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root/msatfinder/msatminer.rc
Revision: 1.1.1.1 (vendor branch)
Committed: Mon Mar 7 15:34:45 2005 UTC (11 years, 5 months ago) by knirirr
Branch: MAIN
CVS Tags: HEAD, HEAD
Changes since 1.1: +0 -0 lines
Log Message:
First import

Line File contents
1 ########################################################################
2 # msatminer.rc - combined configuration file for all msatminer scripts. #
3 # Full editing instructions are included below. #
4 #########################################################################
5
6 # most of these defaults should be acceptable. However, you MUST
7 # edit the parts in the [VIEWER] section (bottom)
8
9 [COMMON]
10
11 # set to 1 to switch on debugging info
12 debug = 0
13
14 # no. of bp either side of each msat to extract
15 flank_size = 300
16
17 # suffix of the genome files
18 genomeglob = "gbk"
19
20 # suffix of your microsatellite fasta files
21 # by default, msatfinder uses the suffix "fasta"
22 msatglob = "fasta"
23
24 # directory variables: it is best to leave these
25 # values as they are. If you change them, the trailing
26 # slash MUST be left on the name
27 mine_dir = "MINE/"
28 repeat_dir = "Repeats/"
29 tab_dir = "Msat_tabs/"
30 bigtab_dir = "Flank_tabs/"
31 fasta_dir = "Fasta/"
32 prime_dir = "Primers/"
33 align_dir = "Aligner/"
34 anno_dir = "Annotations/"
35 count_dir = "Counts/"
36
37 # set this to the url you'd like non-cgi results to be visible
38 # at, if using a web browser to view the final version.
39 # If you don't set it, then you can read the repeat_matrix.html
40 # file in the directory you run msataligner in.
41 url = "http://localhost/msatminer/"
42 url = ""
43
44
45 [DEPENDENCIES]
46
47 # Determine whether primers may be made from the repeat you need eprimer3
48 # (emboss), and primer3_core on your PATH for this to work
49 # (see http://www-genome.wi.mit.edu/genome_software/other/primer3.html)
50 # see eprimer3 documentation for additional flags.
51 # N.B. use "-task 0" if you have EMBOSS v.2.8.0, but "-primers" if you
52 # have a newer version.
53 run_eprimer = 1
54 eprimer_args = "-primer"
55 eprimer = "/usr/bin/eprimer3"
56 primer3core = "/usr/bin/primer3_core"
57
58 # full paths to various executables
59 # check that these are correct for
60 # your system before running
61 bl2seq = "/usr/bin/bl2seq"
62 bl2seq_options = "-F F"
63 blast_type = "blastn"
64 mview = "/usr/local/bin/mview"
65 mview_options = "-html full"
66 dnadist = "/usr/local/bin/dnadist"
67 neighbor = "/usr/local/bin/neighbor"
68 blastall = "/usr/local/bin/blastall"
69 blast_options = "-F F"
70 e_value = "1e-6"
71 formatdb = "/usr/local/bin/formatdb"
72
73
74 [FINDER]
75
76 # the override switch will, if set to 1,
77 # turn off most of the output files.
78 # they can be deactivated individually
79 # with separate switches (see below)
80 override = 0
81
82 # set the thresholds here, in order:
83 # mono, di, tri, tetra, penta, hexa... &c.
84 # msatfinder will find msats of that
85 # no. of units or more
86 threshold = "12,8,5,5,5,5"
87
88 # set the type of msat you want to search
89 # for here, 1=mono, 2=di etc. Default is
90 # for mono-hexa
91 mrange="1,2,3,4,5,6"
92
93 # will write a file.tab file for you
94 # with repeats formatted as embl features
95 # ready for overlay on the genbank doc
96 # inside the artemis annotation tool
97 # contains "feature table", hence "tab"
98 # 0 no artemis files
99 # 1 files for msat only
100 # 2 also produce separate files for msat + flanks
101 artemis = 1
102
103 # Write repeats and flanking areas to
104 # a MINE.db file? 1=yes, etc.
105 mine = 1
106
107 # write fasta files for repeats?
108 fastafile = 1
109
110 # "taxon" information: please see
111 # http://genomics.nerc-oxford.ac.uk/msatminer/#taxon
112 # for details
113 phages = "viruses"
114 viroids = "viruses"
115 plant_viruses = "viruses"
116 megaplasmids = "plasmids"
117
118 # remote link for viewing complete
119 # files, (Genbank, in this case)
120 remote_link="http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
121
122 # this switch turns on the Repeats/$prefix.summary
123 # file, which can grow rather large if your
124 # thresholds are low. It's an essential file, though.
125 sumswitch = 1
126
127 # print out filenames as they are searched
128 screendump = 1
129
130 [ANNOTATOR]
131
132 # suffix for the blast databases that will be generated
133 dbname = "_blastdb"
134
135 # save blast reports used for msat location matching (0=no, 1=yes)
136 save = 0
137
138 # various names are be given to the categories one
139 # sorts the matches into. Define them here.
140 np_degree = "Conserved/Monomorphic"
141 p_degree = "Conserved/Polymorphic"
142 nc_degree = "Not conserved"
143 f1_degree = "One flank conserved"
144 f2_degree = "Two flanks conserved"
145
146 # set to 1 in order to separate (CA)6 into two
147 # columns of 'CA' and '6', &c.
148 expand = 0
149
150 # set $match to 0 in order to turn off the
151 # discarding of small matches.
152 # $multiplier controls the threshold
153 smatch = 1
154 multiplier = 3
155
156 [ALIGNER]
157
158 # run mview. Set to 0 to turn off, or if mview not installed
159 run_mview = 1
160
161 # activate blasts vs. msats or genomes
162 vsgenomes = 1
163 vsmsats = 1
164
165 # add extra headers in the table to make it
166 # clearer when you have a large number of
167 # microsatellites/genomes
168 headers = 1
169
170 # the key explains what colours &c. are used
171 # in the final output. Set to 0 to disable
172 key = 1
173
174 # this value is the hsp length above which it
175 # will be considered to be a valid match.
176 hsp_size = 150
177
178 # background colour for the bl2seq cells
179 # of the final table
180 # Don't choose blue ;-)
181 # no hit (orange)
182 bgcolournohit = "#FF9900"
183 # hit another genome (green)
184 bgcolourhit = "#009933"
185 # hit self (red)
186 bgcolourself = "CC3033"
187 # length($hit) < ($hsp_size + msat length) (yellow)
188 bgcolourpartial = "#FFFF99"
189
190
191 [VIEWER]
192
193 # unlike the rest of the file, these defaults will need
194 # to be edited if you set up a database. dbmaker will
195 # read these and attempt to set up a database (with
196 # cgi viewer) according to these paramters
197
198 # title for your webpage
199 title = "Microsatellite Database"
200
201 # url for the cgi parts your on-line database
202 baseURL = "http://localhost/cgi-bin/"
203
204 # location of the cgi scripts on your server
205 cgiloc = "/var/www/cgi-bin/"
206
207 # the output of msataligner, and any other non-cgi
208 # files, will be copied to this directory in order
209 # to be viewed at the url set at COMMON.url, above
210 msatview = "/var/www/html/msatminer/"
211
212 # name of the stylesheet to use
213 stylesheet = "quickmineoutput.css"
214
215 # details used to connect to your database.
216 # dbtype should be 'Pg' if useing a postgresql database,
217 # or 'mysql' if using a mysql database
218 dbtype = "mysql"
219 dbname = "msatminer"
220
221 # these names should have permission to create tables and insert
222 # data, using: GRANT ALL TO privileged_user ON msatminer.* IDENTIFIED
223 # BY `a_cunning_password` WITH GRANT OPTION;
224 # and will be used by msatdbmaker to create the database
225 gdbusername = "privileged_user"
226 gdbpassword = "a_cunning_password"
227
228 # these names should only have permission to select on the database
229 #using: GRANT SELECT TO unprivileged_user ON msatminer.* IDENTIFIED
230 # BY `another_cunning_password`;
231 # and will be used by msatdbmaker to create the database
232 sdbusername = "unprivileged_user"
233 sdbpassword = "another_cunning_password"
234
235 # the person to whom messages concerning your database should be sent
236 mailto = "you\@your_host"