Camelia, the Perl 6 bug

IRC log for #bioclipse, 2011-01-31

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All times shown according to UTC.

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12:48 samuell On this page ([1]), it says "After you have downloaded and installed the [OSGi] bundle in your OSGi container" ...
12:48 samuell [1]: http://www.osgilook.com/2009/08/24/o​sgi-preferences-service-by-example/
12:48 zarah samuell's link is also http://tinyurl.com/4ulk36s
12:48 samuell What does this mean?
12:48 samuell What is my "OSGi container"?
12:50 samuell Gpox: How do I practically go about installing an OSGi bundle (the preferences service you linked last week) in my plugin?
12:50 samuell (In short words .... just need a pointer, I think)
12:55 samuell (Hmm, seems it is available as an equinox implementation as well, in the Eclipse CVS ... http://dev.eclipse.org/viewcvs/viewvc.cgi/o​rg.eclipse.equinox/compendium/bundles/org.e​clipse.equinox.preferences/?root=RT_Project )
12:55 zarah samuell's link is also http://tinyurl.com/6jj5aba
12:56 Gpox when you run from within eclipse or from a product you specify that you want to use that bundle ie. inlude it in a feature you run
12:58 Gpox to make sure it is started in the 'Run Configurations' dialog under the tab plugins you can choose if the bundle should be auto-started
13:01 samuell Gpox: Ok, but I have to download it first, I guess?
13:01 samuell ... can I just checkout from CVS and import it as an eclipse plugin?
13:02 Gpox looks like the preferences service is included in the spec. and thus is included
13:02 samuell Gpox: Ah, ok
13:03 Gpox add orgeclipse.equinox.preferences bundle or import org.osgi.service.prefs to get it
13:04 Gpox package
13:04 samuell Gpox: Ok, and that is, in feature.xml?
13:05 Gpox in the plugin
13:05 samuell Gpox: Ok, will try if I can figure out where to add things ...
13:06 Gpox Dependencies-> Required Plug-ins or Imported Packages
13:07 samuell Gpox: Ok, and this "dependencies", that is the tab that I get when opening "plugin.xml"?
13:08 Gpox yes
13:08 samuell Ok ...
13:08 samuell Ok, found, and added, org.eclipse.equinox.preferences.source
13:09 Gpox -source
13:10 samuell Hmm, ok ... the one without the "-source" was not there :(
13:12 Gpox it might already be there, if you try and use PreferencesService you should get a warning and be able to use quick fix to add it if it is not there
13:12 samuell Gpox: Ok, will try that!
13:15 samuell Gpox: Yeah, indeed seems like it is already there ... one thing only now ...
13:15 samuell Do you happen to know what that "context" variable is, on http://www.osgilook.com/2009/08/24/o​sgi-preferences-service-by-example/
13:15 zarah samuell's link is also http://tinyurl.com/4ulk36s
13:15 samuell ... they don't show how they initialize it in the code example ...
13:16 samuell ... maybe it's something very basic, that I'm supposed to understand :) ....
13:17 Gpox you get one in the start method of your activator or you can use org.osgi.framework.FrameworkUtil.getB​unlde(this.getClass).getBundleContext
13:18 samuell Gpox: Ok ... also, I just found out it is shown better in the linked docs: http://felix.apache.org/site/apac​he-felix-preferences-service.html
13:19 samuell Gpox: Ah, ok, I have the context variable initialized already, in the start method of the Activator class ...
13:19 samuell Ok ok
13:19 samuell Ok, many thanks Gpox!
13:24 samuell (Ok, will try also the other method you suggested ... )
13:26 samuell ... seems to work fine :)
13:26 samuell Gpox++
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15:03 CIA-91 bioclipse.experimental: Carl Masak master * rf25ef19 / (22 files in 6 dirs): (log message trimmed)
15:03 CIA-91 bioclipse.experimental: replaced shell process with JRI process
15:03 CIA-91 bioclipse.experimental: This makes for a more robust connection with R, and hopefully provides a
15:03 CIA-91 bioclipse.experimental: better way to communicate back and forth between R and Bioclipse,
15:03 CIA-91 bioclipse.experimental: long-term. The console output still needs some fixing-up, and right now
15:03 CIA-91 bioclipse.experimental: Bioclipse dies unless provided with the VM argument
15:03 CIA-91 bioclipse.experimental:  -Djava.library.path="/Library/Frameworks/​R.framework/Resources/library/rJava/jri:"
15:04 samuell All: Is there anything such as a BSL reference?
15:04 samuell BSL Cheat cheet/Refcard?
15:04 * samuell would need it now :">
15:05 samuell Ok ... there's something: http://wiki.bioclipse.net/index.p​hp?title=Scripting_in_Bioclipse_2
15:05 samuell I tried to loop over some results from a method returning List<String> .... but don't get it to work
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15:06 egonw cande: https://github.com/bioclipse/bioclipse.statistics
15:06 egonw samuell: not at this moment, I think... we really need to write the BSL book
15:06 samuell egonw: Ok
15:08 samuell Guess the most comprehensive example collection is egonw 's blog atm :)
15:09 egonw myexperiment.org and gist.github.com has more; i think
15:10 samuell egonw: Well, ok
15:12 olass samuell: there is generated help docu for BSL
15:13 olass masak and egonw wrote perl scripts for this
15:13 samuell olass: Ah ...
15:13 olass see help system...
15:13 olass net.bioclipse.doc plugin if I remember correctly... (egonw?)
15:16 samuell Unfortunately no example on looping over stuff
15:17 samuell I tried:
15:17 samuell for (string in strings) {
15:17 samuell / do stuff ...
15:17 samuell }
15:17 egonw that's groovy talk :)
15:17 samuell egonw: ah, true
15:18 egonw for (i=0; i<strings.length; i++)
15:18 egonw samuell: just google for a JS tutorial
15:18 egonw but I agree this would make a nice book for Oakleave
15:18 samuell egonw: Yeah, already finding some groovy CheatCheets :)
15:18 samuell (Cheat sheets)
15:18 egonw samuell: why not try the Groovy console ?
15:19 egonw ok, bbl
15:20 samuell egonw: Hmm, thought BSL was groovy already ... Never saw the groovy console before :-o
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15:28 olass samuell: BSL is Javascript for now...
15:28 samuell olass: Ok
15:29 olass but there is a groovy console, just not as mature..
15:29 * olass doesn't know its current status
15:29 * samuell didn't get the manager methods to show up with auto-completion, at least ...
15:31 samuell But then I know.
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15:52 CIA-91 bioclipse.statistics: Carl Masak master * r468eae2 / (22 files in 6 dirs): (log message trimmed)
15:52 CIA-91 bioclipse.statistics: replaced shell process with JRI process
15:52 CIA-91 bioclipse.statistics: This makes for a more robust connection with R, and hopefully provides a
15:52 CIA-91 bioclipse.statistics: better way to communicate back and forth between R and Bioclipse,
15:52 CIA-91 bioclipse.statistics: long-term. The console output still needs some fixing-up, and right now
15:52 CIA-91 bioclipse.statistics: Bioclipse dies unless provided with the VM argument
15:52 CIA-91 bioclipse.statistics:  -Djava.library.path="/Library/Frameworks/​R.framework/Resources/library/rJava/jri:"
15:53 egonw mmm... that path looks quite platform dependent... :/
16:11 egonw Gpox: ping
16:11 Gpox egonw: pong
16:11 egonw Gpox: where should net.bioclipse.jama be coming from?
16:11 egonw target platform=
16:12 egonw target platform?
16:12 Gpox yes
16:12 egonw ok, unexpected :)
16:12 egonw given the net.bioclipse.jama name :)
16:13 Gpox we don't have a naming convension for external libs that has been osgi-ified
16:13 egonw I always follow the java pkg names
16:14 egonw but Jama does not really have one, or...
16:15 Gpox use import package instead of Required-Bundle for it. Then it is easy to change the name of the bundle
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16:19 egonw_ you add the net.bioclipse.jama plugin to the statistics_feature...
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16:19 egonw_ that should remain, Gpox?
16:20 Gpox yes
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16:56 CIA-91 bioclipse.statistics: Egon Willighagen master * r4bebd33 / README : Added details on how to get R-support going on Debian - http://bit.ly/eT9vvp
16:56 CIA-91 bioclipse.statistics: Egon Willighagen master * r113cabd / plugins/net.bioclipse.r/plugin.xml : Removed EP that is no longer used - http://bit.ly/eHvQxN
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17:04 samuell olass: Any good idea how to store Galaxy tool config files (or it's data), with the uppmax plugin?
17:04 samuell .... the question is, what is most convenient and smart ...
17:04 olass can you add it to the plugin?
17:05 olass at devel time?
17:05 samuell olass: Yeah, thought about that
17:05 olass just create a folder in the plugin then...
17:05 samuell ... but then one would like to be able to import new definitions later
17:05 olass you can easily do that with a plugin fragment
17:05 olass I can explain tomorrow
17:05 samuell olass: Right ... sounds like an idea
17:06 olass if you like, make the galaxy config a separate plugin
17:06 samuell olass: Indeed
17:06 olass maybe that is the best way to go..
17:06 samuell olass: Sounds reasonablew
17:06 olass yeah, i think so
17:06 samuell Ok, talk more tomorrow
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20:00 egonw olass: ping
20:00 egonw olass: urgent
20:00 olass pong
20:00 egonw there recently was another life sciences workbench introduced...
20:01 egonw do you remember the name?
20:01 olass where?
20:01 olass no, don't remember...
20:01 olass what context?
20:02 egonw something like Jalview...
20:02 egonw but it was something else...
20:02 olass recently?
20:02 egonw 2010, I think
20:03 olass for cheminformatics?
20:03 olass I only know of bioinformatics workbenches...
20:03 olass like http://www.ncbi.nlm.nih.gov/projects/gbench/
20:03 olass and utopia
20:03 olass nothing with chemistry...
20:04 egonw ok, that's enough fo rme..
20:04 egonw I need to go offline
20:05 olass ok
20:05 olass sorry I can't remember more...
20:05 egonw np
20:05 olass wait a sec...
20:05 egonw I emailed some suggested text to Jarl
20:06 olass hmm, never mind
20:06 olass ok, great
20:06 olass I have no clue for bench
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