Packaged version of Chado

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Packaged version of Chado

Eric Rasche-2
Hello All,

 As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I wondered if there would be any community interest in a packaged (.deb) release of chado. I'm not aware of any in existence now.

I would be building it from the SVN repository of Chado. If there's sufficient interest, I could also conceivably add it to the PPAs, and would maintain a simple copy of the Chado repo there, so installation would be as simple as adding a PPA and `apt-get install chado`.

I'm not aware of what the install base demographics of Chado currently are, but if I do package Chado, I'm considering moving actual configuration options into /etc so the variables don't have to be exported for each user.

Cheers,
Eric Rasche

--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a href="tel:4046922048">404-692-2048
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Re: Packaged version of Chado

Scott Cain
Hi Eric,

There actually is a debian package for Chado as part of sid:


It was packaged as part of the effort called Debian Med:


it is less than perfect (some things don't get installed as I recall), but I haven't had any time available to make suggestions for fixing it (if I knew more about packaging I would probably be faster at making suggestions, but it's an activation energy thing).  There is also a GBrowse package; it works well but is getting a little old.

Scott





On Mon, Jun 24, 2013 at 1:23 PM, Eric Rasche <[hidden email]> wrote:
Hello All,

 As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I wondered if there would be any community interest in a packaged (.deb) release of chado. I'm not aware of any in existence now.

I would be building it from the SVN repository of Chado. If there's sufficient interest, I could also conceivably add it to the PPAs, and would maintain a simple copy of the Chado repo there, so installation would be as simple as adding a PPA and `apt-get install chado`.

I'm not aware of what the install base demographics of Chado currently are, but if I do package Chado, I'm considering moving actual configuration options into /etc so the variables don't have to be exported for each user.

Cheers,
Eric Rasche

--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a href="tel:4046922048" target="_blank">404-692-2048
[hidden email]

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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Packaged version of Chado

Stephen Ficklin-2
In reply to this post by Eric Rasche-2
Hi Eric,

Tripal has a Chado installer that puts Chado in the same PostgreSQL databases as Drupal but in the 'chado' schema.  Drupal tables go in the 'public' schema.  This is different from the perl installer which puts Chado in the 'public' schema.  Tripal can be used when Chado resides elsewhere, but for best integration with Drupal it needs to make joins between Chado tables with Drupal tables.  If someone were to install Chado using 'apt-get install' would they have the option of specifying compatibility with Tripal, for example?

Thanks,
Stephen

On 6/24/2013 1:23 PM, Eric Rasche wrote:
Hello All,

 As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I wondered if there would be any community interest in a packaged (.deb) release of chado. I'm not aware of any in existence now.

I would be building it from the SVN repository of Chado. If there's sufficient interest, I could also conceivably add it to the PPAs, and would maintain a simple copy of the Chado repo there, so installation would be as simple as adding a PPA and `apt-get install chado`.

I'm not aware of what the install base demographics of Chado currently are, but if I do package Chado, I'm considering moving actual configuration options into /etc so the variables don't have to be exported for each user.

Cheers,
Eric Rasche

--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:4046922048">404-692-2048
[hidden email]


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Re: Packaged version of Chado

Eric Rasche-2
Hi Stephen,

 I am sure that would be a possibility. I'd like to have Tripal packaged and released through the repositories. If that were the case, installing a tripal package could modify the existing installation(s?) of Chado to move it into the public schema. Since there's a drupal package, there's a lot of room for these tools to have their dependencies specified properly.

On 06/24/2013 01:08 PM, Stephen Ficklin wrote:
Hi Eric,

Tripal has a Chado installer that puts Chado in the same PostgreSQL databases as Drupal but in the 'chado' schema.  Drupal tables go in the 'public' schema.  This is different from the perl installer which puts Chado in the 'public' schema.  Tripal can be used when Chado resides elsewhere, but for best integration with Drupal it needs to make joins between Chado tables with Drupal tables.  If someone were to install Chado using 'apt-get install' would they have the option of specifying compatibility with Tripal, for example?

Thanks,
Stephen

On 6/24/2013 1:23 PM, Eric Rasche wrote:
Hello All,

 As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I wondered if there would be any community interest in a packaged (.deb) release of chado. I'm not aware of any in existence now.

I would be building it from the SVN repository of Chado. If there's sufficient interest, I could also conceivably add it to the PPAs, and would maintain a simple copy of the Chado repo there, so installation would be as simple as adding a PPA and `apt-get install chado`.

I'm not aware of what the install base demographics of Chado currently are, but if I do package Chado, I'm considering moving actual configuration options into /etc so the variables don't have to be exported for each user.

Cheers,
Eric Rasche

--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:4046922048">404-692-2048
[hidden email]


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Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a href="tel:4046922048">404-692-2048
[hidden email]

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Re: Packaged version of Chado

Eric Rasche-2
In reply to this post by Scott Cain
Hi Scott,

Since my organisation uses primarily Debian based distros, I'm happy to help support that effort. I'm updating a personal copy of the installation documentation to reflect installation on newer distributions, and will ask to have that merged once I have a replicable process down.

Perhaps then, if it's agreeable, I can offer suggestions on what's missing/needs to be fixed for libchado-perl on debian med.

Since I'm testing out various configurations in staging environments (Ubuntu LXCs), I have reason and time to devote to helping fix the complex installation process.

On 06/24/2013 01:04 PM, Scott Cain wrote:
Hi Eric,

There actually is a debian package for Chado as part of sid:


It was packaged as part of the effort called Debian Med:


it is less than perfect (some things don't get installed as I recall), but I haven't had any time available to make suggestions for fixing it (if I knew more about packaging I would probably be faster at making suggestions, but it's an activation energy thing).  There is also a GBrowse package; it works well but is getting a little old.

Scott





On Mon, Jun 24, 2013 at 1:23 PM, Eric Rasche <[hidden email]> wrote:
Hello All,

 As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I wondered if there would be any community interest in a packaged (.deb) release of chado. I'm not aware of any in existence now.

I would be building it from the SVN repository of Chado. If there's sufficient interest, I could also conceivably add it to the PPAs, and would maintain a simple copy of the Chado repo there, so installation would be as simple as adding a PPA and `apt-get install chado`.

I'm not aware of what the install base demographics of Chado currently are, but if I do package Chado, I'm considering moving actual configuration options into /etc so the variables don't have to be exported for each user.

Cheers,
Eric Rasche

--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:4046922048" target="_blank">404-692-2048
[hidden email]

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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a href="tel:4046922048">404-692-2048
[hidden email]

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Re: Packaged version of Chado

Stephen Ficklin-2
In reply to this post by Eric Rasche-2
Hi Eric,

Sounds good.  Let me know if you make the package.  I'd be happy to test it.

Stephen

On 6/24/2013 2:13 PM, Eric Rasche wrote:
Hi Stephen,

 I am sure that would be a possibility. I'd like to have Tripal packaged and released through the repositories. If that were the case, installing a tripal package could modify the existing installation(s?) of Chado to move it into the public schema. Since there's a drupal package, there's a lot of room for these tools to have their dependencies specified properly.

On 06/24/2013 01:08 PM, Stephen Ficklin wrote:
Hi Eric,

Tripal has a Chado installer that puts Chado in the same PostgreSQL databases as Drupal but in the 'chado' schema.  Drupal tables go in the 'public' schema.  This is different from the perl installer which puts Chado in the 'public' schema.  Tripal can be used when Chado resides elsewhere, but for best integration with Drupal it needs to make joins between Chado tables with Drupal tables.  If someone were to install Chado using 'apt-get install' would they have the option of specifying compatibility with Tripal, for example?

Thanks,
Stephen

On 6/24/2013 1:23 PM, Eric Rasche wrote:
Hello All,

 As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I wondered if there would be any community interest in a packaged (.deb) release of chado. I'm not aware of any in existence now.

I would be building it from the SVN repository of Chado. If there's sufficient interest, I could also conceivably add it to the PPAs, and would maintain a simple copy of the Chado repo there, so installation would be as simple as adding a PPA and `apt-get install chado`.

I'm not aware of what the install base demographics of Chado currently are, but if I do package Chado, I'm considering moving actual configuration options into /etc so the variables don't have to be exported for each user.

Cheers,
Eric Rasche

--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:4046922048">404-692-2048
[hidden email]


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--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
<a moz-do-not-send="true" href="tel:4046922048">404-692-2048
[hidden email]


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Re: Packaged version of Chado

Siddhartha Basu
In reply to this post by Eric Rasche-2
Hi Eric,
Few questions here ..

* What the package will contain, only the sql part or all the perl
  pieces
* What would be the dependencies, pg server and if perl included what
  packages it will pull down. Will there be in any other language as
  dependencies.
* I am heavily interested in LXC particuraly getting it
  packaged/shared/deployed via docker(http://www.docker.io/). If you
  have made progress with LXC already or do so please share your work,
  it would help me to build a docker image easily.

thanks,
-sidd


On Mon, 24 Jun 2013, Eric Rasche wrote:

>    Hi Scott,
>
>    Since my organisation uses primarily Debian based distros, I'm happy to
>    help support that effort. I'm updating a personal copy of the installation
>    documentation to reflect installation on newer distributions, and will ask
>    to have that merged once I have a replicable process down.
>
>    Perhaps then, if it's agreeable, I can offer suggestions on what's
>    missing/needs to be fixed for libchado-perl on debian med.
>
>    Since I'm testing out various configurations in staging environments
>    (Ubuntu LXCs), I have reason and time to devote to helping fix the complex
>    installation process.
>
>    On 06/24/2013 01:04 PM, Scott Cain wrote:
>
>      Hi Eric,
>      There actually is a debian package for Chado as part of sid:
>        http://packages.debian.org/sid/libchado-perl
>      It was packaged as part of the effort called Debian Med:
>        http://www.debian.org/devel/debian-med/
>      it is less than perfect (some things don't get installed as I recall),
>      but I haven't had any time available to make suggestions for fixing it
>      (if I knew more about packaging I would probably be faster at making
>      suggestions, but it's an activation energy thing).  There is also a
>      GBrowse package; it works well but is getting a little old.
>      Scott
>
>      On Mon, Jun 24, 2013 at 1:23 PM, Eric Rasche <[hidden email]>
>      wrote:
>
>        Hello All,
>
>         As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I
>        wondered if there would be any community interest in a packaged (.deb)
>        release of chado. I'm not aware of any in existence now.
>
>        I would be building it from the SVN repository of Chado. If there's
>        sufficient interest, I could also conceivably add it to the PPAs, and
>        would maintain a simple copy of the Chado repo there, so installation
>        would be as simple as adding a PPA and `apt-get install chado`.
>
>        I'm not aware of what the install base demographics of Chado currently
>        are, but if I do package Chado, I'm considering moving actual
>        configuration options into /etc so the variables don't have to be
>        exported for each user.
>
>        Cheers,
>        Eric Rasche
>        --
>        Eric Rasche
>        Programmer II
>        Center for Phage Technology
>        Texas A&M University
>        College Station, TX 77843
>        404-692-2048
>        [hidden email]
>        ------------------------------------------------------------------------------
>        This SF.net email is sponsored by Windows:
>
>        Build for Windows Store.
>
>        http://p.sf.net/sfu/windows-dev2dev
>        _______________________________________________
>        Gmod-schema mailing list
>        [hidden email]
>        https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>      --
>      ------------------------------------------------------------------------
>      Scott Cain, Ph. D.                                   scott at scottcain
>      dot net
>      GMOD Coordinator (http://gmod.org/)                     216-392-3087
>      Ontario Institute for Cancer Research
>
>    --
>    Eric Rasche
>    Programmer II
>    Center for Phage Technology
>    Texas A&M University
>    College Station, TX 77843
>    404-692-2048
>    [hidden email]

> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
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> [hidden email]
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Re: Packaged version of Chado

Eric Rasche-2
Hi Siddhartha,

* I'm working on packaging them now and finding...lots of
interdependencies with GMODTools, etc. This has caused me to expand the
scope of work to packaging Chado, Tripal, GMODTools, etc. The packages
will contain everything required to completely deploy a Chado instance.
The Chado package will depend on gmodtools, and Tripal will depend on
Chado and Drupal (etc).
I'm also trying to re-write the Makefile.PL since it's less of a normal
Perl makefile and more of an installation script. Most of the actual
Makefile components can be extracted into preinst/postinst debian helper
scripts, since there's no building of software.

* The dependencies that are currently listed in the .deb are: perl,
postgresql. I will have to work through the required dependencies and
search out examples of packages that have perl-module dependencies. I'm
not aware of what is the correct procedure for handling those; it is
possible the user has installed perl modules via the system repos, and
possible they've done it via CPAN. Some people are very picky that all
their modules are installed from CPAN, and some would rather have the
system maintain them. I can't blame them for that.

* Sure! I have Chado deployed in LXC already, but not Tripal/Drupal as
I'm not in control of some of the network infrastructure. Thus, I
couldn't get an IP address for the container and my networking skill
level isn't high enough that I knew how to access the container other
than at the terminal. Please feel free to contact me privately (as this
would be off topic for this mailing list) and we can discuss deployment
of LXCs and Docker.

Cheers,
Eric

On 06/25/2013 11:24 AM, Siddhartha Basu wrote:

> Hi Eric,
> Few questions here ..
>
> * What the package will contain, only the sql part or all the perl
>   pieces
> * What would be the dependencies, pg server and if perl included what
>   packages it will pull down. Will there be in any other language as
>   dependencies.
> * I am heavily interested in LXC particuraly getting it
>   packaged/shared/deployed via docker(http://www.docker.io/). If you
>   have made progress with LXC already or do so please share your work,
>   it would help me to build a docker image easily.
>
> thanks,
> -sidd
>
>
> On Mon, 24 Jun 2013, Eric Rasche wrote:
>
>>    Hi Scott,
>>
>>    Since my organisation uses primarily Debian based distros, I'm happy to
>>    help support that effort. I'm updating a personal copy of the installation
>>    documentation to reflect installation on newer distributions, and will ask
>>    to have that merged once I have a replicable process down.
>>
>>    Perhaps then, if it's agreeable, I can offer suggestions on what's
>>    missing/needs to be fixed for libchado-perl on debian med.
>>
>>    Since I'm testing out various configurations in staging environments
>>    (Ubuntu LXCs), I have reason and time to devote to helping fix the complex
>>    installation process.
>>
>>    On 06/24/2013 01:04 PM, Scott Cain wrote:
>>
>>      Hi Eric,
>>      There actually is a debian package for Chado as part of sid:
>>        http://packages.debian.org/sid/libchado-perl
>>      It was packaged as part of the effort called Debian Med:
>>        http://www.debian.org/devel/debian-med/
>>      it is less than perfect (some things don't get installed as I recall),
>>      but I haven't had any time available to make suggestions for fixing it
>>      (if I knew more about packaging I would probably be faster at making
>>      suggestions, but it's an activation energy thing).  There is also a
>>      GBrowse package; it works well but is getting a little old.
>>      Scott
>>
>>      On Mon, Jun 24, 2013 at 1:23 PM, Eric Rasche <[hidden email]>
>>      wrote:
>>
>>        Hello All,
>>
>>         As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I
>>        wondered if there would be any community interest in a packaged (.deb)
>>        release of chado. I'm not aware of any in existence now.
>>
>>        I would be building it from the SVN repository of Chado. If there's
>>        sufficient interest, I could also conceivably add it to the PPAs, and
>>        would maintain a simple copy of the Chado repo there, so installation
>>        would be as simple as adding a PPA and `apt-get install chado`.
>>
>>        I'm not aware of what the install base demographics of Chado currently
>>        are, but if I do package Chado, I'm considering moving actual
>>        configuration options into /etc so the variables don't have to be
>>        exported for each user.
>>
>>        Cheers,
>>        Eric Rasche
>>        --
>>        Eric Rasche
>>        Programmer II
>>        Center for Phage Technology
>>        Texas A&M University
>>        College Station, TX 77843
>>        404-692-2048
>>        [hidden email]
>>        ------------------------------------------------------------------------------
>>        This SF.net email is sponsored by Windows:
>>
>>        Build for Windows Store.
>>
>>        http://p.sf.net/sfu/windows-dev2dev
>>        _______________________________________________
>>        Gmod-schema mailing list
>>        [hidden email]
>>        https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>      --
>>      ------------------------------------------------------------------------
>>      Scott Cain, Ph. D.                                   scott at scottcain
>>      dot net
>>      GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>      Ontario Institute for Cancer Research
>>
>>    --
>>    Eric Rasche
>>    Programmer II
>>    Center for Phage Technology
>>    Texas A&M University
>>    College Station, TX 77843
>>    404-692-2048
>>    [hidden email]
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> ------------------------------------------------------------------------------
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>
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--
Eric Rasche Programmer II Center for Phage Technology Texas A&M
University College Station, TX 77843 tel:404-692-2048 [hidden email]

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Re: Packaged version of Chado

Scott Cain
Hi Eric,

I'll include some comments inline.

Scott



On Tue, Jun 25, 2013 at 12:35 PM, Eric Rasche <[hidden email]> wrote:
Hi Siddhartha,

* I'm working on packaging them now and finding...lots of
interdependencies with GMODTools, etc. This has caused me to expand the
scope of work to packaging Chado, Tripal, GMODTools, etc. The packages
will contain everything required to completely deploy a Chado instance.
The Chado package will depend on gmodtools, and Tripal will depend on
Chado and Drupal (etc).
 
I'm also trying to re-write the Makefile.PL since it's less of a normal
Perl makefile and more of an installation script. Most of the actual
Makefile components can be extracted into preinst/postinst debian helper
scripts, since there's no building of software.

Yes, Makefile.PL definitely grew way past the typical use of Makefile.PL for perl modules, and I regret that to some extent.  I would certainly be willing to help you re-engineer this, as it would make sense to redo general Chado installer at the same time.  It's one of those things that I've thought about doing for a long time, but since it works (if in a goofy way), I haven't devoted any time to reworking it.
 

* The dependencies that are currently listed in the .deb are: perl,
postgresql. I will have to work through the required dependencies and
search out examples of packages that have perl-module dependencies. I'm
not aware of what is the correct procedure for handling those; it is
possible the user has installed perl modules via the system repos, and
possible they've done it via CPAN. Some people are very picky that all
their modules are installed from CPAN, and some would rather have the
system maintain them. I can't blame them for that.

Obviously, the Debian people think everything should be in a package, but I can't blame you for listing fewer dependencies in your package.  Since the Debian Med folks packaged Chado already, there are already Sid packages for everything that is a Chado dependency.
 

* Sure! I have Chado deployed in LXC already, but not Tripal/Drupal as
I'm not in control of some of the network infrastructure. Thus, I
couldn't get an IP address for the container and my networking skill
level isn't high enough that I knew how to access the container other
than at the terminal. Please feel free to contact me privately (as this
would be off topic for this mailing list) and we can discuss deployment
of LXCs and Docker.

Cheers,
Eric

On 06/25/2013 11:24 AM, Siddhartha Basu wrote:
> Hi Eric,
> Few questions here ..
>
> * What the package will contain, only the sql part or all the perl
>   pieces
> * What would be the dependencies, pg server and if perl included what
>   packages it will pull down. Will there be in any other language as
>   dependencies.
> * I am heavily interested in LXC particuraly getting it
>   packaged/shared/deployed via docker(http://www.docker.io/). If you
>   have made progress with LXC already or do so please share your work,
>   it would help me to build a docker image easily.
>
> thanks,
> -sidd
>
>
> On Mon, 24 Jun 2013, Eric Rasche wrote:
>
>>    Hi Scott,
>>
>>    Since my organisation uses primarily Debian based distros, I'm happy to
>>    help support that effort. I'm updating a personal copy of the installation
>>    documentation to reflect installation on newer distributions, and will ask
>>    to have that merged once I have a replicable process down.
>>
>>    Perhaps then, if it's agreeable, I can offer suggestions on what's
>>    missing/needs to be fixed for libchado-perl on debian med.
>>
>>    Since I'm testing out various configurations in staging environments
>>    (Ubuntu LXCs), I have reason and time to devote to helping fix the complex
>>    installation process.
>>
>>    On 06/24/2013 01:04 PM, Scott Cain wrote:
>>
>>      Hi Eric,
>>      There actually is a debian package for Chado as part of sid:
>>        http://packages.debian.org/sid/libchado-perl
>>      It was packaged as part of the effort called Debian Med:
>>        http://www.debian.org/devel/debian-med/
>>      it is less than perfect (some things don't get installed as I recall),
>>      but I haven't had any time available to make suggestions for fixing it
>>      (if I knew more about packaging I would probably be faster at making
>>      suggestions, but it's an activation energy thing).  There is also a
>>      GBrowse package; it works well but is getting a little old.
>>      Scott
>>
>>      On Mon, Jun 24, 2013 at 1:23 PM, Eric Rasche <[hidden email]>
>>      wrote:
>>
>>        Hello All,
>>
>>         As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I
>>        wondered if there would be any community interest in a packaged (.deb)
>>        release of chado. I'm not aware of any in existence now.
>>
>>        I would be building it from the SVN repository of Chado. If there's
>>        sufficient interest, I could also conceivably add it to the PPAs, and
>>        would maintain a simple copy of the Chado repo there, so installation
>>        would be as simple as adding a PPA and `apt-get install chado`.
>>
>>        I'm not aware of what the install base demographics of Chado currently
>>        are, but if I do package Chado, I'm considering moving actual
>>        configuration options into /etc so the variables don't have to be
>>        exported for each user.
>>
>>        Cheers,
>>        Eric Rasche
>>        --
>>        Eric Rasche
>>        Programmer II
>>        Center for Phage Technology
>>        Texas A&M University
>>        College Station, TX 77843
>>        <a href="tel:404-692-2048" value="+14046922048">404-692-2048
>>        [hidden email]
>>        ------------------------------------------------------------------------------
>>        This SF.net email is sponsored by Windows:
>>
>>        Build for Windows Store.
>>
>>        http://p.sf.net/sfu/windows-dev2dev
>>        _______________________________________________
>>        Gmod-schema mailing list
>>        [hidden email]
>>        https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>      --
>>      ------------------------------------------------------------------------
>>      Scott Cain, Ph. D.                                   scott at scottcain
>>      dot net
>>      GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>      Ontario Institute for Cancer Research
>>
>>    --
>>    Eric Rasche
>>    Programmer II
>>    Center for Phage Technology
>>    Texas A&M University
>>    College Station, TX 77843
>>    <a href="tel:404-692-2048" value="+14046922048">404-692-2048
>>    [hidden email]
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

--
Eric Rasche Programmer II Center for Phage Technology Texas A&M
University College Station, TX 77843 tel:<a href="tel:404-692-2048" value="+14046922048">404-692-2048 [hidden email]

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--
------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Packaged version of Chado

Scott Cain
In reply to this post by Eric Rasche-2
Hi Eric,

I'll include some comments inline.

Scott



On Tue, Jun 25, 2013 at 12:35 PM, Eric Rasche <[hidden email]> wrote:
Hi Siddhartha,

* I'm working on packaging them now and finding...lots of
interdependencies with GMODTools, etc. This has caused me to expand the
scope of work to packaging Chado, Tripal, GMODTools, etc. The packages
will contain everything required to completely deploy a Chado instance.
The Chado package will depend on gmodtools, and Tripal will depend on
Chado and Drupal (etc).
 
I'm also trying to re-write the Makefile.PL since it's less of a normal
Perl makefile and more of an installation script. Most of the actual
Makefile components can be extracted into preinst/postinst debian helper
scripts, since there's no building of software.

Yes, Makefile.PL definitely grew way past the typical use of Makefile.PL for perl modules, and I regret that to some extent.  I would certainly be willing to help you re-engineer this, as it would make sense to redo general Chado installer at the same time.  It's one of those things that I've thought about doing for a long time, but since it works (if in a goofy way), I haven't devoted any time to reworking it.
 

* The dependencies that are currently listed in the .deb are: perl,
postgresql. I will have to work through the required dependencies and
search out examples of packages that have perl-module dependencies. I'm
not aware of what is the correct procedure for handling those; it is
possible the user has installed perl modules via the system repos, and
possible they've done it via CPAN. Some people are very picky that all
their modules are installed from CPAN, and some would rather have the
system maintain them. I can't blame them for that.

Obviously, the Debian people think everything should be in a package, but I can't blame you for listing fewer dependencies in your package.  Since the Debian Med folks packaged Chado already, there are already Sid packages for everything that is a Chado dependency.
 

* Sure! I have Chado deployed in LXC already, but not Tripal/Drupal as
I'm not in control of some of the network infrastructure. Thus, I
couldn't get an IP address for the container and my networking skill
level isn't high enough that I knew how to access the container other
than at the terminal. Please feel free to contact me privately (as this
would be off topic for this mailing list) and we can discuss deployment
of LXCs and Docker.

Cheers,
Eric

On 06/25/2013 11:24 AM, Siddhartha Basu wrote:
> Hi Eric,
> Few questions here ..
>
> * What the package will contain, only the sql part or all the perl
>   pieces
> * What would be the dependencies, pg server and if perl included what
>   packages it will pull down. Will there be in any other language as
>   dependencies.
> * I am heavily interested in LXC particuraly getting it
>   packaged/shared/deployed via docker(http://www.docker.io/). If you
>   have made progress with LXC already or do so please share your work,
>   it would help me to build a docker image easily.
>
> thanks,
> -sidd
>
>
> On Mon, 24 Jun 2013, Eric Rasche wrote:
>
>>    Hi Scott,
>>
>>    Since my organisation uses primarily Debian based distros, I'm happy to
>>    help support that effort. I'm updating a personal copy of the installation
>>    documentation to reflect installation on newer distributions, and will ask
>>    to have that merged once I have a replicable process down.
>>
>>    Perhaps then, if it's agreeable, I can offer suggestions on what's
>>    missing/needs to be fixed for libchado-perl on debian med.
>>
>>    Since I'm testing out various configurations in staging environments
>>    (Ubuntu LXCs), I have reason and time to devote to helping fix the complex
>>    installation process.
>>
>>    On 06/24/2013 01:04 PM, Scott Cain wrote:
>>
>>      Hi Eric,
>>      There actually is a debian package for Chado as part of sid:
>>        http://packages.debian.org/sid/libchado-perl
>>      It was packaged as part of the effort called Debian Med:
>>        http://www.debian.org/devel/debian-med/
>>      it is less than perfect (some things don't get installed as I recall),
>>      but I haven't had any time available to make suggestions for fixing it
>>      (if I knew more about packaging I would probably be faster at making
>>      suggestions, but it's an activation energy thing).  There is also a
>>      GBrowse package; it works well but is getting a little old.
>>      Scott
>>
>>      On Mon, Jun 24, 2013 at 1:23 PM, Eric Rasche <[hidden email]>
>>      wrote:
>>
>>        Hello All,
>>
>>         As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I
>>        wondered if there would be any community interest in a packaged (.deb)
>>        release of chado. I'm not aware of any in existence now.
>>
>>        I would be building it from the SVN repository of Chado. If there's
>>        sufficient interest, I could also conceivably add it to the PPAs, and
>>        would maintain a simple copy of the Chado repo there, so installation
>>        would be as simple as adding a PPA and `apt-get install chado`.
>>
>>        I'm not aware of what the install base demographics of Chado currently
>>        are, but if I do package Chado, I'm considering moving actual
>>        configuration options into /etc so the variables don't have to be
>>        exported for each user.
>>
>>        Cheers,
>>        Eric Rasche
>>        --
>>        Eric Rasche
>>        Programmer II
>>        Center for Phage Technology
>>        Texas A&M University
>>        College Station, TX 77843
>>        <a href="tel:404-692-2048" value="+14046922048">404-692-2048
>>        [hidden email]
>>        ------------------------------------------------------------------------------
>>        This SF.net email is sponsored by Windows:
>>
>>        Build for Windows Store.
>>
>>        http://p.sf.net/sfu/windows-dev2dev
>>        _______________________________________________
>>        Gmod-schema mailing list
>>        [hidden email]
>>        https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>      --
>>      ------------------------------------------------------------------------
>>      Scott Cain, Ph. D.                                   scott at scottcain
>>      dot net
>>      GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087">216-392-3087
>>      Ontario Institute for Cancer Research
>>
>>    --
>>    Eric Rasche
>>    Programmer II
>>    Center for Phage Technology
>>    Texas A&M University
>>    College Station, TX 77843
>>    <a href="tel:404-692-2048" value="+14046922048">404-692-2048
>>    [hidden email]
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
>
> http://p.sf.net/sfu/windows-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

--
Eric Rasche Programmer II Center for Phage Technology Texas A&M
University College Station, TX 77843 tel:<a href="tel:404-692-2048" value="+14046922048">404-692-2048 [hidden email]

------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Packaged version of Chado

Siddhartha Basu
In reply to this post by Eric Rasche-2
Hi Eric,

On Tue, 25 Jun 2013, Eric Rasche wrote:

> Hi Siddhartha,
>
> * I'm working on packaging them now and finding...lots of
> interdependencies with GMODTools, etc. This has caused me to expand the
> scope of work to packaging Chado, Tripal, GMODTools, etc. The packages
> will contain everything required to completely deploy a Chado instance.
> The Chado package will depend on gmodtools, and Tripal will depend on
> Chado and Drupal (etc).
> I'm also trying to re-write the Makefile.PL since it's less of a normal
> Perl makefile and more of an installation script. Most of the actual
> Makefile components can be extracted into preinst/postinst debian helper
> scripts, since there's no building of software.
>
> * The dependencies that are currently listed in the .deb are: perl,
> postgresql. I will have to work through the required dependencies and
> search out examples of packages that have perl-module dependencies. I'm
> not aware of what is the correct procedure for handling those; it is
> possible the user has installed perl modules via the system repos, and
> possible they've done it via CPAN. Some people are very picky that all
> their modules are installed from CPAN, and some would rather have the
> system maintain them. I can't blame them for that.
>
> * Sure! I have Chado deployed in LXC already, but not Tripal/Drupal as
> I'm not in control of some of the network infrastructure. Thus, I
> couldn't get an IP address for the container and my networking skill
> level isn't high enough that I knew how to access the container other
> than at the terminal. Please feel free to contact me privately (as this
> would be off topic for this mailing list) and we can discuss deployment
> of LXCs and Docker.
I am still playing around with this new technology. Would get in
touch(offlist) when i progress a bit more.

thanks,
-siddhartha

>
> Cheers,
> Eric
>
> On 06/25/2013 11:24 AM, Siddhartha Basu wrote:
> > Hi Eric,
> > Few questions here ..
> >
> > * What the package will contain, only the sql part or all the perl
> >   pieces
> > * What would be the dependencies, pg server and if perl included what
> >   packages it will pull down. Will there be in any other language as
> >   dependencies.
> > * I am heavily interested in LXC particuraly getting it
> >   packaged/shared/deployed via docker(http://www.docker.io/). If you
> >   have made progress with LXC already or do so please share your work,
> >   it would help me to build a docker image easily.
> >
> > thanks,
> > -sidd
> >
> >
> > On Mon, 24 Jun 2013, Eric Rasche wrote:
> >
> >>    Hi Scott,
> >>
> >>    Since my organisation uses primarily Debian based distros, I'm happy to
> >>    help support that effort. I'm updating a personal copy of the installation
> >>    documentation to reflect installation on newer distributions, and will ask
> >>    to have that merged once I have a replicable process down.
> >>
> >>    Perhaps then, if it's agreeable, I can offer suggestions on what's
> >>    missing/needs to be fixed for libchado-perl on debian med.
> >>
> >>    Since I'm testing out various configurations in staging environments
> >>    (Ubuntu LXCs), I have reason and time to devote to helping fix the complex
> >>    installation process.
> >>
> >>    On 06/24/2013 01:04 PM, Scott Cain wrote:
> >>
> >>      Hi Eric,
> >>      There actually is a debian package for Chado as part of sid:
> >>        http://packages.debian.org/sid/libchado-perl
> >>      It was packaged as part of the effort called Debian Med:
> >>        http://www.debian.org/devel/debian-med/
> >>      it is less than perfect (some things don't get installed as I recall),
> >>      but I haven't had any time available to make suggestions for fixing it
> >>      (if I knew more about packaging I would probably be faster at making
> >>      suggestions, but it's an activation energy thing).  There is also a
> >>      GBrowse package; it works well but is getting a little old.
> >>      Scott
> >>
> >>      On Mon, Jun 24, 2013 at 1:23 PM, Eric Rasche <[hidden email]>
> >>      wrote:
> >>
> >>        Hello All,
> >>
> >>         As I'm installing Chado/Tripal/etc to an Ubuntu 12.04 LTS server, I
> >>        wondered if there would be any community interest in a packaged (.deb)
> >>        release of chado. I'm not aware of any in existence now.
> >>
> >>        I would be building it from the SVN repository of Chado. If there's
> >>        sufficient interest, I could also conceivably add it to the PPAs, and
> >>        would maintain a simple copy of the Chado repo there, so installation
> >>        would be as simple as adding a PPA and `apt-get install chado`.
> >>
> >>        I'm not aware of what the install base demographics of Chado currently
> >>        are, but if I do package Chado, I'm considering moving actual
> >>        configuration options into /etc so the variables don't have to be
> >>        exported for each user.
> >>
> >>        Cheers,
> >>        Eric Rasche
> >>        --
> >>        Eric Rasche
> >>        Programmer II
> >>        Center for Phage Technology
> >>        Texas A&M University
> >>        College Station, TX 77843
> >>        404-692-2048
> >>        [hidden email]
> >>        ------------------------------------------------------------------------------
> >>        This SF.net email is sponsored by Windows:
> >>
> >>        Build for Windows Store.
> >>
> >>        http://p.sf.net/sfu/windows-dev2dev
> >>        _______________________________________________
> >>        Gmod-schema mailing list
> >>        [hidden email]
> >>        https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >>
> >>      --
> >>      ------------------------------------------------------------------------
> >>      Scott Cain, Ph. D.                                   scott at scottcain
> >>      dot net
> >>      GMOD Coordinator (http://gmod.org/)                     216-392-3087
> >>      Ontario Institute for Cancer Research
> >>
> >>    --
> >>    Eric Rasche
> >>    Programmer II
> >>    Center for Phage Technology
> >>    Texas A&M University
> >>    College Station, TX 77843
> >>    404-692-2048
> >>    [hidden email]
> >> ------------------------------------------------------------------------------
> >> This SF.net email is sponsored by Windows:
> >>
> >> Build for Windows Store.
> >>
> >> http://p.sf.net/sfu/windows-dev2dev
> >> _______________________________________________
> >> Gmod-schema mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
> > ------------------------------------------------------------------------------
> > This SF.net email is sponsored by Windows:
> >
> > Build for Windows Store.
> >
> > http://p.sf.net/sfu/windows-dev2dev
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> --
> Eric Rasche Programmer II Center for Phage Technology Texas A&M
> University College Station, TX 77843 tel:404-692-2048 [hidden email]
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Windows:
>
> Build for Windows Store.
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