NAME

       sepp.config - Configuration file for sepp

SYNOPSIS

       /etc/sepp/sepp.config

DESCRIPTION

       The configuration file of run_sepp.py(1) is at /etc/sepp/sepp.config. It contains paths of programs it
       uses as well as parameters for its dependencies and for itself. It is made of several sections, of which
       title is put inside brackets. Sections are separated by blank lines. In each section, each variable is
       set on a separate line. Now we list the sections and the variables they contain.

pplacer

       The section begins with [pplacer], and it has the following field:

       path=
           The absolute path to the pplacer executable.

hmmalign

       The section begins with [hmmalign], and it has the following field:

       path=
           The absolute path to the hmmalign executable.

hmmsearch

       The section begins with [hmmsearch], and it has the following fields:

       path=
           The absolute path to the hmmsearch executable.

       piped=
           A boolean True or False, indicating whether the human-readable output of hmmsearch should be directed
           to a file (True) instead of stdout (False).

       elim=
           An integer, indicating the E-limit for hmmsearch.

       filters=
           A boolean True or False, indicating whether filters in hmmsearch should be turned off (True) or not
           (False).

hmmbuild

       The section begins with [hmmbuild], and it has the following field:

       path=
           The absolute path to the hmmbuild executable.

jsonmerger

       The section begins with [jsonmerger], and it has the following field:

       path=
           The absolute path to the seppJsonMerger jar.

exhaustive

       The section begins with [exhaustive], and it has the following fields:

       strategy=
           A string "hierarchical", "normal" "midpoint" or "centroid" , indicating the decomposition strategy to
           follow.

       minsubsetsize=
           An integer, indicating the smallest possible value for a subset.

       placementminsubsetsizefacotr=
           An integer, used to compute the size in the decomposition of a tree based on placement subsets.

       placer=
           A string, indicating the name of the placer to use. Currently only "pplacer" is supported.

       weight_placement_by_alignment=
           A boolean True or False, indicating whether to apply weights while caring for fragments or not.

FILES

       /etc/sepp/sepp.config

       ~/.sepp/sepp.config, if existing, overrides the one in /etc/sepp.

SEE ALSO

       run_sepp.py(1)