Re: [Seqan-dev] source code for the apps

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Dear all,

we (the SeqAn developers) cannot easily go back to the 1.3 build system.

Everything originates from to (1) not much thought at the beginning of the project and (2) the library being developed in an academic group where research and publishing papers is the source of funding and not building software (sadly).

Since we are very interested in getting current SeqAn releases into Debian and other distributions, let us see how we can remove some of the headache for you distribution builders!

We would like to have both the apps and the library in Debian.

Would the following be feasible?

1. The SeqAn team provides a "seqan-src-1.4.1.tar.gz" that essentially is a tarballed version of the whole SVN tag.
2. The seqan-dev package is built from this using the -DSEQAN_RELEASE_LIBRARY flag to cmake.
3. The SeqAn team adjusts the build system with a -DSEQAN_IS_DEBIAN_BUILD=TRUE flag that allows to build the apps using the headers from the seqan-dev built earlier.

I have some (but limited, mostly from backports) experience with building Debian packages. Would it be possible for us to maintain our own "debian" folder with build scripts that you can use to base your package upon?

We could branch 1.4.1 and do a 1.4.2 release including the modifications to the build system for making the Debian developers' lives easier.

Cheers,
Manuel

________________________________________
From: Andreas Tille [andreas@an3as.eu]
Sent: Wednesday, August 28, 2013 3:22 PM
To: Holtgrewe, Manuel
Cc: Filippo Rusconi; SeqAn Development
Subject: Re: [Seqan-dev] source code for the apps

Hi Manuel,

thanks for your quick reaction and the instructions how to build seqan
1.4.1.  The problem is, that creating Debian packages works a bit
different here.  In Debian you usually start from a downloaded upstream
tarball and as usual this worked for seqan perfectly in the past.  There
are for sure ways to work around this by writing a script that fakes an
upstream tarball by creating this from svn but this is on one hand extra
work on the other hand it does not create byte identical tarballs (which
is quite a tricky topic even if the single files you are using are byte
identical).  So creating the tarball from SVN is only the second best
choice for us.

Moreover the two step build process (using
-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS and
-DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY for different things) would
also create extra hassle for us.  I had a quick look onto the SVN you
mentioned below and I have no good idea what might be the best way to
proceed from here.  It seems what we are really interested in and what
somehow fits your 1.3.x series release tarballs can be found inside the
core directory.  The other directories seem to contain extra byteload
which needs extra checking and verifying for licenses etc by our
ftpmasters - so the new way you are releasing seqan creates a lot of
work on our side.

I see the following options for us:

  1. Keep on using seqan release tarball and provide only the library
     for our users while droping the apps.

  2. Create the library package as described in 1. and checkout the
     apps from SVN creating seqan-apps_1.4.1.orig.tar.bz2 and build
     Debian packages from this depending from seqan-dev package.
     This probably needs us to tweak the build system for the apps
     a bit.

  3. Checkout http://svn.seqan.de/seqan/tags/seqan-1.4.1/core, create
     seqan_1.4.1.orig.tar.bz2 and create seqan-dev + seqan-apps
     package from this unique source which is mimicking the source
     tarball as of previous versions but also will probably need us
     to tweak the build system (not checked yet)

  4. You would consider adding a source tarball seqan-apps we could
     take in a similar way as in 2.

  5. You would consider to releas as in the past including the apps.

The 1. option would be the least work for everybody but probably not in
the interest of our users.  The 5. option would be the most comfortable
solution from a Debian perspective.

What do you think?

Kind regards and thanks again for your quick response

      Andreas.

On Wed, Aug 28, 2013 at 02:26:55PM +0200, Holtgrewe, Manuel wrote:
> Dear Fillipo,
>
> we do not ship the whole SeqAn project from source any more in a tarball but you can still get it from SVN.
>
> (tl;dr: Skip to the instructions starting with "svn co" below).
>
> You can get the 1.4.1 version from here
>
> http://svn.seqan.de/seqan/tags/seqan-1.4.1/
>
> You can find more information on building applications in the following two documents:
>
> http://trac.seqan.de/wiki/Tutorial/GettingStarted/LinuxMakefiles
> http://trac.seqan.de/wiki/BuildManual/UsingTheSeqAnBuildSystem
>
> I just checked and the following sequence of commands built all applications and installed them with an install prefix (similar to an autoconf ./configure --prefix=)
>
> svn co http://svn.seqan.de/seqan/tags/seqan-1.4.1 seqan-1.4.1
> mkdir -p seqan-1.4.1-build/release
> cd seqan-1.4.1-build/release
> cmake ../../seqan-1.4.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../../seqan-1.4.1-install -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_APPS
> make -j 8 install
>
> Similar, you could use the following sequence to get a library install:
>
> svn co http://svn.seqan.de/seqan/tags/seqan-1.4.1 seqan-1.4.1
> mkdir -p seqan-1.4.1-build/library
> cd seqan-1.4.1-build/library
> cmake ../../seqan-1.4.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=../../seqan-lib-1.4.1-install -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE_LIBRARY
> make docs
> make install
>
> Feel free to ask if you hit a brick wall (I successfully compiled everything on Debian 7.1).
>
> Cheers,
> Manuel
> ________________________________________
> From: Filippo Rusconi [listes.rusconi@laposte.net]
> Sent: Wednesday, August 28, 2013 1:34 PM
> To: seqan-dev@lists.fu-berlin.de
> Cc: Andreas Tille
> Subject: [Seqan-dev] source code for the apps
>
> Greetings Fellow Seqan Users and Developers,
>
> I'm currently packaging the OpenMS software suite for Debian. That
> software depends on Seqan.
>
> Since release 1.10, OpenMS depends on Seqan 1.4.1. In Debian, we
> currently have seqan 1.3.1 in the form of two packages: seqan-dev
> (header files of the lib) and seqan-apps (binary programs) [[ CC
> Andreas, who is the package maintainer ]].
>
> Before being able to package OpenMS for Debian, we thus have to have
> seqan 1.4.1 packaged for Debian. The problem is that apparently the
> apps are no more shipped in the source tarball. I see at
> http://packages.seqan.de/ that the Seqan
> software is now shipped in two forms:
>
> 1/ header files in the lib source bundle
>
> 2/ binary images in the apps bundle.
>
> Where can we get the source of the apps, so that we can continue
> having both the library and the apps nicely packaged in Debian ?
>
> Thank you for your kind help,
>
> Filippo Rusconi
>
> --
> Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu
> Researcher at CNRS and Debian Developer <lopippo@debian.org>
> Author of ``massXpert''     at http://www.massxpert.org
>
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> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>

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