sepp.config - Configuration file for sepp

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.

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.

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

The section begins with [hmmalign], and it has the following field: path= The absolute path to the hmmalign executable.

The section begins with [hmmbuild], and it has the following field: path= The absolute path to the hmmbuild executable.

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).

The section begins with [jsonmerger], and it has the following field: path= The absolute path to the seppJsonMerger jar.

sepp.config - Configuration file for sepp

The section begins with [pplacer], and it has the following field: path= The absolute path to the pplacer executable.

run_sepp.py(1) sepp SEPP.CONFIG(5)

/etc/sepp/sepp.config