jalview packages for Debian

Hello all,

Ages ago, I started to package jalview for the Debian operating
system (http://www.debian.org). The original "Intention to package"
can be found there:

http://bugs.debian.org/507436

Several things stopped me at that time, the most important one being
the difficulty to package jmol for Debian, as many parts of its
dependencies had unclear copyright/licenses. This has now been cleared
up (not by me), and I'm finally back to packaging jalview. However,
I'm hitting one problem now: the origin of the code for the
min-jaba-client.jar library. I found most of the source code there:

http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source.jar

Unfortunately, that jar contains already compiled classes, and in
particular the compbio.util package, for which I can't find source
code as of now. Is it available somewhere ? If not, could someone
please make it available at a well-defined location ?

For now, I'm stuck at this point; it seems that it's the last bit
that prevents me from compiling jalview at this point, but I'm unsure.
In any case, it is a show stopper (see below).

Any help would be greatly appreciated !

Cheers,

     Vincent

----- Why do I need the source code ? -----

The Debian Social contract [1] requires that all bits of software we
distribute must come along with its source code. Hence, we cannot
distribute code only in a compiled JAR form.

[1]: http://www.debian.org/social_contract

Hello Vincent,

I am sorry to hear that you are having troubles. The jar that is missing is a part of the JABAWS package http://www.compbio.dundee.ac.uk/jabaws as you know.

However, as this is just a utility jar, there is no separate download for it as yet. I did not realize someone will want it that way. Please bear with me and I will make you a separate source download. Is that what you need - just a jar file with the source code for this? I am sorry I am not familiar with the Debian packaging process.

Regards,
Peter

Dr Peter Troshin
Bioinformatics Software Developer
Phone: +44 (0)1382 388589
Fax: +44 (0)1382 385764
The Barton Group
College of Life Sciences
Medical Sciences Institute
University of Dundee
Dundee
DD1 5EH
UK

···

On 14/04/2011 23:31, Vincent Fourmond wrote:

  Hello all,

  Ages ago, I started to package jalview for the Debian operating
system (http://www.debian.org). The original "Intention to package"
can be found there:

  http://bugs.debian.org/507436

  Several things stopped me at that time, the most important one being
the difficulty to package jmol for Debian, as many parts of its
dependencies had unclear copyright/licenses. This has now been cleared
up (not by me), and I'm finally back to packaging jalview. However,
I'm hitting one problem now: the origin of the code for the
min-jaba-client.jar library. I found most of the source code there:

http://www.compbio.dundee.ac.uk/jabaws/archive/jaba-client-source.jar

  Unfortunately, that jar contains already compiled classes, and in
particular the compbio.util package, for which I can't find source
code as of now. Is it available somewhere ? If not, could someone
please make it available at a well-defined location ?

  For now, I'm stuck at this point; it seems that it's the last bit
that prevents me from compiling jalview at this point, but I'm unsure.
In any case, it is a show stopper (see below).

  Any help would be greatly appreciated !

  Cheers,

      Vincent

----- Why do I need the source code ? -----

The Debian Social contract [1] requires that all bits of software we
distribute must come along with its source code. Hence, we cannot
distribute code only in a compiled JAR form.

[1]: http://www.debian.org/social_contract

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Hello Peter !

I am sorry to hear that you are having troubles. The jar that is missing
is a part of the JABAWS package http://www.compbio.dundee.ac.uk/jabaws
as you know.

However, as this is just a utility jar, there is no separate download
for it as yet. I did not realize someone will want it that way. Please
bear with me and I will make you a separate source download. Is that
what you need - just a jar file with the source code for this?

  This is exactly what I need - the source for the embedded
compbio-annotations-1.0.jar and compbio-util-1.3.jar in
jaba-client-source.jar.

  Actually, could you simply offer for download an updated
jaba-client-source.jar with simply all the sources in ?

  Now that I'm at it, I'll push my luck into asking you to version the
download location: if you could name it jaba-client-source-1.1.jar (1.1
is the jabaws version, isn't it ?), that would be fantastic: that
enables all the version-tracking facilities that Debian provide to keep
track with what we call "upstream" versions.

I am sorry I am not familiar with the Debian packaging process.

  No problems ! Debian and all distributions in general are somehow
demanding on what can be packaged, in addition to the copyright/license
requirements. These demands may seem silly from a developer point of
view, but once you've turned to packaging, you see the reason behind all
that. The page http://wiki.debian.org/UpstreamGuide contains a (rather
lengthy) reading on how to make the job easy for packagers to package
the software you write. In most cases, it boils down to basically one
thing: avoid to distribute code-less compiled stuff (such as the
aforementionned ones). Actually, this is a problem of a particular
magnitude for Java software specifically, with the ease to distribute
compiled code that will run everywhere. [1]

  Many thanks !

  Vincent

[1] For those interested, I have written a long post on that topic some
time ago:

http://vince-debian.blogspot.com/2009/03/java-packaging-nightmare.html

···

On 15/04/11 11:37, Peter Troshin wrote:

--
Vincent Fourmond, Doctor in Physics
http://vince-debian.blogspot.com/

Hi Vincent,

Good day for you then! You will get everything you asked for (:-))

Now seriously - thank you for taking trouble explaining why you need this and making good suggestions!
I will let you know the details once all of this is ready.

Cheers,
Peter

···

On 15/04/2011 11:13, Vincent Fourmond wrote:

   Hello Peter !

On 15/04/11 11:37, Peter Troshin wrote:

I am sorry to hear that you are having troubles. The jar that is missing
is a part of the JABAWS package http://www.compbio.dundee.ac.uk/jabaws
as you know.

However, as this is just a utility jar, there is no separate download
for it as yet. I did not realize someone will want it that way. Please
bear with me and I will make you a separate source download. Is that
what you need - just a jar file with the source code for this?

   This is exactly what I need - the source for the embedded
compbio-annotations-1.0.jar and compbio-util-1.3.jar in
jaba-client-source.jar.

   Actually, could you simply offer for download an updated
jaba-client-source.jar with simply all the sources in ?

   Now that I'm at it, I'll push my luck into asking you to version the
download location: if you could name it jaba-client-source-1.1.jar (1.1
is the jabaws version, isn't it ?), that would be fantastic: that
enables all the version-tracking facilities that Debian provide to keep
track with what we call "upstream" versions.

I am sorry I am not familiar with the Debian packaging process.

   No problems ! Debian and all distributions in general are somehow
demanding on what can be packaged, in addition to the copyright/license
requirements. These demands may seem silly from a developer point of
view, but once you've turned to packaging, you see the reason behind all
that. The page http://wiki.debian.org/UpstreamGuide contains a (rather
lengthy) reading on how to make the job easy for packagers to package
the software you write. In most cases, it boils down to basically one
thing: avoid to distribute code-less compiled stuff (such as the
aforementionned ones). Actually, this is a problem of a particular
magnitude for Java software specifically, with the ease to distribute
compiled code that will run everywhere. [1]

   Many thanks !

  Vincent

[1] For those interested, I have written a long post on that topic some
time ago:

http://vince-debian.blogspot.com/2009/03/java-packaging-nightmare.html

Hi Vincent, Peter and Steffen.

It is really good to hear that Jalview will finally be available as a package on Debian, Vincent.

Could you join jalview-dev (http://www.jalview.org/mailman/listinfo/jalview-dev) and post a link to a prototype .deb, or the details of the repository where its uploaded, so I can do some testing ? Unfortunately, there may be a few run-time issues that will need fixing, and we currently lack an automated test suite to catch these issues.

Jim.

···

On 15/04/2011 11:33, Peter Troshin wrote:

Hi Vincent,

Good day for you then! You will get everything you asked for (:-))

Now seriously - thank you for taking trouble explaining why you need
this and making good suggestions!
I will let you know the details once all of this is ready.

Cheers,
Peter

On 15/04/2011 11:13, Vincent Fourmond wrote:

    Hello Peter !

On 15/04/11 11:37, Peter Troshin wrote:

I am sorry to hear that you are having troubles. The jar that is missing
is a part of the JABAWS package http://www.compbio.dundee.ac.uk/jabaws
as you know.

However, as this is just a utility jar, there is no separate download
for it as yet. I did not realize someone will want it that way. Please
bear with me and I will make you a separate source download. Is that
what you need - just a jar file with the source code for this?

    This is exactly what I need - the source for the embedded
compbio-annotations-1.0.jar and compbio-util-1.3.jar in
jaba-client-source.jar.

    Actually, could you simply offer for download an updated
jaba-client-source.jar with simply all the sources in ?

    Now that I'm at it, I'll push my luck into asking you to version the
download location: if you could name it jaba-client-source-1.1.jar (1.1
is the jabaws version, isn't it ?), that would be fantastic: that
enables all the version-tracking facilities that Debian provide to keep
track with what we call "upstream" versions.

I am sorry I am not familiar with the Debian packaging process.

    No problems ! Debian and all distributions in general are somehow
demanding on what can be packaged, in addition to the copyright/license
requirements. These demands may seem silly from a developer point of
view, but once you've turned to packaging, you see the reason behind all
that. The page http://wiki.debian.org/UpstreamGuide contains a (rather
lengthy) reading on how to make the job easy for packagers to package
the software you write. In most cases, it boils down to basically one
thing: avoid to distribute code-less compiled stuff (such as the
aforementionned ones). Actually, this is a problem of a particular
magnitude for Java software specifically, with the ease to distribute
compiled code that will run everywhere. [1]

    Many thanks !

  Vincent

[1] For those interested, I have written a long post on that topic some
time ago:

http://vince-debian.blogspot.com/2009/03/java-packaging-nightmare.html

Hi Vincent, Peter, Steffen, and Jim,

I am also potentially very interested in a Jalview debian package. It would be really great to get it. Is there any news on this initiative?

Cheers,
Hervé

···

On 04/15/2011 03:08 PM, Jim Procter wrote:

Hi Vincent, Peter and Steffen.

It is really good to hear that Jalview will finally be available as a
package on Debian, Vincent.

Could you join jalview-dev
(http://www.jalview.org/mailman/listinfo/jalview-dev) and post a link to
a prototype .deb, or the details of the repository where its uploaded,
so I can do some testing ? Unfortunately, there may be a few run-time
issues that will need fixing, and we currently lack an automated test
suite to catch these issues.

Jim.

On 15/04/2011 11:33, Peter Troshin wrote:

Hi Vincent,

Good day for you then! You will get everything you asked for (:-))

Now seriously - thank you for taking trouble explaining why you need
this and making good suggestions!
I will let you know the details once all of this is ready.

Cheers,
Peter

On 15/04/2011 11:13, Vincent Fourmond wrote:

     Hello Peter !

On 15/04/11 11:37, Peter Troshin wrote:

I am sorry to hear that you are having troubles. The jar that is missing
is a part of the JABAWS package http://www.compbio.dundee.ac.uk/jabaws
as you know.

However, as this is just a utility jar, there is no separate download
for it as yet. I did not realize someone will want it that way. Please
bear with me and I will make you a separate source download. Is that
what you need - just a jar file with the source code for this?

     This is exactly what I need - the source for the embedded
compbio-annotations-1.0.jar and compbio-util-1.3.jar in
jaba-client-source.jar.

     Actually, could you simply offer for download an updated
jaba-client-source.jar with simply all the sources in ?

     Now that I'm at it, I'll push my luck into asking you to version the
download location: if you could name it jaba-client-source-1.1.jar (1.1
is the jabaws version, isn't it ?), that would be fantastic: that
enables all the version-tracking facilities that Debian provide to keep
track with what we call "upstream" versions.

I am sorry I am not familiar with the Debian packaging process.

     No problems ! Debian and all distributions in general are somehow
demanding on what can be packaged, in addition to the copyright/license
requirements. These demands may seem silly from a developer point of
view, but once you've turned to packaging, you see the reason behind all
that. The page http://wiki.debian.org/UpstreamGuide contains a (rather
lengthy) reading on how to make the job easy for packagers to package
the software you write. In most cases, it boils down to basically one
thing: avoid to distribute code-less compiled stuff (such as the
aforementionned ones). Actually, this is a problem of a particular
magnitude for Java software specifically, with the ease to distribute
compiled code that will run everywhere. [1]

     Many thanks !

  Vincent

[1] For those interested, I have written a long post on that topic some
time ago:

http://vince-debian.blogspot.com/2009/03/java-packaging-nightmare.html

_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

Hi Hervé

Hi Vincent, Peter, Steffen, and Jim,

I am also potentially very interested in a Jalview debian package. It
would be really great to get it. Is there any news on this initiative?

not in the last few months. I have some code scrubbing to do on a dependent library before the Jalview source is fully compliant with Debian's free from source policy. Steffen and I did discuss the situation at ISMB, and in principle, Jalview could be included directly as a non-free package, but I'm not sure if Vincent continued with that strategy.

Either way, we should have something in the near future. However, this package will most likely only provide the Jalview desktop - do you want a separate package for the applet too ? (e.g. for provisioning web servers that use it).

Jim.

···

On 26/08/2011 20:56, Hervé Ménager wrote:

Hi Jim,

Hi Hervé

Hi Vincent, Peter, Steffen, and Jim,

I am also potentially very interested in a Jalview debian package. It
would be really great to get it. Is there any news on this initiative?

not in the last few months. I have some code scrubbing to do on a
dependent library before the Jalview source is fully compliant with
Debian's free from source policy. Steffen and I did discuss the
situation at ISMB, and in principle, Jalview could be included directly
as a non-free package, but I'm not sure if Vincent continued with that
strategy.

Good, thanks a lot for keeping us updated on this.

Either way, we should have something in the near future. However, this
package will most likely only provide the Jalview desktop - do you want
a separate package for the applet too ? (e.g. for provisioning web
servers that use it).

Yes indeed, this is what I would like to get, am I so predictable? :wink:
I would be glad to get it, so if any contribution is needed, e.g. to test it, do not hesitate to contact me!

Hervé

···

On 08/27/2011 09:48 AM, Jim Procter wrote:

On 26/08/2011 20:56, Hervé Ménager wrote:

Jim.