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

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

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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