forked from rvosa/supersmart-phylota
-
Notifications
You must be signed in to change notification settings - Fork 5
/
supersmart.ini
121 lines (99 loc) · 4.01 KB
/
supersmart.ini
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
; THIS FILE CONTAINS EXTENDED CONFIGURABLE OPTIONS FOR THE SUPERSMART PIPELINE THAT
; CANNOT BE SET VIA THE COMMAND-LINE INTERFACE FOR THE INDIVIDUAL PIPELINE STEPS
; 1 . GENERAL OPTIONS
; number of cores available
NODES=4
; overall verbosity level
VERBOSITY=-v
; random seed (for reproducibility of results)
RANDOM_SEED=1234
; 2. PIPELINE RUN OPTIONS
; (such as choice of analysis tools, extended run parameters etc.)
; substitution models for inference tools
EXAML_MODEL=GAMMA
RAXML_MODEL=GTRGAMMA
PHYML_MODEL=GTR
; number of RAXML runs and bootstraps
RAXML_RUNS=100
; ExaBayes (backbone tool) options
EXABAYES_NUMRUNS=4
EXABAYES_NUMCHAINS=1
EXABAYES_NUMGENS=100000
; BEAST options
BEAST_TEMPLATE_FILE=data/BEAST/starbeast.xml
; defines the preferred multiple sequence alignment tool. note that this is
; a short name, not an executable location. possible values are:
; mafft clustalw kalign muscle probalign probcons tcoffee amap
MSA_TOOL=muscle
; treePL smoothing level
TREEPL_SMOOTH=100
; parameters for merging clusters. In principle we could use 'blast', 'inparanoid'
; or 'feature'. When blasting, we retain superclusters whose reciprocal overlap is
; specified as MERGE_OVERLAP. We will only retain alignments whose divergence does
; not exceed BACKBONE_MAX_DISTANCE (to prevent saturation) and we will join alignments
; such that each of the BACKBONE_EXEMPLARS exemplar species per genus participates in at
; least BACKBONE_MIN_COVERAGE alignments, which we try to increase up to BACKBONE_MAX_COVERAGE,
; if available.
ALN_MERGE=blast
MERGE_OVERLAP=0.51
BACKBONE_MAX_DISTANCE=0.1
BACKBONE_MIN_COVERAGE=3
BACKBONE_MAX_COVERAGE=10
BACKBONE_EXEMPLARS=2
; parameters for genus trees. within the genera we might accept more rapidly evolving
; loci, hence the CLADE_MAX_DISTANCE might exceed BACKBONE_MAX_DISTANCE. This is
; because we might assume less saturation. The CLADE_MIN_DENSITY specifies how
; many of the clade members must minimally be present to accept the alignment.
; CLADE_MIN_COVERAGE and CLADE_MAX_COVERAGE sets minimum and maximum marker coverage
; per taxon. CLADE_MAX_HAPLOTYPES sets the maximum number of additional haplotypes to add to
; each species in a genus tree
CLADE_MAX_DISTANCE=0.3
CLADE_MIN_DENSITY=0.2
CLADE_MIN_COVERAGE=2
CLADE_MAX_COVERAGE=10
CLADE_MAX_HAPLOTYPES=3
; Configuration for setting up the database and parsing the sequences.
; If variables whose names end with DIR or FILE point to relative paths, and
; prefixing them with the value of environment variable $SUPERSMART_HOME turns
; these into absolute paths that point to something (which is the intended
; behaviour), then the Config.pm object that operates on this file will return
; those absolute paths instead. This is because some of the steps are done on a
; cluster where different nodes will see a different directory layout.
; text file containing the GB release number on which this build is based
GB_RELNUM_FILE=data/GB_CURRENT_RELEASE/GB_FLATFILES/GB_Release_Number
GB_RELNUM=
; defines the minimum 'best practice score' for fossil records from the fossil
; table to be used as calibration points in the tree calibration
FOSSIL_BEST_PRACTICE_CUTOFF=0.0
; burnin fraction for computing consensus trees
; from a posterior distribution
BURNIN=0.1
; how node heights are summarized in a consensus tree. Options are the same as
; for TreeAnnotator, i.e. 'keep', 'median', 'mean' or 'ca'
NODE_HEIGHTS=ca
; 3. INSTALLATION OPTIONS
; (Most likely, you won't need to change anything here.)
; names of executables used by the pipeline
EXAML_BIN=examl
EXABAYES_BIN=exabayes
EXAML_PARSER_BIN=parse-examl
EXABAYES_PARSER_BIN=parse-exabayes
PHYML_BIN=phyml
BLASTP_BIN=blastp
BLASTN_BIN=blastn
MAKEBLASTDB_BIN=makeblastdb
MPIRUN_BIN=mpirun
MYSQL_BIN=mysql
PERL_BIN=perl
CURL_BIN=curl
WGET_BIN=wget
GUNZIP_BIN=gunzip
MUSCLE_BIN=muscle
EXABAYES_CONSENSE_BIN=consense-exabayes
TREEPL_BIN=treePL
BEAST_BIN=beast
TREEANNOTATOR_BIN=treeannotator
; Configuration settings for interaction with the mysql database in the
; supersmart pipeline
DATABASE_FILE=data/phylota.sqlite
RDBMS=SQLite