Re: [base] Base1PluginExecutor
Johan Enell wrote: > It is correct that reporterlists isn't imported by the > Base1PluginExecuter. I have added a ticket, http://base.thep.lu.se/ticket/943 > . > > There is no workaround. Hi Johan Thanks for clearing this up for me. Could you or anyone else give me some brief tips on imlpementing the function? For example some example code which does something similar in another BASE plugin would be helpful - I could then try to write the code myself. Alternatively, maybe there are other plugins/BASE functions which do the same thing as MGH, particularly the fold ratio and p-value functions? Many thanks Nick. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Base1PluginExecutor
Hi Nick,
It is correct that reporterlists isn't imported by the
Base1PluginExecuter. I have added a ticket, http://base.thep.lu.se/ticket/943
.
There is no workaround.
/Johan
On 7 mar 2008, at 15.41, Nick Loman wrote:
> Bob MacCallum wrote:
>
>> The tricks are (in no particular order)
>>
>> * share the plugin definition and configuration to everyone
>>
>> * configure the plugin using the the config files in
>> Root's "/BASE 1 plugin configuration files" folder.
>
> Hi
>
> Thanks for replies Bob/Nicklas.
>
> I had to make the following changes to the MGH stuff so far and have
> got
> a little further.
>
> BASE was getting upset because the first entry in the definition
> was missing the 'maxChannels' parameter. Therefore, I deleted all
> the BASEfile definitions apart from the last one which has a value
> for 'maxChannels' and managed to configure the plugin successfully.
>
> I had to make the following change to basefile-genelist.pl and
> basefile-general.pl to get it to read the BASEfile correctly.
>
> 89c86
> < elsif($currentsection eq "BASEfile") {
> ---
>> elsif($currentsection eq "BASEfile" or $currentsection eq
> 'settings') {
> 93d89
>
> Now although the PNG files are created correctly and copied to the
> folder, the actual reporterlist information is not being imported
> into BASE.
>
> The stdout output from the script is as follows:
>
> BASEfile
> sectionreporterlist
> columnsreporterIdscore
> ECs4755 0.256762034483983
> ECs3012 0.119996549971508
> ECs2479 0.286847065875626
> ...
>
> Now, looking at the BASE 2.5.0 sourcecode, there is no case in
> "importData()" which handles a reporterlist section. So perhaps I
> should
> not be surprised no data is being imported?
>
> Can anyone confirm whether this is the case, and whether there is any
> workaround?
>
> Many thanks
>
> Nick.
>
> -
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Re: [base] Base1PluginExecutor
Bob MacCallum wrote:
> The tricks are (in no particular order)
>
> * share the plugin definition and configuration to everyone
>
> * configure the plugin using the the config files in
> Root's "/BASE 1 plugin configuration files" folder.
Hi
Thanks for replies Bob/Nicklas.
I had to make the following changes to the MGH stuff so far and have got
a little further.
BASE was getting upset because the first entry in the definition
was missing the 'maxChannels' parameter. Therefore, I deleted all
the BASEfile definitions apart from the last one which has a value
for 'maxChannels' and managed to configure the plugin successfully.
I had to make the following change to basefile-genelist.pl and
basefile-general.pl to get it to read the BASEfile correctly.
89c86
< elsif($currentsection eq "BASEfile") {
---
> elsif($currentsection eq "BASEfile" or $currentsection eq
'settings') {
93d89
Now although the PNG files are created correctly and copied to the
folder, the actual reporterlist information is not being imported into BASE.
The stdout output from the script is as follows:
BASEfile
sectionreporterlist
columnsreporterIdscore
ECs4755 0.256762034483983
ECs3012 0.119996549971508
ECs2479 0.286847065875626
...
Now, looking at the BASE 2.5.0 sourcecode, there is no case in
"importData()" which handles a reporterlist section. So perhaps I should
not be surprised no data is being imported?
Can anyone confirm whether this is the case, and whether there is any
workaround?
Many thanks
Nick.
-
This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
The BASE general discussion mailing list
basedb-users@lists.sourceforge.net
unsubscribe: send a mail with subject "unsubscribe" to
[EMAIL PROTECTED]
Re: [base] Base1PluginExecutor
The tricks are (in no particular order) * share the plugin definition and configuration to everyone * configure the plugin using the the config files in Root's "/BASE 1 plugin configuration files" folder. Nicklas Nordborg writes: > Nick Loman wrote: > > Hi there > > > > Could I trouble someone to give me a very brief walk-through as to how > > BASE1PluginExecutor should be configured? > > http://base.thep.lu.se/chrome/site/latest/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation.base1 > > - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ > ___ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] -- Bob MacCallum | VectorBase Developer | Kafatos/Christophides Groups | Division of Cell and Molecular Biology | Imperial College London | Phone +442075941945 | Email [EMAIL PROTECTED] - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
Re: [base] Base1PluginExecutor
Nick Loman wrote: > Hi there > > Could I trouble someone to give me a very brief walk-through as to how > BASE1PluginExecutor should be configured? http://base.thep.lu.se/chrome/site/latest/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation.base1 - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
[base] Base1PluginExecutor
Hi there Could I trouble someone to give me a very brief walk-through as to how BASE1PluginExecutor should be configured? I want to use the MGH plugins described here: http://pga.mgh.harvard.edu/Parabiosys/resources/software_tools/base_plugins.php I've downloaded and copied the perl scripts into /www/plugins/molbio.mgh.harvard.edu-dpark/ But how do I hook up the perl scripts and the supplied definition files into BASE 2.5.0 ? Here is an example definition file: BASEfile section plugin uniqueName molbio.mgh.harvard.edu/dpark/limitint versionNumber 1.1.1 nameMGH: limit intensity descr Enforces a minimum value for spot intensities. Replaces all intensities below the min value specified below with that min value. Implemented in Perl by [EMAIL PROTECTED] execNamemolbio.mgh.harvard.edu/dpark/basefile-general.pl usedColumns position\treporter\treporterId usedFields _allIntensities geneAverages0 serialFormat0 url minChannels 1 maxChannels 0 leaveStdin 0 leaveStdout 0 columns positionvalueType namecommonName options defaultValueenumOptions removed % 1 h plugin limitint0 2 f minval min value 4 50 0 I presume I need to point BASE1PluginExecutor at this file somehow? Alternatively, are there any other plugins which will perform Fold Ratio and p-value tests? Many thanks for your tiem! Nick. - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
