Re: Query about maker web

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Re: Query about maker web

Carson Hinton Holt
Re: Query about maker web First , just incase this affects your setup.  I updated the MAKER download yesterday to version 2.0.2.  So you will want to use the most recent version.  Versions 2.0.1 and above let you view results via JBrowse and GBrowse in addition to Apollo.

For the latest version you may want to clear the MWAS/config directory, and redo setup, because the server.opt file may now have more things that need to be configured, specifically JBROWSE_ROOT and GBROWSE_CONFIG.

Apollo must be installed from source rather than from the package to use the webstart version.  You can check the source out using subversion.

svn co https://gmod.svn.sourceforge.net/svnroot/gmod/apollo/trunk apollo

Other details on using Apollo or how the webstart works can be found at http://gmod.org/wiki/Apollo_Tutorial .

You will need to have apache ant installed to compile the source.  Before compiling copy maker/Apollo/gff3.tiers to /apollo/conf/gff3.tiers.  This will set up colors for the apollo webstart, othwise everything will be the same shade of grey.  Then go to the directory /apollo/src/java/ and type ant jar to compile.

Then run sudo mwas_server APOLLO.

I know the second problem you are describing about the tarball occurred on in earlier version of the web interface and should be fixed by upgrading.

If you need more help just ask because I know that the web interface documentation is sparse for now.  I will be improving that soon.

Thanks,
Carson


On 6/17/10 3:28 AM, "Jenny Barna" <jcjb@...> wrote:



Hello

I have been setting up maker for Michael Akam, who says you
demonstrated it at a conference a few days ago. I got the
command line working and also got a lot of the web interface
working. Leaving aside for the moment the less essential problems,
right now there are two I have not solved that would be quite
a problem if they want to use this on the web:

a) When I set up the server I found that the apollo web start
could not be installed correctly because
webstart_generator.pl

does not exist. Google indicates that it is nowhere to be
found except mentioned in manuals at your web site:

~/Documents/Software/Apollo/bin/webstart_generator.pl

and I can't find it anywhere. So they would not be able to
view the results (which have formed OK). Can you help with that?

b) So if I try to download the tarball instead, so they could use
apollo locally, stream.cgi gives a blank screen. Up till now
I debugged all the problems (eg extra needed perl libs or permission
problems etc) via on-screen errors but this one has none.
The apache log and/or running it at the command line says

....
[Thu Jun 17 09:16:21 2010] stream.cgi: Use of uninitialized value
$username in concatenation (.) or string at
/prg/computing/cgi-bin/maker/lib/stream.pm line 165.
[Thu Jun 17 09:16:21 2010] stream.cgi: Use of uninitialized value $_ in
substitution (s///) at /prg/computing/cgi-bin/maker/lib/stream.pm line
110.
...

(This is with either no accounts at all or a guest account).

Many thanks in advance!


Jenny Barna            | Email                 jcjb@...
SBS Computing Facility | Web computing.bio.cam.ac.uk
Dept of Biochemistry   | Telephone (Direct)   +44 1223 333644
Tennis Court Road      | Switchboard          +44 1223 333600
Cambridge, CB2 1QW, UK | Fax:                 +44 1223 333345



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Re: Query about maker web

Carson Hinton Holt
Re: Query about maker web GBrowse 2 is now the official release of GBrowse as of about a month ago (not alpha any more or even beta for that matter).  Thank you Scott Cain and others for all the hard work adding many useful and much desired new features ;-)  The easiest way to install the latest version 2.10 (MWAS requires at least 2.09) would be as follows:
sudo cpan
install Bio::Graphics::Browser2

In MAKER you need to have GBROWSE_MASTER set in the maker/MWAS/config/server.ctl file to something like -->
GBROWSE_MASTER:/etc/gbrowse2/Gbrowse.conf

You then run -->
sudo mwas_server GBROWSE

This will set up values in the GBrowse congiguration file for you.  The MAKER produced links should then function as expected.

Thank,
Carson

On 6/21/10 8:08 AM, "Jenny Barna" <jcjb@...> wrote:

On Thu, 17 Jun 2010, Carson Holt wrote:

> If you need more help just ask because I know that the web interface documentation is sparse for now.  I will be improving that soon.

The data download now fine with new release thanks.

I thought maybe better to set up GBrowse for them. I guessed from
the syntax in MWS.pm you use alpha release 2, which I installed.

Could you give me a clue as to how I configure which end (or both ends)
to show the outputs as I can see MWS.pm constructs urls like

http://hostname/cgi-bin/gb2/gbrowse/MWAS_2_12/?name=contig...

but my gbrowse is converting it to the non-workable

hostname/cgi-bin/gb2/gbrowse/yeast_advanced/?name=contig...

from which I guess I need to edit /etc/gbrowse2/GBrowse.conf
to set up the MWAS results as another data source?
or something?

TIA


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Re: Query about maker web

Carson Hinton Holt
Re: [maker-devel] Query about maker web Some other things you may want to install for them.  JBrowse (JBROWSE_ROOT indicated in the server.ctl file).  Also optional, functional annotations require InterProScan from the EBI, as well as wu-blast.  If you don’t have wu-blast, you still get most functionality without, and I expect to fix my functional annotation module to support NCBI BLAST shortly.

Thanks,
Carson


On 6/21/10 1:35 PM, "Carson Holt" <carson.holt@...> wrote:

GBrowse 2 is now the official release of GBrowse as of about a month ago (not alpha any more or even beta for that matter).  Thank you Scott Cain and others for all the hard work adding many useful and much desired new features ;-)  The easiest way to install the latest version 2.10 (MWAS requires at least 2.09) would be as follows:
sudo cpan
install Bio::Graphics::Browser2

In MAKER you need to have GBROWSE_MASTER set in the maker/MWAS/config/server.ctl file to something like -->
GBROWSE_MASTER:/etc/gbrowse2/Gbrowse.conf

You then run -->
sudo mwas_server GBROWSE

This will set up values in the GBrowse congiguration file for you.  The MAKER produced links should then function as expected.

Thank,
Carson

On 6/21/10 8:08 AM, "Jenny Barna" <jcjb@...> wrote:

On Thu, 17 Jun 2010, Carson Holt wrote:

> If you need more help just ask because I know that the web interface documentation is sparse for now.  I will be improving that soon.

The data download now fine with new release thanks.

I thought maybe better to set up GBrowse for them. I guessed from
the syntax in MWS.pm you use alpha release 2, which I installed.

Could you give me a clue as to how I configure which end (or both ends)
to show the outputs as I can see MWS.pm constructs urls like

http://hostname/cgi-bin/gb2/gbrowse/MWAS_2_12/?name=contig...

but my gbrowse is converting it to the non-workable

hostname/cgi-bin/gb2/gbrowse/yeast_advanced/?name=contig...

from which I guess I need to edit /etc/gbrowse2/GBrowse.conf
to set up the MWAS results as another data source?
or something?

TIA



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