Re: [base] basedb-users Digest, Vol 70, Issue 1

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Hi Jari

Thank you for your comments.

I am using BASE 2.17.2 which is running on a Linux/Ubuntu server.

I have found that RMAExpress runs perfectly with most Affymetrix files, but
I get this error when analysing data from Affymetrix GeneChip Human Gene
1.0 ST or Affymetrix GeneChip Mouse Gene 1.0 ST arrays, so I believe that
the error must lie with the configuration of the ST arrays within base.

I preloaded the probes as reporters into the database from a cdf file for
each array, and the reporters are visible in the database.

Yet somehow the RMAExpress plugin is failing with these arrays.

I would appreciate any comments or suggestions.

Thanks

Ross

On 5 March 2015 at 00:18, <bas...@li...>
wrote:

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> Today's Topics:
>
>    1. Re: BASE reporter fields problem (Nicklas Nordborg)
>    2. BASE 3.4 has been released (Nicklas Nordborg)
>    3. RMAexpress (Ross Chapman)
>    4. Re: RMAexpress (Jari H?kkinen)
>    5. BASE 3.4.1 has been released (Nicklas Nordborg)
>    6. (no subject) (Ross Chapman)
>    7. Re: Problem with RMAexpress plugin [Was: (no subject)]
>       (Jari H?kkinen)
>
>
> ---------- Forwarded message ----------
> From: Nicklas Nordborg <nic...@me...>
> To: BASE ML <bas...@li...>
> Cc:
> Date: Mon, 12 Jan 2015 07:50:46 +0100
> Subject: Re: [base] BASE reporter fields problem
> On 2015-01-12 07:25, Ross Chapman wrote:
>
>> Hi all
>>
>> I recently moved a BASE2 database to a new server by copying the full
>> database and all installation files along with plugin files.
>>
>> When I try to run some custom plugins on the new instance, I receive an
>> error stating that there is an unknown reporter field being requested in
>> the new database version. The same plugins still work fine on the
>> original BASE2 application.
>>
>> Can you point me to where the reporter fields are set and how I can
>> correct the annotations in the new instance.
>>
>
> This should be in the extended-properties.xml file that is found in the
> WEB-INF/classes directory in your BASE installation. See
> http://base.thep.lu.se/chrome/site/latest/html/appendix/
> extendedproperties.html for some more information.
>
> /Nicklas
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Nicklas Nordborg <nic...@me...>
> To: BASE ML <bas...@li...>, BASE dev <
> bas...@li...>, <
> bas...@li...>
> Cc:
> Date: Wed, 14 Jan 2015 14:41:58 +0100
> Subject: [base] BASE 3.4 has been released
> Hello all,
>
> After fixing a few issues with the beta version, BASE 3.4.0 has now
> been released. One new feature is the possibility to install skins. Check
> out the example skins at
> http://baseplugins.thep.lu.se/wiki/net.sf.basedb.skincollection
>
> For a complete list of changes, see:
> http://base.thep.lu.se/query?milestone=BASE+3.4&group=type
>
> Installation/upgrade instructions:
> http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html
>
> As usual, the program can be downloaded from:
> http://base.thep.lu.se/wiki/DownloadPage
>
> /Nicklas
>
>
>
>
> ---------- Forwarded message ----------
> From: Ross Chapman <ros...@mi...>
> To: bas...@li...
> Cc:
> Date: Tue, 3 Feb 2015 16:55:30 +1100
> Subject: [base] RMAexpress
> Hi all
>
> I am having problems running the RMAexpress plug in after migrating BASE2
> to a new server.
>
>
> The plug in fails with the following error:
>
> java.io.IOException: Unexpected exit of RMAExpress sub-process. Return
> value: 127
> at se.lu.thep.affymetrix.RMAExpress.runBinary(RMAExpress.java:156)
> at
> se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:262)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
> at java.lang.Thread.run(Thread.java:745)
>
> Can you suggest a possible cause and solution?
>
> Many thanks
>
> Ross
>
> --
> Dr Ross Chapman
> Senior Bioinformatician
> MIMR-PHI Institute of Medical Research
> 27-31 Wright Street, Clayton, VIC 3168
>
> (03) 99024766
>
>
> ---------- Forwarded message ----------
> From: "Jari Häkkinen" <jar...@me...>
> To: bas...@li...
> Cc:
> Date: Tue, 03 Feb 2015 14:20:45 +0100
> Subject: Re: [base] RMAexpress
> Hi,
>
> Did you also move the underlying RMAexpress binary to the new server? You
> probably need to recompile RMAExpress (http://rmaexpress.bmbolstad.com/)
> for your new server.
>
>
> Jari
>
>
> On 2015-02-03 06:55, Ross Chapman wrote:
>
>> Hi all
>>
>> I am having problems running the RMAexpress plug in after migrating
>> BASE2 to a new server.
>>
>>
>> The plug in fails with the following error:
>>
>> java.io.IOException: Unexpected exit of RMAExpress sub-process. Return
>> value: 127
>> at se.lu.thep.affymetrix.RMAExpress.runBinary(RMAExpress.java:156)
>> at
>> se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(
>> AbstractExternalBinaryPlugin.java:262)
>> at
>> net.sf.basedb.core.PluginExecutionRequest.invoke(
>> PluginExecutionRequest.java:116)
>> at
>> net.sf.basedb.core.InternalJobQueue$JobRunner.
>> run(InternalJobQueue.java:510)
>> at java.lang.Thread.run(Thread.java:745)
>>
>> Can you suggest a possible cause and solution?
>>
>> Many thanks
>>
>> Ross
>>
>> --
>> Dr Ross Chapman
>> Senior Bioinformatician
>> MIMR-PHI Institute of Medical Research
>> 27-31 Wright Street, Clayton, VIC 3168
>> (03) 99024766
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Dive into the World of Parallel Programming. The Go Parallel Website,
>> sponsored by Intel and developed in partnership with Slashdot Media, is
>> your
>> hub for all things parallel software development, from weekly thought
>> leadership blogs to news, videos, case studies, tutorials and more. Take a
>> look and join the conversation now. http://goparallel.sourceforge.net/
>>
>>
>>
>> _______________________________________________
>> The BASE general discussion mailing list
>> bas...@li...
>> unsubscribe: send a mail with subject "unsubscribe" to
>> bas...@li...
>>
>>
> --
> "For a successful technology, reality must take precedence over public
> relations, for nature cannot be fooled." - Richard P. Feynman, Rogers
> Commission Report 1986
>
>
>
>
> ---------- Forwarded message ----------
> From: Nicklas Nordborg <nic...@me...>
> To: <bas...@li...>, BASE ML <
> bas...@li...>, BASE dev <
> bas...@li...>
> Cc:
> Date: Tue, 10 Feb 2015 13:06:18 +0100
> Subject: [base] BASE 3.4.1 has been released
> Hello all,
>
> We have released BASE 3.4.1 today. This is a bugfix release that
> fixes a few minor problems.
>
> For a complete list of changes, see:
> http://base.thep.lu.se/query?milestone=BASE+3.4.1&group=type
>
> Installation/upgrade instructions:
> http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html
>
> As usual, the program can be downloaded from:
> http://base.thep.lu.se/wiki/DownloadPage
>
> /Nicklas
>
>
>
>
> ---------- Forwarded message ----------
> From: Ross Chapman <ros...@mi...>
> To: bas...@li...
> Cc:
> Date: Wed, 4 Mar 2015 14:33:04 +1100
> Subject: [base] (no subject)
> Hi all
>
> I am trying to analyse some data from an Affymetrix GeneChip Mouse Gene
> 1.0 ST Array [MoGene-1_0-st-v1] chip using the RMAexpress plugin and the
> CDF file downloaded from Affymetrix.  The analysis fails with an exception
> (below).
>
> Can you advise me of what the underlying problem might be and of any
> potential solution.
>
> Many thanks
>
> Ross Chapman
>
> net.sf.basedb.core.BaseException: Unable to import root bioassay.
> at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:218)
> at
> se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:263)
> at
> net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116)
> at
> net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: java.io.FileNotFoundException:
> /tmp/tomcat6-tomcat6-tmp/RMAExpress plug-in/3983/rma.txt (No such file or
> directory)
> at java.io.FileInputStream.open(Native Method)
> at java.io.FileInputStream.<init>(FileInputStream.java:146)
> at java.io.FileInputStream.<init>(FileInputStream.java:101)
> at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:167)
> ... 4 more
>
> --
> Dr Ross Chapman
> Senior Bioinformatician
> MIMR-PHI Institute of Medical Research
> 27-31 Wright Street, Clayton, VIC 3168
>
> (03) 99024766
>
>
> ---------- Forwarded message ----------
> From: "Jari Häkkinen" <jar...@me...>
> To: bas...@li...
> Cc:
> Date: Wed, 04 Mar 2015 14:18:16 +0100
> Subject: Re: [base] Problem with RMAexpress plugin [Was: (no subject)]
> It looks like the result file from RMAExpressConsole is not available when
> the result is stored into the database:
>
> > /tmp/tomcat6-tomcat6-tmp/RMAExpress plug-in/3983/rma.txt (No such file
> > or directory)
>
> You need to check that the file is created and readable.
>
> Which versions of BASE and RMAexpress are you running? Are you running in
> a linux environment?
>
>
> Jari
>
>
> On 2015-03-04 04:33, Ross Chapman wrote:
>
>> Hi all
>>
>> I am trying to analyse some data from an Affymetrix GeneChip Mouse Gene
>> 1.0 ST Array [MoGene-1_0-st-v1] chip using the RMAexpress plugin and the
>> CDF file downloaded from Affymetrix.  The analysis fails with an
>> exception (below).
>>
>> Can you advise me of what the underlying problem might be and of any
>> potential solution.
>>
>> Many thanks
>>
>> Ross Chapman
>>
>> net.sf.basedb.core.BaseException: Unable to import root bioassay.
>> at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:218)
>> at
>> se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(
>> AbstractExternalBinaryPlugin.java:263)
>> at
>> net.sf.basedb.core.PluginExecutionRequest.invoke(
>> PluginExecutionRequest.java:116)
>> at
>> net.sf.basedb.core.InternalJobQueue$JobRunner.
>> run(InternalJobQueue.java:510)
>> at java.lang.Thread.run(Thread.java:745)
>> Caused by: java.io.FileNotFoundException:
>> /tmp/tomcat6-tomcat6-tmp/RMAExpress plug-in/3983/rma.txt (No such file
>> or directory)
>> at java.io.FileInputStream.open(Native Method)
>> at java.io.FileInputStream.<init>(FileInputStream.java:146)
>> at java.io.FileInputStream.<init>(FileInputStream.java:101)
>> at se.lu.thep.affymetrix.RMAExpress.storeResult(RMAExpress.java:167)
>> ... 4 more
>>
>> --
>> Dr Ross Chapman
>> Senior Bioinformatician
>> MIMR-PHI Institute of Medical Research
>> 27-31 Wright Street, Clayton, VIC 3168
>> (03) 99024766
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> Dive into the World of Parallel Programming The Go Parallel Website,
>> sponsored
>> by Intel and developed in partnership with Slashdot Media, is your hub
>> for all
>> things parallel software development, from weekly thought leadership
>> blogs to
>> news, videos, case studies, tutorials and more. Take a look and join the
>> conversation now. http://goparallel.sourceforge.net/
>>
>>
>>
>> _______________________________________________
>> The BASE general discussion mailing list
>> bas...@li...
>> unsubscribe: send a mail with subject "unsubscribe" to
>> bas...@li...
>>
>>
> --
> "For a successful technology, reality must take precedence over public
> relations, for nature cannot be fooled." - Richard P. Feynman, Rogers
> Commission Report 1986
>
>
>
>
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website,
> sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for
> all
> things parallel software development, from weekly thought leadership blogs
> to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> basedb-users mailing list
> bas...@li...
> https://lists.sourceforge.net/lists/listinfo/basedb-users
>
>

-- 
Dr Ross Chapman
Senior Bioinformatician
MIMR-PHI Institute of Medical Research
27-31 Wright Street, Clayton, VIC 3168

(03) 99024766