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)