DBWatcher (was 'MINORE: Anyone gotten this to work?')

Frederic Plewniak plewniak at igbmc.u-strasbg.fr
Mon Jun 3 07:56:26 EST 1996


Greg wrote:
> 
> Question: has anyone modified this program to run on Solaris (or even Irix
> for that matter). It seems like a really useful idea which I could
> find immediate use for. Alternatively, is there a similar publicly
> available service running on the 'net somewhere?
> 


It is not exactly what MINORE does but I have just written a C program
running on Solaris (DBWatcher 1.00) which does something similar with
local databases. I am still documenting it but you can already dowload
the current pre-release version :

      ftp://ftp-igbmc.u-strasbg.fr/pub/DBWatcher/dbwatcher.tar.Z


Current features include :

      1) Performs BLAST searches and keeps track of previous
         searches to report **only novel similarities**

      2) Checks for database updates, sequence modification,
         settings changes and performs searches **only when necessary**

      3) Searches are arranged in jobs and results for each job are
         sent to **one or several** e-mail addresses.


DBWatcher comes with a companion program, SetDBWatcher, which provides
an X Graphical User Interface for managing the jobs.
(SetDBWatcher requires the NCBI ToolKit for compilation.)

FYI, here is a first draft of the README.DBWatcher file :


################################################################################

       DBWatcher
       version 1.0 for Sun/Solaris (May 1996)

################################################################################
Frederic PLEWNIAK
Plewniak at igbmc.u-strasbg.fr
CNRS - LGME 6520
IGBMC - Strasbourg, France
--------------------------------------------------------------------------------

DBwatcher is a program handling  periodic BLAST searches to find similarities to
your own sequences.  It  keeps  track of the previous searches and only performs
new ones when necessary  (i.e. when the database has been updated,  the sequence
has been modified, or when settings have been changed).

Only  novel  similarities are reported, thus saving the time of browsing through
bulky result files.  When executed daily (as a cron job) it ensures that you are
informed as soon as new sequences similar to yours are incorporated into a given
database. This is most valuable in association with an automatic database update
procedure.

Results are sent by electronic mail to one or several addresses making DBWatcher
particularly suitable for collaborative database survey as well as for users who
do not have access to locally maintained databases.


--------------------------------------------------------------------------------
REQUIREMENTS
================================================================================
DBWAtcher requires a working version of the BLAST programs which can be obtained
from ncbi.nlm.nih.gov anonymous ftp site in the /blast directory. Alternatively,
DBWatcher can use the GCG versions of the BLAST programs.

The following environment variables should be set to their appropriate value for
both regular and GCG versions :

        $BLASTDB        : Directory containing the BLAST databases
        $BLASTMAT       : Directory containing the BLAST comparison matrices
        $BLASTFILTER    : Directory containing the seg and xnu filter programs

For more information concerning BLAST programs, please consult the BLAST help at
http://www.ncbi.nlm.nih.gov/BLAST/blast_help.html  or the BLAST documentation in
the GCG Program Manual.

This version has only been tested with GCG BLAST programs on Sun/Solaris 2.5 but
it should be portable to other Unix boxes.
Binaries are provided for Sun/Solaris 2.5.

Of course,  these requirements are only for the site  actually running the BLAST
programs and DBWatcher. Remote sites only need an e-mail box to receive results.


--------------------------------------------------------------------------------
SETTING UP JOBS
================================================================================
DBWatcher jobs can be created manually or with the SetDBWatcher GUI if you have
access to X/Motif libraries.
SetDBWatcher takes care of everything including available programs and databases
so you don't have to worry too much about creating and managing your jobs.
Here are some instructions though, just in case you might want to do things by
hand or develop your own way of setting up jobs.

Jobs are stored in the DBWatcher Home Directory as follows :

                          DBWatcher Home Directory
                                     |
                     ---------------------------------- ...
                     |                                |
                   user1                            user2
                     |                                |
       ---------------------------                    |
       |                         |                    |
      Job1                   anotherjob             Myjob
       |                         |                    |
  -----------------       ----------------      ----------------
  |     |    |    |       |     |    |   |      |     |    |   |
config seqs log  tmp    config seqs log tmp   config seqs log tmp
        |    |    |             |    |   |            |    |   |
     ----  ----  ----           |    |   |         ----  ----  ----
     |  |  |  |  |  |           |    |   |         |  |  |  |  |  |
     s1 s2 s1 s2 s1 s2       myseq myseq myseq     sX sY sX sY sX sY



Directories user1, user2, etc should be named after the username of the
user who
will be responsible for running DBWatcher.

There might be any number of job directories in users' directories,  having any
valid UNIX directory name.

In each job directory there should be the following :
        config          : config file
        seqs/           : sequences directory
        log/            : log directory used to keep track of previous searches
                          files in this directory are created automatically.
        tmp/            : directory used to store the last results
                          files in this directory are created automatically.

Sequences in the seqs/ directory should be in FastA (Pearson) format.

The config file should have the following format :

        - 1st line : Job name (any character accepted)
        - 2nd line : Blast program name
        - 3rd line : Database name
        - 4th line : Extra parameters
        - 5th line : P(N) threshold above which results are not reported
        - 6th line : e-mail addresses to send the results

-----------------Example of config file----------------------------------------
Job Name
gcg_blastn
gbnew
V=250 B=250 -filter seg
1e-3
John.Smith at institute.dom.xx Anyone at anywhere.xx
-----------------End of example------------------------------------------------

Best regards,
Fred

Frederic PLEWNIAK
Plewniak at igbmc.u-strasbg.fr
CNRS - LGME 6520
IGBMC - Strasbourg, France




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