaxy-dev] deleting and free space

you can go to options. then click on show deleted datasets. then this will make appear all datasets that have been "deleted" but are not yet removed from the disk. You will see something like this: "This dataset has been deleted. Click here to undelete or here to immediately remove it from disk

[galaxy-dev] deleting and free space

Hi, I have my own local galaxy installed and things are great. However, I am running of space, is there a better way to free space from the GUI? I have been deleting sets/files from my history but it looks like the Usage still going up. I manually run the following scripts but still nothing

Re: [galaxy-dev] ASN.1 (text and binary) formats in Galaxy & Tool Shed

On Tue, Feb 19, 2013 at 6:45 PM, Nicola Soranzo wrote: > Il giorno mar, 19/02/2013 alle 14.15 +, Peter Cock ha scritto: >> On Tue, Feb 19, 2013 at 2:00 PM, James Taylor wrote: >> > On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote: >> >>I think it could make sense to define generic 'asn1' and

Re: [galaxy-dev] can't run instance for CloudMan

Stefano, Could you clarify what you did differently? The public URL provided by Amazon *should* be the primary interface to your cluster. -Dannon On Tue, Feb 19, 2013 at 12:55 PM, stefano cardinale wrote: > Hello, > thanks, I managed to run the instances by using BioCloudCentral on the same

Re: [galaxy-dev] can't run instance for CloudMan

Hello, thanks, I managed to run the instances by using BioCloudCentral on the same SecurityGroup and Keys I already set up, which were fine. For some reason pointing the browser to the address provided by Amazon, as described in your Wiki CloudMan thread, did not work, but finally I found some

Re: [galaxy-dev] ASN.1 (text and binary) formats in Galaxy & Tool Shed

Il giorno mar, 19/02/2013 alle 14.15 +, Peter Cock ha scritto: > On Tue, Feb 19, 2013 at 2:00 PM, James Taylor wrote: > > On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock > > wrote: > >>I think it could make sense to define generic 'asn1' and > >>'asn1-binary' formats in the Galaxy core (name su

Re: [galaxy-dev] KeyError ['tools'] on importing workflow from locally installed repository

Jorrit, Thank you for uncovering that issue, I've commited a fix in the stable branch of galaxy-central at 8887:d5896e8a60fa. To apply that changeset, you'll need to run the following commands from your Galaxy directory: $ hg pull -b stable https://bitbucket.org/galaxy/galaxy-central/ $ hg up

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Tue, Feb 19, 2013 at 5:26 PM, Nate Coraor wrote: > On Feb 19, 2013, at 12:18 PM, Peter Cock wrote: > Nate wrote: >>> Hi Peter, >>> >>> This is due to the annoying way in which Mercurial handles symlinks. We're >>> going to graft the changesets that caused this up to stable shortly, but in >>>

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Feb 19, 2013, at 12:18 PM, Peter Cock wrote: > On Tue, Feb 19, 2013 at 5:08 PM, Nate Coraor wrote: >> On Feb 19, 2013, at 11:23 AM, Peter Cock wrote: >> >>> Hi all, >>> >>> I've got an hg puzzle, can anyone on the Galaxy team explain the >>> cause of this and what action I can take to avoid

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Tue, Feb 19, 2013 at 5:08 PM, Nate Coraor wrote: > On Feb 19, 2013, at 11:23 AM, Peter Cock wrote: > >> Hi all, >> >> I've got an hg puzzle, can anyone on the Galaxy team explain the >> cause of this and what action I can take to avoid it? >> >> Starting with a clean checkout, >> >> $ hg clone

Re: [galaxy-dev] Changing job command line.

On Feb 14, 2013, at 7:26 AM, James wrote: > Hi Nate, > > Thanks for your reply, > > I guess the idea is that the job is prepared in the interface which lets a > user select > the grid. This is currently located in my galaxy instance as a if statement > in the > default job dispatcher. Just be

Re: [galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

On Feb 19, 2013, at 11:23 AM, Peter Cock wrote: > Hi all, > > I've got an hg puzzle, can anyone on the Galaxy team explain the > cause of this and what action I can take to avoid it? > > Starting with a clean checkout, > > $ hg clone https://bitbucket.org/galaxy/galaxy-central > warning: bitbuc

Re: [galaxy-dev] Datasets linked into Galaxy do not work

On Feb 14, 2013, at 4:38 AM, Sarah Diehl wrote: > Hi Nate, > > copied datasets do work and I run Galaxy from the server root. Hi Sarah, I'm having trouble replicating this issue. Could you send along (privately) the relevant portions of your proxy server configuration, and universe_wsgi.ini?

Re: [galaxy-dev] Searching tool shed for file format definitions?

Hi Peter, This is not yet available, but something I've been planning to do for quite a while. I've opened the following Trello card for this. I'm not exactly sure yet how this will be implemented as I haven't thought this completely though. Of course, ideas from the community are always wel

[galaxy-dev] Galaxy hg repository problem "abort: path ... traverses symbolic link"

Hi all, I've got an hg puzzle, can anyone on the Galaxy team explain the cause of this and what action I can take to avoid it? Starting with a clean checkout, $ hg clone https://bitbucket.org/galaxy/galaxy-central warning: bitbucket.org certificate with fingerprint 24:9c:45:8b:9c:aa:ba:55:4e:01:

[galaxy-dev] Searching tool shed for file format definitions?

Hello all, I was wondering how people keep track of the available file format definitions in the tool shed(s)? For core file types defined in Galaxy, I can just view the datatypes_conf.xml file and/or the classes in lib/galaxy/datatypes/ - but how can I do something similar on a Galaxy Tool Shed?

Re: [galaxy-dev] shall we need to download dataset when we install our local Galaxy?

Hi! You'll probably find this page helpful in configuring your local instance with tools and references: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup In short, yes, to use these references locally you'll need to retrieve them and configure your galaxy to use them. -Dannon On Mon, Fe

[galaxy-dev] shall we need to download dataset when we install our local Galaxy?

hi: When we running a local installation of Galaxy,there are some reference dataset ,such as Human Feb. 2009 (GRCh37/hg19) (hg19),A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1),and so on.Shall we download these datasets and save in our computer ? This is my first use Galaxy,it is very goo

Re: [galaxy-dev] Deploying LOC files for tool built-in data during a tool installation

Hello Jean-Frédéric, Sorry for the delay in this response. Please see my inline comments. On Feb 8, 2013, at 10:33 AM, Jean-Frédéric Berthelot wrote: > Hi list, > > The tool I am currently wrapping has built-in data, which may be used by the > tool users (through a relevant + .LOC file confi

Re: [galaxy-dev] ASN.1 (text and binary) formats in Galaxy & Tool Shed

On Tue, Feb 19, 2013 at 2:00 PM, James Taylor wrote: > On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote: >> Would a pull request implementing this be acceptable? > > Yes. My understanding is that ASN is a completely flexible metaformat, > like XML, and so should be under either Text or Data, wit

Re: [galaxy-dev] Tool wrapper XSD

Hey Pierre, If you are going to write one and want a starting point, here is the schema I used for incorporating Galaxy tools into a Java web service workflow framework called TINT: https://github.com/jmchilton/TINT/blob/master/projects/TropixGalaxy/schema/galaxy.xsd It is mostly a subset of act

Re: [galaxy-dev] Tool wrapper XSD

On Tue, Feb 19, 2013 at 3:39 AM, Pierre Pericard wrote: > Is there a Galaxy XML tool wrapper XSD ? No, but if anyone would like to make such a schema we would be happy to include it. -- James Taylor, Assistant Professor, Biology/CS, Emory University _

Re: [galaxy-dev] ASN.1 (text and binary) formats in Galaxy & Tool Shed

On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote: > Would a pull request implementing this be acceptable? Yes. My understanding is that ASN is a completely flexible metaformat, like XML, and so should be under either Text or Data, with appropriate subtypes defined for blast, et cetera. -- Jame

Re: [galaxy-dev] Merge internal head to release_2012.02.08

Thanks Dannon. One more tip: If you commit your changes on the default branch, you will need to merge them with stable, i.e. `hg update release_2013.02.08` followed by `hg merge ` --nate On Feb 19, 2013, at 7:27 AM, Dannon Baker wrote: > Derrick, > > The new update process outlined works wi

Re: [galaxy-dev] Merge internal head to release_2012.02.08

Derrick, The new update process outlined works with local changes the same way as the 'hg pull -u' used previously. The only difference is that it updates to a particular tag, instead of whatever is at the galaxy-dist tip. 'hg pull -u' that you've used before is actually just shorthand for doing

Re: [galaxy-dev] environment variables and paths for toolshed tools

On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster wrote: > On Feb 19, 2013, at 5:10 AM, Peter Cock wrote: > > Yes, the complete directory hierarchy and content of the original > repository revision is preserved when it installed into Galaxy. > >> Based on a sample of one, it seems the installation

Re: [galaxy-dev] environment variables and paths for toolshed tools

Hi Peter, see below... On Feb 19, 2013, at 5:10 AM, Peter Cock wrote: > On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster wrote: >> Hi Peter, >> >> Thanks for your thoughts on this. I've created the following Trello card >> for this enhancement. >> >> https://trello.com/card/galaxy-tool-enha

[galaxy-dev] ASN.1 (text and binary) formats in Galaxy & Tool Shed

Hello all, Although they are these days also offering XML for many tools, the NCBI still make heavy use of the older ASN.1 file format (both as plain text and binary). This crops up in BLAST (e.g. as the BLAST archive format, or as dustmasker output), in the Entrez Utilities (e.g. for sequence dat

Re: [galaxy-dev] environment variables and paths for toolshed tools

On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster wrote: > Hi Peter, > > Thanks for your thoughts on this. I've created the following Trello card for > this enhancement. > > https://trello.com/card/galaxy-tool-enhancement-to-accommodate-repository-install-dir/506338ce32ae458f6d15e4b3/636 > > The

[galaxy-dev] all the data files in .loc files needed to download ?

Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn shenwiyn___ Please keep all replies on the list by using "reply all" in your mail client. To

[galaxy-dev] Tool wrapper XSD

Hi everyone, Is there a Galaxy XML tool wrapper XSD ? Thanks, Pierre -- Pierre Pericard IE CDD - Projet Peptisan Service Informatique et Bio-informatique (SIB) Station Biologique de Roscoff CNRS - UPMC Place Georges Teissier CS 90074 29688 ROSCOFF CEDEX FRANCE Tel : (+33) 2 98 29 56 46 http:/

Re: [galaxy-dev] changing datasets file_path storage location

On Tuesday, February 19, 2013, Derrick Lin wrote: > Thanks Peter, > > Our data is backup and we are planning to shutdown the galaxy for moving > data to the new place, change the file_path value in universe config, then > start the galaxy again. > > My only concern is if the existing value of file