[Seqan-dev] [andreas@an3as.eu: Re: source code for the apps]

[Filippo Rusconi <listes.rusconi@laposte.net>]

Greetings everybody,

here is a mail from Andreas Tille, who is not subscribed to the
mailing list.

Filippo Rusconi

----- Forwarded message from Andreas Tille <andreas@an3as.eu> -----

Date: Wed, 28 Aug 2013 15:22:09 +0200
From: Andreas Tille <andreas@an3as.eu>
To: "Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>
Cc: Filippo Rusconi <lopippo@debian.org>, SeqAn Development <seqan-dev@lists.fu-berlin.de>
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
> 

-- 
http://fam-tille.de

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