[apollo] Re: [Gmod-schema] problem of adopting Apollo to Chado

Scott Cain Thu, 25 Jun 2009 13:22:44 -0700

Hi Hee Shin,

I cc'ed this to the Apollo mailing list because I don't know theanswer either. I can see several Apollo packages that are marked"hidden" in the sourceforge download admin page, but it's not clear tome which one would be the previous version; I guessed 1.10.0, but thatisn't available.


Scott

On Jun 25, 2009, at 3:48 PM, heekim wrote:


I would like to use more stable version.
Would please how to download the previous version.
I couldn't find in the sourceforge.net.
I only see 1.11.0.
Thak you.

Hee Shin


Jonathan Crabtree-4 wrote:


Hi Hee,

This is a known bug in Apollo 1.11.0. I've committed a patch forit to

CVS

(see revision 1.7 of DNAUtils.java), but it hasn't made its wayinto a new

release yet:

http://gmod.cvs.sourceforge.net/viewvc/gmod/apollo/src/java/org/bdgp/util/DNAUtils.java?view=log

You may want to join the Apollo mailing list if you have notalready doneso, so that you can see the ongoing discussion on this topic. Inbrief,this is not the only problem with the 1.11.0 release and judging bythe

CVS

logs I think Ed (the main Apollo developer) is busy ironing out therest

of

them as we speak. You may want to consider waiting for the nextrelease,downgrading to a previous release, or running off the CVS HEAD,depending

on
your inclination and time constraints...

Jonathan

On Thu, Jun 25, 2009 at 2:36 PM, heekim <[email protected]> wrote:


in the debugging mode, i was able to catch what to do.
I made progress.
I had another error that I dont understand.
it says,
"FATAL: Exception in Apollo.mainRun() thread

java.lang.IllegalArgumentException: Could not find complement for'N'"


this is my setup,
I created the instance called "beetle" which inherited RiceInstance.
<chadodb>
      <name>BeetleBase Chado KSU server</name>

<adapter>apollo.dataadapter.chado.jdbc.PostgresChadoAdapter</adapter>

<url>jdbc:postgresql://xxx.xxx.xxx.xxx:5432/BeetleBase3_Hans_Marce</url>

      <dbName>BeetleBase3_Hans_Marce</dbName>
      <dbUser>postgres</dbUser>
      <dbInstance>beetle</dbInstance>
      <style>gff3.style</style>
<!--  <sequenceTypes>
      <type>gene</type>
      <type>golden_path_region</type>
      </sequenceTypes> -->
      </chadodb>

Thank you.

Hee Shin



Scott Cain-4 wrote:


Hi Hee Shin,

You can turn on debugging by changing 'INFO' to 'DEBUG' in the
log4j.properties file in the conf directory.  Please try again with
debugging turned on so we can see the complete list of steps that
Apollo goes through.  Also, there have been some reports about

problems with the most recent release of Apollo when it comes touse

with Chado (v 1.11).  You might want to try version 1.10 as well.

Scott


On Fri, Jun 19, 2009 at 5:21 PM, heekim<[email protected]> wrote:

Hi,

I am modifying chado-adapter.xml to adopt Apollo to Chado.
However, whenever I define <dbInstance>beetle</dbInstance>, itshows

an

error; FATAL: Failed to read config file conf/apollo.cfg.

I also tried it with/without <chadoInstance id="beetle">,however, it

still
have the same error.

I hope that I can adopt Apollo to Chado.
Thank you.

Hee Shin

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Ontario Institute for Cancer Research




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[apollo] Re: [Gmod-schema] problem of adopting Apollo to Chado

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