Packging jModelTest for Debian and versioning

[Andreas Tille]

Hi,

I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in the field of medicine
and biology. You can find an overview about the biological software we
have just packaged for Debian on our biology task page[1].

Since I was asked to package jModelTest I checked what might be the
latest version. At

https://code.google.com/p/jmodeltest2/wiki/Updates

I found

"20 Feb 2015 Version 2.1.7 rev 20150220"

which seems to be the latest download that is available at your Google
drive download location. In addition at Github a release
jModelTest-2.1.7-20141120 is available. While I would really prefer
releases from Github since this simplifies things a lot this does not
seem to be tha lastet release.

It would help if you could confirm that the codebase officially moved
from Google Code to Github and if so if all released states would be
properly tagged.

Kind regards

Andreas.

[1] http://blends.debian.org/med/tasks/bio

[Diego Darriba]

Hi Andreas,

As you said, jModelTest has been officially migrated to github, since
google code is going away:

https://github.com/ddarriba/jmodeltest

I tagged the last releases, available at Google Drive together with the
PhyML binaries. jModelTest requires PhyML to be available, but it can be
configured for using a system wide installed version by setting the flag
`global-phyml-exe` in the configuration file:

https://github.com/ddarriba/jmodeltest2/blob/v2.1.7r20150222/src/main/resources/conf/jmodeltest.conf

Don't hesitate on asking me if you have any question or you need me to do
any further change in the code.

Best Regards,
Diego.

Post by Andreas Tille
Hi,
I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in the field of medicine
and biology. You can find an overview about the biological software we
have just packaged for Debian on our biology task page[1].
Since I was asked to package jModelTest I checked what might be the
latest version. At
https://code.google.com/p/jmodeltest2/wiki/Updates
I found
"20 Feb 2015 Version 2.1.7 rev 20150220"
which seems to be the latest download that is available at your Google
drive download location. In addition at Github a release
jModelTest-2.1.7-20141120 is available. While I would really prefer
releases from Github since this simplifies things a lot this does not
seem to be tha lastet release.
It would help if you could confirm that the codebase officially moved
from Google Code to Github and if so if all released states would be
properly tagged.
Kind regards
Andreas.
[1] http://blends.debian.org/med/tasks/bio

[Andreas Tille]

Hi Diego,

it took some time since the last mail exchange but as I mentioned before
we need to work on the third party JARs to build them from source as
separate packages. I managed to do this now for alter.jar, pal.jar and
prottest.jar (fetching latest version 3.4 instead of 3.0 - hope this is
fine). The only remaining bio-related JAR is lib/readseq.jar.

We had some previous discussion on the Debian Med mailing list[2] which
lead to the conclusion that this code could at best shipped under
non-free if the authors are not responsive. Since we did not got any
response from the authors we somehow assume that the readseq2 project is
possibly dead.

You might check whether jmodeltest would be able to use

https://github.com/rdpstaff/ReadSeq

instead to not relay on a non-free project with uncertain maintenance
status.

Kind regards

Andreas.


[2] https://lists.debian.org/debian-med/2014/02/msg00205.html

Post by Diego Darriba
Hi Andreas,
As you said, jModelTest has been officially migrated to github, since
https://github.com/ddarriba/jmodeltest
I tagged the last releases, available at Google Drive together with the
PhyML binaries. jModelTest requires PhyML to be available, but it can be
configured for using a system wide installed version by setting the flag
https://github.com/ddarriba/jmodeltest2/blob/v2.1.7r20150222/src/main/resources/conf/jmodeltest.conf
Don't hesitate on asking me if you have any question or you need me to do
any further change in the code.
Best Regards,
Diego.

Post by Andreas Tille
Hi,
I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in the field of medicine
and biology. You can find an overview about the biological software we
have just packaged for Debian on our biology task page[1].
Since I was asked to package jModelTest I checked what might be the
latest version. At
https://code.google.com/p/jmodeltest2/wiki/Updates
I found
"20 Feb 2015 Version 2.1.7 rev 20150220"
which seems to be the latest download that is available at your Google
drive download location. In addition at Github a release
jModelTest-2.1.7-20141120 is available. While I would really prefer
releases from Github since this simplifies things a lot this does not
seem to be tha lastet release.
It would help if you could confirm that the codebase officially moved
from Google Code to Github and if so if all released states would be
properly tagged.
Kind regards
Andreas.
[1] http://blends.debian.org/med/tasks/bio

[Diego Darriba]

Hi Andreas,

Thanks for the advice. ReadSeq should be fine, even though according to its README file it does not
parse PHYLIP format. I will check it within the next days and hopefully by the end of this week
there will be a new release. I believe we can even proceed without readseq2/ReadSeq, using ALTER
directly. I'll let you know.

Best Regards,
Diego.

Post by Andreas Tille
Hi Diego,
it took some time since the last mail exchange but as I mentioned before
we need to work on the third party JARs to build them from source as
separate packages. I managed to do this now for alter.jar, pal.jar and
prottest.jar (fetching latest version 3.4 instead of 3.0 - hope this is
fine). The only remaining bio-related JAR is lib/readseq.jar.
We had some previous discussion on the Debian Med mailing list[2] which
lead to the conclusion that this code could at best shipped under
non-free if the authors are not responsive. Since we did not got any
response from the authors we somehow assume that the readseq2 project is
possibly dead.
You might check whether jmodeltest would be able to use
https://github.com/rdpstaff/ReadSeq
instead to not relay on a non-free project with uncertain maintenance
status.
Kind regards
Andreas.
[2] https://lists.debian.org/debian-med/2014/02/msg00205.html

Post by Diego Darriba
Hi Andreas,
As you said, jModelTest has been officially migrated to github, since
https://github.com/ddarriba/jmodeltest
I tagged the last releases, available at Google Drive together with the
PhyML binaries. jModelTest requires PhyML to be available, but it can be
configured for using a system wide installed version by setting the flag
https://github.com/ddarriba/jmodeltest2/blob/v2.1.7r20150222/src/main/resources/conf/jmodeltest.conf
Don't hesitate on asking me if you have any question or you need me to do
any further change in the code.
Best Regards,
Diego.

Post by Andreas Tille
Hi,
I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in the field of medicine
and biology. You can find an overview about the biological software we
have just packaged for Debian on our biology task page[1].
Since I was asked to package jModelTest I checked what might be the
latest version. At
https://code.google.com/p/jmodeltest2/wiki/Updates
I found
"20 Feb 2015 Version 2.1.7 rev 20150220"
which seems to be the latest download that is available at your Google
drive download location. In addition at Github a release
jModelTest-2.1.7-20141120 is available. While I would really prefer
releases from Github since this simplifies things a lot this does not
seem to be tha lastet release.
It would help if you could confirm that the codebase officially moved
from Google Code to Github and if so if all released states would be
properly tagged.
Kind regards
Andreas.
[1] http://blends.debian.org/med/tasks/bio

[Diego Darriba]

Hi Andreas,

I added a new tagged revision after removing the dependency on ReadSeq. I also fixed the license in
several files where it was missing, and I removed the PhyML binaries from the repository. I am not
sure how you deal with that dependency, which is present also in ProtTest, but let me know if I
should do something about it. I replaced the binaries with a README file in
src/main/resources/exe/phyml that explains how to place the PhyML binary in the distribution.

Best,
Diego.

Post by Andreas Tille
Hi Diego,
it took some time since the last mail exchange but as I mentioned before
we need to work on the third party JARs to build them from source as
separate packages. I managed to do this now for alter.jar, pal.jar and
prottest.jar (fetching latest version 3.4 instead of 3.0 - hope this is
fine). The only remaining bio-related JAR is lib/readseq.jar.
We had some previous discussion on the Debian Med mailing list[2] which
lead to the conclusion that this code could at best shipped under
non-free if the authors are not responsive. Since we did not got any
response from the authors we somehow assume that the readseq2 project is
possibly dead.
You might check whether jmodeltest would be able to use
https://github.com/rdpstaff/ReadSeq
instead to not relay on a non-free project with uncertain maintenance
status.
Kind regards
Andreas.
[2] https://lists.debian.org/debian-med/2014/02/msg00205.html

Post by Diego Darriba
Hi Andreas,
As you said, jModelTest has been officially migrated to github, since
https://github.com/ddarriba/jmodeltest
I tagged the last releases, available at Google Drive together with the
PhyML binaries. jModelTest requires PhyML to be available, but it can be
configured for using a system wide installed version by setting the flag
https://github.com/ddarriba/jmodeltest2/blob/v2.1.7r20150222/src/main/resources/conf/jmodeltest.conf
Don't hesitate on asking me if you have any question or you need me to do
any further change in the code.
Best Regards,
Diego.

Post by Andreas Tille
Hi,
I'm writing you on behalf of the Debian Med team that has the objective
to package all free software that is relevant in the field of medicine
and biology. You can find an overview about the biological software we
have just packaged for Debian on our biology task page[1].
Since I was asked to package jModelTest I checked what might be the
latest version. At
https://code.google.com/p/jmodeltest2/wiki/Updates
I found
"20 Feb 2015 Version 2.1.7 rev 20150220"
which seems to be the latest download that is available at your Google
drive download location. In addition at Github a release
jModelTest-2.1.7-20141120 is available. While I would really prefer
releases from Github since this simplifies things a lot this does not
seem to be tha lastet release.
It would help if you could confirm that the codebase officially moved
from Google Code to Github and if so if all released states would be
properly tagged.
Kind regards
Andreas.
[1] http://blends.debian.org/med/tasks/bio

[Andreas Tille]

Hi Diego,

Post by Diego Darriba
I added a new tagged revision after removing the dependency on ReadSeq. I also fixed the license in
several files where it was missing,

Thanks a lot for your really helpful support.

Post by Diego Darriba
and I removed the PhyML binaries from the repository. I am not
sure how you deal with that dependency, which is present also in ProtTest, but let me know if I
should do something about it.

We use a dependency from the Debian package of phyml 20141029.

Post by Diego Darriba
I replaced the binaries with a README file in
src/main/resources/exe/phyml that explains how to place the PhyML binary in the distribution.

/usr/bin/phyml should be found.

It might be helpful if you could add a test suite checking whether phyml
is easily found.

Kind regards

Andreas.

[Diego Darriba]

Hi Andreas,

jModelTest searches for the binaries in the local path, unless it is
configured for using the global path, since the phyml version installed
by the user might not be compatible. I will change the default behavior
such that it searches for global binaries first, and tests the suitability.

Do you use any standard test suite? Could you send me an example of
other software that already incorporates this?

Best,
Diego.

Post by Andreas Tille
Hi Diego,

Post by Diego Darriba
I added a new tagged revision after removing the dependency on ReadSeq. I also fixed the license in
several files where it was missing,

Thanks a lot for your really helpful support.

Post by Diego Darriba
and I removed the PhyML binaries from the repository. I am not
sure how you deal with that dependency, which is present also in ProtTest, but let me know if I
should do something about it.

We use a dependency from the Debian package of phyml 20141029.

Post by Diego Darriba
I replaced the binaries with a README file in
src/main/resources/exe/phyml that explains how to place the PhyML binary in the distribution.

/usr/bin/phyml should be found.
It might be helpful if you could add a test suite checking whether phyml
is easily found.
Kind regards
Andreas.

[Andreas Tille]

Hi Diego,

Post by Diego Darriba
jModelTest searches for the binaries in the local path, unless it is
configured for using the global path, since the phyml version installed
by the user might not be compatible. I will change the default behavior
such that it searches for global binaries first, and tests the suitability.

This would be a very sensible enhancement.

Post by Diego Darriba
Do you use any standard test suite? Could you send me an example of
other software that already incorporates this?

I think there is no such thing as a standard test suite. I admit I have
no experience with Java but in Python and R there are at least four
different test frameworks (in both) I have seen used by authors of such
software.

May be others here on this list might be able to provide some input -
otherwise a web search might uncover what would fit your application
best (which I feel unable to decide).

Thanks a lot for your support

Andreas.

[Andreas Tille]

Hi Diego,

Post by Diego Darriba
I added a new tagged revision after removing the dependency on ReadSeq.

I checked this out and noticed that the BrowserLauncher is now the only
thing left for packaging to fullfill all prerequisites for jmodeltest.
I guess it is this project:

http://browserlaunch2.sourceforge.net/

right?

BTW, I noticed that the build process is a bit picky about non-ASCII
characters. As I said I have no detailed experience with Java source
code but I needed to apply this patch

https://anonscm.debian.org/cgit/debian-med/jmodeltest.git/tree/debian/patches/encoding.patch

to enable building the source code. I agree that it is not really nice
to mix up proper Spanish names but lacking a better solution I went
for this one for the moment.

Kind regards

Andreas.

[Andreas Tille]

Hi Diego,

I think I forgot to CC you in my last mail. I wonder what the status of
jmodeltest might be. Any estimation when we can expect a new version
without netbeans dependencies?

Kind regards

Andreas.

Post by Andreas Tille
Hi Diego,

Post by Diego Darriba
I added a new tagged revision after removing the dependency on ReadSeq.

I checked this out and noticed that the BrowserLauncher is now the only
thing left for packaging to fullfill all prerequisites for jmodeltest.
http://browserlaunch2.sourceforge.net/
right?
BTW, I noticed that the build process is a bit picky about non-ASCII
characters. As I said I have no detailed experience with Java source
code but I needed to apply this patch
https://anonscm.debian.org/cgit/debian-med/jmodeltest.git/tree/debian/patches/encoding.patch
to enable building the source code. I agree that it is not really nice
to mix up proper Spanish names but lacking a better solution I went
for this one for the moment.
Kind regards
Andreas.
--
http://fam-tille.de

[Diego Darriba]

Hi Andreas,

I have just released a new revision. There was no dependency on Netbeans library in jModelTest (that
was in ProtTest, instead). The new version allows for using the PhyML binary located at /usr/bin/phyml.
The changes are listed here:

https://github.com/ddarriba/jmodeltest2/blob/master/src/main/resources/CHANGELOG

Please let me know if there is anything else missing.

Thank you,
Diego.

Post by Andreas Tille
Hi Diego,
I think I forgot to CC you in my last mail. I wonder what the status of
jmodeltest might be. Any estimation when we can expect a new version
without netbeans dependencies?
Kind regards
Andreas.

Post by Andreas Tille
Hi Diego,

Post by Diego Darriba
I added a new tagged revision after removing the dependency on ReadSeq.

I checked this out and noticed that the BrowserLauncher is now the only
thing left for packaging to fullfill all prerequisites for jmodeltest.
http://browserlaunch2.sourceforge.net/
right?
BTW, I noticed that the build process is a bit picky about non-ASCII
characters. As I said I have no detailed experience with Java source
code but I needed to apply this patch
https://anonscm.debian.org/cgit/debian-med/jmodeltest.git/tree/debian/patches/encoding.patch
to enable building the source code. I agree that it is not really nice
to mix up proper Spanish names but lacking a better solution I went
for this one for the moment.
Kind regards
Andreas.
--
http://fam-tille.de

[Andreas Tille]

Hi Diego,

Post by Diego Darriba
I have just released a new revision. There was no dependency on Netbeans library in jModelTest (that
was in ProtTest, instead).

Ahh sorry, I mixed this up. The netbeans dependency from ProtTest just
prevented me from backporting to current Debian stable. It would be
nice if you could ping me if you have removed the netbeans dependency -
I think I remember that you intended to get rid of netbeans.

Post by Diego Darriba
The new version allows for using the PhyML binary located at /usr/bin/phyml.
https://github.com/ddarriba/jmodeltest2/blob/master/src/main/resources/CHANGELOG

These changes look good. I can remove the encoding patch.

Post by Diego Darriba

Post by Andreas Tille
I checked this out and noticed that the BrowserLauncher is now the only
thing left for packaging to fullfill all prerequisites for jmodeltest.
http://browserlaunch2.sourceforge.net/
right?

You did not confirmed this. This is the only missing dependency in the
current jmodeltest which prevents me from creating the package.

Kind regards

Andreas.

[Diego Darriba López]

Hi Andreas,

I though I have already answered. Sorry for that. Effectively, that is the project for BrowserLauncher.

I will upload the next release for ProtTest in the next days. The dependency has been removed, but there is also a recently found bug I need to fix.

Best,
Diego.


On Fri, Jan 15, 2016 at 11:12:40PM +0100, Andreas Tille wrote:
Hi Diego,

Post by Diego Darriba
I have just released a new revision. There was no dependency on Netbeans library in jModelTest (that
was in ProtTest, instead).

Ahh sorry, I mixed this up. The netbeans dependency from ProtTest just
prevented me from backporting to current Debian stable. It would be
nice if you could ping me if you have removed the netbeans dependency -
I think I remember that you intended to get rid of netbeans.

Post by Diego Darriba
The new version allows for using the PhyML binary located at /usr/bin/phyml.
https://github.com/ddarriba/jmodeltest2/blob/master/src/main/resources/CHANGELOG

These changes look good. I can remove the encoding patch.

Post by Diego Darriba

Post by Andreas Tille
I checked this out and noticed that the BrowserLauncher is now the only
thing left for packaging to fullfill all prerequisites for jmodeltest.
http://browserlaunch2.sourceforge.net/
right?

You did not confirmed this. This is the only missing dependency in the
current jmodeltest which prevents me from creating the package.

Kind regards

Andreas.

[Andreas Tille]

Hi Diego,

Post by Diego Darriba López
I though I have already answered. Sorry for that. Effectively, that is the project for BrowserLauncher.

OK, I've packaged this and uploaded to the Debian new queue.

Post by Diego Darriba López
I will upload the next release for ProtTest in the next days. The dependency has been removed, but there is also a recently found bug I need to fix.

Sounds good!

Thanks for your kind cooperation

Andreas.

[Andreas Tille]

Hi Diego,

I wonder whether I missed something but I have not found any new
protest3 version which is not using netbeans. May be you simply
forgot to tag it on Github?

Kind regards and thanks for your cooperation

Andreas.

Post by Andreas Tille
Hi Diego,

Post by Diego Darriba López
I though I have already answered. Sorry for that. Effectively, that is the project for BrowserLauncher.

OK, I've packaged this and uploaded to the Debian new queue.

Post by Diego Darriba López
I will upload the next release for ProtTest in the next days. The dependency has been removed, but there is also a recently found bug I need to fix.

Sounds good!
Thanks for your kind cooperation
Andreas.
--
http://fam-tille.de

[Diego Darriba]

Hi Andreas,

Sorry for the delay. The netbeans dependencies where removed time ago, but I could not work in the
new release. It is now ready and you can find it in the github repository. Hopefully everything is
OK now. The only thing to be taken into account is that you would need to set "global-phyml-exe =
true" in prottest.properties in order to use PhyML from the path.

Kind Regards,
Diego.

Post by Andreas Tille
Hi Diego,
I wonder whether I missed something but I have not found any new
protest3 version which is not using netbeans. May be you simply
forgot to tag it on Github?
Kind regards and thanks for your cooperation
Andreas.

Post by Andreas Tille
Hi Diego,

Post by Diego Darriba López
I though I have already answered. Sorry for that. Effectively, that is the project for BrowserLauncher.

OK, I've packaged this and uploaded to the Debian new queue.

Post by Diego Darriba López
I will upload the next release for ProtTest in the next days. The dependency has been removed, but there is also a recently found bug I need to fix.

Sounds good!
Thanks for your kind cooperation
Andreas.
--
http://fam-tille.de

[Andreas Tille]

Hi Diego,

thanks a lot for your support. Prottest now builds fine under Debian
stable and I'll upload a backport to Jessie soon. I also noticed that
jmodeltest now can be build easily and I'm in the process of preparing
packages. When doing so I noticed some glitches you might be interested
in:

1. Please review the patch I'm using at
https://anonscm.debian.org/git/debian-med/jmodeltest.git/tree/debian/patches/do_not_chmod_anything_in_usr_bin.patch
The original build.xml removes executable bit from every file
in /usr/bin which is probably not what you want and if the
user that builds jmodeltest has root permissions (and is not
in a chrooted system where Debian builds are happening) the
system in question might become disfunctional.

2. When I start runjmodeltest-gui the window displays:

WARNING: PhyML binary is not in the list of compatibility:
/usr/bin/phyml v3:320+dfsg-2~bpo8+1
Compatible versions: 20130103 20131022 20141009 20141029 20150501 20151222
jModelTest will try to continue execution anyway, but it might fail.

I have no idea how you do ther version verfification in
jmodeltest. I just can say that we packaged what can be
found here:

https://github.com/stephaneguindon/phyml/releases

Could you confirm that this phyml version would work?

I'll probably come up with more questions regarding proper usage
of mpj but that's it for now.

Thanks a lot for your cooperation

Andreas.

Post by Diego Darriba
Hi Andreas,
Sorry for the delay. The netbeans dependencies where removed time ago, but I could not work in the
new release. It is now ready and you can find it in the github repository. Hopefully everything is
OK now. The only thing to be taken into account is that you would need to set "global-phyml-exe =
true" in prottest.properties in order to use PhyML from the path.
Kind Regards,
Diego.

Post by Andreas Tille
Hi Diego,
I wonder whether I missed something but I have not found any new
protest3 version which is not using netbeans. May be you simply
forgot to tag it on Github?
Kind regards and thanks for your cooperation
Andreas.

Post by Andreas Tille
Hi Diego,

Post by Diego Darriba López
I though I have already answered. Sorry for that. Effectively, that is the project for BrowserLauncher.

OK, I've packaged this and uploaded to the Debian new queue.

Post by Diego Darriba López
I will upload the next release for ProtTest in the next days. The dependency has been removed, but there is also a recently found bug I need to fix.

Sounds good!
Thanks for your kind cooperation
Andreas.
--
http://fam-tille.de