SeqAn for Debian
================

Quoting upstream namely Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
in a private mail to Andreas Tille <andreas@fam-tille.de> and
Filippo Rusconi <lopippo@debian.org> at Wed, 27 Nov 2013 09:38:30 +0100:

  The SeqAn apps are a pretty diverse collection. Some are just simple
  tools for Bioinformaticians, some are results from our research. The
  tools should be useful for useful but from the research result, only
  some are. I would suggest placing the following binaries in /usr/bin
  since they are tools useful for and used by users/scientists:

    alf
    gustaf
    insegt
    masai_indexer
    masai_mapper
    masai_output_pe
    masai_output_se
    mason
    micro_razers
    pair_align
    rabema_build_gold_standard
    rabema_evaluate
    rabema_prepare_sam
    razers
    razers3
    sak
    seqan_tcoffee
    snp_store
    splazers
    stellar
    tree_recon

    [list was sorted and wildcard expanded (masai_*, rabema_*) by
     Andreas Tille]

  The other binaries could live happily in /usr/bin/seqan. If there is a
  collision, one could prefix seqan_ to the binary name.

According to this advise all binary applications are moved to
/usr/lib/seqan/bin and the ones mentioned above symlinked to /usr/bin.
Manpages were created using help2man for the symlinked binaried.

If you set your PATH like

  PATH=${PATH}:/usr/lib/seqan/bin

you can call all seqan tools straight from command line with exception
of /usr/lib/seqan/bin/join since there is a /usr/bin/join inside the
coreutils package which will be found first so you need to explicitly
specify the full path.

If there are good reasons to provide any additional binary under /usr/bin
please file a bug report using `reportbug seqan` and let us know about
your preference.

 -- Andreas Tille <tille@debian.org>  Wed, 27 Nov 2013 10:26:17 +0100

Note: some apps are not built for some architectures due to memory limitations:

Apps not built for mips & mipsel:
 - yara

Apps not built for armhf:
 - yara

Apps not built for sh4:
 - yara
 - razers3

Apps not built for armel:
 - yara

Apps not built for kfreebsd-i386:
 - yara

Apps not built for hurd-i386:
 - yara

Apps not built for ia64:
 - searchjoin (assembler errors)

Sending patches to improve the build experience on any of these architectures
would be welcome by the Debian-Med team and upstream.

  -- Michael R. Crusoe <michael.crusoe@gmail.com>  Fri, 03 Nov 2017 09:29:40 -0700
