SEALS
A System for Easy Analysis of Lots of Sequences


http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html

Version 0.82

Roland Walker
National Center for Biotechnology Information
walker@ncbi.nlm.nih.gov

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README

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 Special warning regarding SEALS scripts involving Entrez retrievals:

   gi2fasta
   gi2asn1
   gi2genbank
   gi2defline
   gi2abstract
   gi2sibling
   boundtable2fasta

   taxnode2gi           #  these cause load to a much lesser
   taxnode2amino_gi     #  extent
   taxnode2nucleic_gi   #

   tax_filt             #  these cause excessive load only
   tax_break            #  if your taxonomy index ('megatable')
   tax_collector        #  becomes outdated

 If you are performing retrievals on a large scale, you must set up your
 local fasta indexes ("hints").  This will reduce load on the NCBI servers, 
 and give you a speed increase of many orders of magnitude.  Hints are
 created with the command 'fasta2index' and stored on the path specified 
 under the fasta2index option '-fast_index_path'. (See the readme for 
 fasta2index.  At a minimum, indexes for the nr and nt databases which 
 are less than 60 days old must be installed.  The recommendation is that
 indexes be created for all available indexes which contain gi numbers.

 If you are retrieving fasta records which are in your hints databases, the 
 retrieval will occur on your local system only.  Other retrievals will
 search Entrez through the NCBI servers.
 
 Be very careful with large operations that may cause overloading of the
 NCBI servers.  In the interest of providing reliable service to all, NCBI 
 must request that large retrieval operations be planned carefully to 
 minimize impact on NCBI systems.  Large retrievals should be scheduled to
 run outside of the normal business hours at NCBI, namely 8 AM to 9 PM, 
 Eastern Standard Time.

 All transactions are logged.  Your site administrator will be contacted
 if overuse occurs.  Continued abuse of NCBI servers may result in limited 
 access for your site.
 

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To install the SEALS package, change to the seals/install directory and follow
the instructions in the README in that directory.

If you are not the SEALS administrator, but wish to use an already installed 
version of SEALS, you only need to 
  
  0 be using tcsh as your shell 

  1 add a line sourcing .seals_login.tcshrc (from this directory), as 
    near to the end of your ~/.login as possible

  2 add a line sourcing .seals_shell.tcshrc (from this directory), as 
    near to the beginning of your ~/.tcshrc as possible.  If you don't
    have a ~/.tcshrc, create one that sources .seals_shell.tcshrc
    and your ~/.cshrc, if any.

When you are done with all that, create a new login shell, and execute 

   seals

with no arguments to see a list of scripts.  

   seals --status

will give you some status information about your installation, and

   seals --describe

will return single-line descriptions of each command.

The rwidget man page will give you a very important overview of the SEALS
command-line interface.  Please read it.

The listing returned by

   seals --bugs

is recommended reading as well.

For most programs, a readme will be given if the program is executed without 
arguments.  In all cases, executing

  command --help

will give you a readme.

NOTES:

There are a few scripts missing, and blastmore is not in this release.  These 
programs must be prettified a bit more before I am happy with distributing 
them.  There are also many scripts here which are not described in the ISMB 
paper.  The best reference is the output of the 'seals' command.

gi2report is not included, because the report format is longer supported by 
NCBI.

If you have difficulties with retrievals using gi2fasta, etc, there may be
a problem with the Entrez server.  Please try 'entrezping' to see if the 
server is up.

There are man pages available for gref, but other programs have no 
documentation other than the built-in README.

There will be more docs whenever I get the change to write them, and a 1.0
release to go with our paper in Bioinformatics (formerly CABIOS), which is in 
preparation.  If you have any specific needs, especially regarding things 
mentioned in the paper but not listed, but also any suggestions, thoughts, or 
bug reports, write me without hesitation.

Roland

Roland Walker
walker@nbci.nlm.nih.gov