File: README.Apollo

package info (click to toggle)
libchado-perl 1.31-6
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, bullseye, sid
  • size: 44,716 kB
  • sloc: sql: 282,721; xml: 192,553; perl: 25,524; sh: 102; python: 73; makefile: 57
file content (96 lines) | stat: -rw-r--r-- 4,017 bytes parent folder | download | duplicates (5)
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
Note that this document is quite old, and while it may still work
this way, it can't be guaranteed.  Most people who use Apollo
with Chado do not do it this way anymore and instead use the 
adapter that comes with Apollo (sometimes known as the "Crabtree
adapter" after the original author Jonathan Crabtree).  For 
more information on it, see the Apollo tutorial at the GMOD
website:

  http://gmod.org/wiki/Apollo_Tutorial

Scott
9/20/2011



This needs to be better documented, but here is a start:

In order to use Apollo read/write with chado, here are things that need to
be done:

  - grant privileges to users to several tables (list here) --in the  
    meantime, you can grant all using sqlt and the template, 
    bin/privileges.tmpl 

    sqlt -f PostgreSQL -t TTSchema --template bin/privileges.tmpl modules/nofuncs.sql | psql <databasename>

    You can edit the template to grant privileges to just specific
    users instead of PUBLIC, which of course would be a lot more secure.

  - insert several ad hoc cv terms found in 
    modules/sequence/apollo-bridge/cv_inserts.sql. This file
    contains sql commands to insert several controlled vocabulary terms
    that Apollo expects to be in the database.  This file can be recreated
    with additional terms as needed by editing the file
    modules/sequence/apollo-bridge/ad_hoc_cv and running the perl script
    modules/sequence/apollo-bridge/insert_ad_doc_cv.pl.  The resulting 
    sql file can be inserted into the database with this command:

      $ psql $DBNAME < modules/sequence/apollo-bridge/cv_inserts.sql 

  - insert a few misc items like those found in 
    modules/sequence/apollo-bridge/apollo.inserts
    
    Essentially, Apollo and chado have to agree about what the names
    of the programs in the analysis table are, and there needs to be a
    few terms in the cv table.

    About naming analysis results: there are no restrictions on what you
    name them, however the GFF3 bulk loader will insert them typically 
    one of two ways:

    1. If you specify the -a (--analysis) flag with an argument, the 
    loader will look for an entry in the analysis table where
    analysis.name is equal to the argument supplied with -a.

    2. If you don't give an argument with -a, the loader will look
    for analysis.name that is equal to the GFF source and type concatentated
    with and underscore between them, ie 'source_type', eg, 'Rice_cDNA_match'.

    The inserts in the db table are there so that dbxref entries in GFF files
    I typically process.  They can be ignored unless you are loading
    GFF files with Dbxref entries.

    Then there is the uniquename_id_generator sequence, for which
    integers for building uniquenames are used. Then there are two
    interts in to cvtermprop for the suffix and prefix for uniquename
    generation.  Generated uniquenames with be of the form:

        $prefix . (int from uniquename_id sequence) . $suffix

    For exmple, if you insert 'RICE' for the prefix and 'X' for the suffix, 
    the resulting name of the first feature will be 'RICE000001X';

  - add the functions and triggers to chado.  Use the perl script:

      % /usr/local/bin/gmod_apollo_triggers.pl create

    Note that this script can also be used to drop and add the triggers
    in case you want to do some bulk loading and want to disactivate
    the triggers for that. 

  - modify the Apollo configuration file, chado-adapter.xml.  IS THERE
    DOCUMENTATION FOR DOING THAT IN APOLLO'S DOCS?  Yes, there is
    a section for connecteding directly to flybase chado in the apollo
    doc directory: doc/html/userguide.html but it is somewhat out of date.
    I need to work with Mark to update it (it will probably need me to 
    write it and have Mark proof it).


I understand that these directions are somewhat vague.  Getting Apollo to
work with chado requires a little hands on tinkering.  If you find yourself
having difficulties, please contact me.

Scott Cain
cain@cshl.edu
4/29/05