gbrowse_syn /tmp folder creation

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gbrowse_syn /tmp folder creation

Jayaraman, Pushkala

Hello,

We have installed gbrowse2 on a solaris server with custom installation paths to each of the files and folders..

Directory Paths

For future reference, here is where you've installed GBrowse's various components:

GBrowse documentation, stylesheets and in-memory databases.

/rgd_home/3.0/WWW/gbrowse2

GBrowse configuration files

/rgd_home/3.0/WWW/gbrowse2-config/GBrowse.conf

Preinstalled sample database(s)

/rgd_home/3.0/WWW/gbrowse2-example-databases

Online tutorial and sample data files

/rgd_home/3.0/WWW/gbrowse2/tutorial.

GBrowse CGI (web) scripts

·         /usr/local/apache2/cgi-bin/gbrowse

·         /usr/local/apache2/cgi-bin/gbrowse_img

·         /usr/local/apache2/cgi-bin/gbrowse_details

Temporary directories for cached images and sessions.

/rgd_home/3.0/WWW/gbrowse2-tmp

 

 

 

 

 

I was trying to build the synteny viewer (gbrowse_syn) and I rememberd from the tutorial that I needed to create a /tmp folder and a /gbrowse2 folder inside that tmp folder.

On the default installation I know it is to be created under /var/www

For the paths that I have pasted above, where would I have to create that /tmp folder?

This question is referring to this particular set of instructions:

 

Activating the Oryza Data Source

1) Make sure the temporary image directory specified in the config files exists and is world-writable

$sudo mkdir /var/www/tmp

$sudo mkdir /var/www/tmp/gbrowse2

$sudo chmod 777 /var/www/tmp/gbrowse2

 

 

 

 

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 


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Re: gbrowse_syn /tmp folder creation

Sheldon McKay
Hi Pushkala,

Given your paths, I think the place to put it would be

/rgd_home/3.0/WWW/tmp/gbrowse2

You might also want to try editing the configuration files (should be
under /rgd_home/3.0/WWW/gbrowse2-config/synteny) to use the same temp
folder as gbrowse, '/gbrowse2-tmp'.

Sheldon


Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Tue, Jun 1, 2010 at 5:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello,
>
> We have installed gbrowse2 on a solaris server with custom installation
> paths to each of the files and folders..
>
> Directory Paths
>
> For future reference, here is where you've installed GBrowse's various
> components:
>
> GBrowse documentation, stylesheets and in-memory databases.
>
> /rgd_home/3.0/WWW/gbrowse2
>
> GBrowse configuration files
>
> /rgd_home/3.0/WWW/gbrowse2-config/GBrowse.conf
>
> Preinstalled sample database(s)
>
> /rgd_home/3.0/WWW/gbrowse2-example-databases
>
> Online tutorial and sample data files
>
> /rgd_home/3.0/WWW/gbrowse2/tutorial.
>
> GBrowse CGI (web) scripts
>
> ·         /usr/local/apache2/cgi-bin/gbrowse
>
> ·         /usr/local/apache2/cgi-bin/gbrowse_img
>
> ·         /usr/local/apache2/cgi-bin/gbrowse_details
>
> Temporary directories for cached images and sessions.
>
> /rgd_home/3.0/WWW/gbrowse2-tmp
>
>
>
>
>
>
>
>
>
>
>
> I was trying to build the synteny viewer (gbrowse_syn) and I rememberd from
> the tutorial that I needed to create a /tmp folder and a /gbrowse2 folder
> inside that tmp folder.
>
> On the default installation I know it is to be created under /var/www
>
> For the paths that I have pasted above, where would I have to create that
> /tmp folder?
>
> This question is referring to this particular set of instructions:
>
>
>
> Activating the Oryza Data Source
>
> 1) Make sure the temporary image directory specified in the config files
> exists and is world-writable
>
> $sudo mkdir /var/www/tmp
>
> $sudo mkdir /var/www/tmp/gbrowse2
>
> $sudo chmod 777 /var/www/tmp/gbrowse2
>
>
>
>
>
>
>
>
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>

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Re: gbrowse_syn /tmp folder creation

Jayaraman, Pushkala
Thanks Sheldon,
I would also like to ask you another question:
Would we be able to activate fastcgi to work with gbrowse_syn?
For now, I see that /gb2/gbrowse_syn/oryza seems to work, but /fgb2/gbrowse_syn/oryza doesn't..
Can I get it to work? Presuming that I have the default configurations on my system, what changes do I have to make?

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Wednesday, June 02, 2010 8:20 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: gbrowse_syn /tmp folder creation

Hi Pushkala,

Given your paths, I think the place to put it would be

/rgd_home/3.0/WWW/tmp/gbrowse2

You might also want to try editing the configuration files (should be
under /rgd_home/3.0/WWW/gbrowse2-config/synteny) to use the same temp
folder as gbrowse, '/gbrowse2-tmp'.

Sheldon


Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Tue, Jun 1, 2010 at 5:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Hello,
>
> We have installed gbrowse2 on a solaris server with custom installation
> paths to each of the files and folders..
>
> Directory Paths
>
> For future reference, here is where you've installed GBrowse's various
> components:
>
> GBrowse documentation, stylesheets and in-memory databases.
>
> /rgd_home/3.0/WWW/gbrowse2
>
> GBrowse configuration files
>
> /rgd_home/3.0/WWW/gbrowse2-config/GBrowse.conf
>
> Preinstalled sample database(s)
>
> /rgd_home/3.0/WWW/gbrowse2-example-databases
>
> Online tutorial and sample data files
>
> /rgd_home/3.0/WWW/gbrowse2/tutorial.
>
> GBrowse CGI (web) scripts
>
> ·         /usr/local/apache2/cgi-bin/gbrowse
>
> ·         /usr/local/apache2/cgi-bin/gbrowse_img
>
> ·         /usr/local/apache2/cgi-bin/gbrowse_details
>
> Temporary directories for cached images and sessions.
>
> /rgd_home/3.0/WWW/gbrowse2-tmp
>
>
>
>
>
>
>
>
>
>
>
> I was trying to build the synteny viewer (gbrowse_syn) and I rememberd from
> the tutorial that I needed to create a /tmp folder and a /gbrowse2 folder
> inside that tmp folder.
>
> On the default installation I know it is to be created under /var/www
>
> For the paths that I have pasted above, where would I have to create that
> /tmp folder?
>
> This question is referring to this particular set of instructions:
>
>
>
> Activating the Oryza Data Source
>
> 1) Make sure the temporary image directory specified in the config files
> exists and is world-writable
>
> $sudo mkdir /var/www/tmp
>
> $sudo mkdir /var/www/tmp/gbrowse2
>
> $sudo chmod 777 /var/www/tmp/gbrowse2
>
>
>
>
>
>
>
>
>
>
>
> Pushkala Jayaraman
>
> Programmer/Analyst
>
> Rat Genome Database
>
> Human and Molecular Genetics Center
>
> Medical College of Wisconsin
>
> Email: [hidden email]
>
> Work: 414-955-2229
>
> www.rgd.mcw.edu
>
>




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Re: gbrowse_syn /tmp folder creation

Sheldon McKay
Hi Pushkala,

Although fastcgi is currently not currently supported for gbrowse_syn,
I will add it to the list of near-term feature requests.

Sheldon

Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Wed, Jun 2, 2010 at 6:48 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Thanks Sheldon,
> I would also like to ask you another question:
> Would we be able to activate fastcgi to work with gbrowse_syn?
> For now, I see that /gb2/gbrowse_syn/oryza seems to work, but /fgb2/gbrowse_syn/oryza doesn't..
> Can I get it to work? Presuming that I have the default configurations on my system, what changes do I have to make?
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Sheldon McKay [mailto:[hidden email]]
> Sent: Wednesday, June 02, 2010 8:20 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: gbrowse_syn /tmp folder creation
>
> Hi Pushkala,
>
> Given your paths, I think the place to put it would be
>
> /rgd_home/3.0/WWW/tmp/gbrowse2
>
> You might also want to try editing the configuration files (should be
> under /rgd_home/3.0/WWW/gbrowse2-config/synteny) to use the same temp
> folder as gbrowse, '/gbrowse2-tmp'.
>
> Sheldon
>
>
> Sheldon McKay, PhD
> Scientific Lead, iPlant Collaborative
> BIO5 Institute, University of Arizona
> Email: [hidden email]
> Google Voice:  (203) 701-9204
>
>
>
> On Tue, Jun 1, 2010 at 5:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Hello,
>>
>> We have installed gbrowse2 on a solaris server with custom installation
>> paths to each of the files and folders..
>>
>> Directory Paths
>>
>> For future reference, here is where you've installed GBrowse's various
>> components:
>>
>> GBrowse documentation, stylesheets and in-memory databases.
>>
>> /rgd_home/3.0/WWW/gbrowse2
>>
>> GBrowse configuration files
>>
>> /rgd_home/3.0/WWW/gbrowse2-config/GBrowse.conf
>>
>> Preinstalled sample database(s)
>>
>> /rgd_home/3.0/WWW/gbrowse2-example-databases
>>
>> Online tutorial and sample data files
>>
>> /rgd_home/3.0/WWW/gbrowse2/tutorial.
>>
>> GBrowse CGI (web) scripts
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse_img
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse_details
>>
>> Temporary directories for cached images and sessions.
>>
>> /rgd_home/3.0/WWW/gbrowse2-tmp
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> I was trying to build the synteny viewer (gbrowse_syn) and I rememberd from
>> the tutorial that I needed to create a /tmp folder and a /gbrowse2 folder
>> inside that tmp folder.
>>
>> On the default installation I know it is to be created under /var/www
>>
>> For the paths that I have pasted above, where would I have to create that
>> /tmp folder?
>>
>> This question is referring to this particular set of instructions:
>>
>>
>>
>> Activating the Oryza Data Source
>>
>> 1) Make sure the temporary image directory specified in the config files
>> exists and is world-writable
>>
>> $sudo mkdir /var/www/tmp
>>
>> $sudo mkdir /var/www/tmp/gbrowse2
>>
>> $sudo chmod 777 /var/www/tmp/gbrowse2
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Pushkala Jayaraman
>>
>> Programmer/Analyst
>>
>> Rat Genome Database
>>
>> Human and Molecular Genetics Center
>>
>> Medical College of Wisconsin
>>
>> Email: [hidden email]
>>
>> Work: 414-955-2229
>>
>> www.rgd.mcw.edu
>>
>>
>
>
>
>
>

------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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gbrowse_syn sample data source links?

Jayaraman, Pushkala
In Gbrowse_syn wiki,
Could I have the orthology test data download link?
Or through the svn?
Pushkala

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Thursday, June 03, 2010 7:21 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: gbrowse_syn /tmp folder creation

Hi Pushkala,

Although fastcgi is currently not currently supported for gbrowse_syn,
I will add it to the list of near-term feature requests.

Sheldon

Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Wed, Jun 2, 2010 at 6:48 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Thanks Sheldon,
> I would also like to ask you another question:
> Would we be able to activate fastcgi to work with gbrowse_syn?
> For now, I see that /gb2/gbrowse_syn/oryza seems to work, but /fgb2/gbrowse_syn/oryza doesn't..
> Can I get it to work? Presuming that I have the default configurations on my system, what changes do I have to make?
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Sheldon McKay [mailto:[hidden email]]
> Sent: Wednesday, June 02, 2010 8:20 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: gbrowse_syn /tmp folder creation
>
> Hi Pushkala,
>
> Given your paths, I think the place to put it would be
>
> /rgd_home/3.0/WWW/tmp/gbrowse2
>
> You might also want to try editing the configuration files (should be
> under /rgd_home/3.0/WWW/gbrowse2-config/synteny) to use the same temp
> folder as gbrowse, '/gbrowse2-tmp'.
>
> Sheldon
>
>
> Sheldon McKay, PhD
> Scientific Lead, iPlant Collaborative
> BIO5 Institute, University of Arizona
> Email: [hidden email]
> Google Voice:  (203) 701-9204
>
>
>
> On Tue, Jun 1, 2010 at 5:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Hello,
>>
>> We have installed gbrowse2 on a solaris server with custom installation
>> paths to each of the files and folders..
>>
>> Directory Paths
>>
>> For future reference, here is where you've installed GBrowse's various
>> components:
>>
>> GBrowse documentation, stylesheets and in-memory databases.
>>
>> /rgd_home/3.0/WWW/gbrowse2
>>
>> GBrowse configuration files
>>
>> /rgd_home/3.0/WWW/gbrowse2-config/GBrowse.conf
>>
>> Preinstalled sample database(s)
>>
>> /rgd_home/3.0/WWW/gbrowse2-example-databases
>>
>> Online tutorial and sample data files
>>
>> /rgd_home/3.0/WWW/gbrowse2/tutorial.
>>
>> GBrowse CGI (web) scripts
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse_img
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse_details
>>
>> Temporary directories for cached images and sessions.
>>
>> /rgd_home/3.0/WWW/gbrowse2-tmp
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> I was trying to build the synteny viewer (gbrowse_syn) and I rememberd from
>> the tutorial that I needed to create a /tmp folder and a /gbrowse2 folder
>> inside that tmp folder.
>>
>> On the default installation I know it is to be created under /var/www
>>
>> For the paths that I have pasted above, where would I have to create that
>> /tmp folder?
>>
>> This question is referring to this particular set of instructions:
>>
>>
>>
>> Activating the Oryza Data Source
>>
>> 1) Make sure the temporary image directory specified in the config files
>> exists and is world-writable
>>
>> $sudo mkdir /var/www/tmp
>>
>> $sudo mkdir /var/www/tmp/gbrowse2
>>
>> $sudo chmod 777 /var/www/tmp/gbrowse2
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Pushkala Jayaraman
>>
>> Programmer/Analyst
>>
>> Rat Genome Database
>>
>> Human and Molecular Genetics Center
>>
>> Medical College of Wisconsin
>>
>> Email: [hidden email]
>>
>> Work: 414-955-2229
>>
>> www.rgd.mcw.edu
>>
>>
>
>
>
>
>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
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Re: gbrowse_syn /tmp folder creation

Jayaraman, Pushkala
In reply to this post by Sheldon McKay
Hello Sheldon,
I had another question:

If I have to modify my data source conf file so that it uses data from the mysql database that I set up on a server that is not localhost.. is this how I will write it? I keep getting an internal server error..
(considering that this is the way it has been set on the filesystem:)


GBrowse documentation, stylesheets and in-memory databases.
    /usr/local/gbrowse2/htdocs

GBrowse configuration files
    /usr/local/gbrowse2/etc/GBrowse.conf

Preinstalled sample database(s)
    /usr/local/gbrowse2/databases

Online tutorial and sample data files
    /usr/local/gbrowse2/htdocs/tutorial.

GBrowse CGI (web) scripts

        * /usr/local/apache3/cgi-bin/gbrowse
        * /usr/local/apache3/cgi-bin/gbrowse_img
        * /usr/local/apache3/cgi-bin/gbrowse_details

Installation and configuration manual
    GBrowse 2.0 HOWTO

Temporary directories for cached images and sessions.
    /usr/local/gbrowse2/tmp






[GENERAL]
description   = Domestic rice chromosome 3
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -dsn dbi:mysql:database=rice;host=forte.hmgc.mcw.edu
                -user rgdselect
                -pass rgdselusrdv1a

# Web site configuration info
tmpimages   = /usr/local/gbrowse2/tmp/gbrowse2

[GENERAL]
description   = Wild rice chromosome 3
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -dsn dbi:mysql:database=wild_rice;host=forte.hmgc.mcw.edu
                -user rgdselect
                -pass rgdselusrdv1a

# Web site configuration info
tmpimages   = /usr/local/gbrowse2/tmp/gbrowse2




[GENERAL]
description =  BLASTZ alignments for Oryza sativa

# The synteny database
join        = dbi:mysql:database=rice_synteny;host=forte.hmgc.mcw.edu;user=rgdselect;pass=rgdselusrdv1a

# This option maps the relationship between the species data sources, names and descriptions
# The value for "name" (the first column) is the symbolic name that gbrowse_syn users to identify each species.
# This value is also used in two other places in the gbrowse_syn configuration:
# the species name in the "examples" directive and the species name in the .aln file
# The value for "conf. file" is the basename of the corresponding gbrowse .conf files.
# This value is also used to identify the species configuration stanzas at the bottom of the configuration file.

#                 name          conf. file            Description
source_map =      rice          rice_synteny          "Domesic Rice (O. sativa)"
                  wild_rice     wild_rice_synteny     "Wild Rice"

tmpimages     = /usr/local/gbrowse2/tmp/gbrowse2
imagewidth    = 800
stylesheet    = /usr/local/gbrowse2/htdocs/css/gbrowse_transparent.css
cache time    = 1

config_extension = conf





Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu

-----Original Message-----
From: Sheldon McKay [mailto:[hidden email]]
Sent: Thursday, June 03, 2010 7:21 AM
To: Jayaraman, Pushkala
Cc: [hidden email]
Subject: Re: gbrowse_syn /tmp folder creation

Hi Pushkala,

Although fastcgi is currently not currently supported for gbrowse_syn,
I will add it to the list of near-term feature requests.

Sheldon

Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: [hidden email]
Google Voice:  (203) 701-9204



On Wed, Jun 2, 2010 at 6:48 PM, Jayaraman, Pushkala <[hidden email]> wrote:

> Thanks Sheldon,
> I would also like to ask you another question:
> Would we be able to activate fastcgi to work with gbrowse_syn?
> For now, I see that /gb2/gbrowse_syn/oryza seems to work, but /fgb2/gbrowse_syn/oryza doesn't..
> Can I get it to work? Presuming that I have the default configurations on my system, what changes do I have to make?
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Sheldon McKay [mailto:[hidden email]]
> Sent: Wednesday, June 02, 2010 8:20 AM
> To: Jayaraman, Pushkala
> Cc: [hidden email]
> Subject: Re: gbrowse_syn /tmp folder creation
>
> Hi Pushkala,
>
> Given your paths, I think the place to put it would be
>
> /rgd_home/3.0/WWW/tmp/gbrowse2
>
> You might also want to try editing the configuration files (should be
> under /rgd_home/3.0/WWW/gbrowse2-config/synteny) to use the same temp
> folder as gbrowse, '/gbrowse2-tmp'.
>
> Sheldon
>
>
> Sheldon McKay, PhD
> Scientific Lead, iPlant Collaborative
> BIO5 Institute, University of Arizona
> Email: [hidden email]
> Google Voice:  (203) 701-9204
>
>
>
> On Tue, Jun 1, 2010 at 5:51 PM, Jayaraman, Pushkala <[hidden email]> wrote:
>> Hello,
>>
>> We have installed gbrowse2 on a solaris server with custom installation
>> paths to each of the files and folders..
>>
>> Directory Paths
>>
>> For future reference, here is where you've installed GBrowse's various
>> components:
>>
>> GBrowse documentation, stylesheets and in-memory databases.
>>
>> /rgd_home/3.0/WWW/gbrowse2
>>
>> GBrowse configuration files
>>
>> /rgd_home/3.0/WWW/gbrowse2-config/GBrowse.conf
>>
>> Preinstalled sample database(s)
>>
>> /rgd_home/3.0/WWW/gbrowse2-example-databases
>>
>> Online tutorial and sample data files
>>
>> /rgd_home/3.0/WWW/gbrowse2/tutorial.
>>
>> GBrowse CGI (web) scripts
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse_img
>>
>> ·         /usr/local/apache2/cgi-bin/gbrowse_details
>>
>> Temporary directories for cached images and sessions.
>>
>> /rgd_home/3.0/WWW/gbrowse2-tmp
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> I was trying to build the synteny viewer (gbrowse_syn) and I rememberd from
>> the tutorial that I needed to create a /tmp folder and a /gbrowse2 folder
>> inside that tmp folder.
>>
>> On the default installation I know it is to be created under /var/www
>>
>> For the paths that I have pasted above, where would I have to create that
>> /tmp folder?
>>
>> This question is referring to this particular set of instructions:
>>
>>
>>
>> Activating the Oryza Data Source
>>
>> 1) Make sure the temporary image directory specified in the config files
>> exists and is world-writable
>>
>> $sudo mkdir /var/www/tmp
>>
>> $sudo mkdir /var/www/tmp/gbrowse2
>>
>> $sudo chmod 777 /var/www/tmp/gbrowse2
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Pushkala Jayaraman
>>
>> Programmer/Analyst
>>
>> Rat Genome Database
>>
>> Human and Molecular Genetics Center
>>
>> Medical College of Wisconsin
>>
>> Email: [hidden email]
>>
>> Work: 414-955-2229
>>
>> www.rgd.mcw.edu
>>
>>
>
>
>
>
>

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