Ubuntu Manpage: getData - retrieves databases from the Internet

NAME

       getData - retrieves databases from the Internet

SYNOPSIS

       getData [ --mirrordir <path> ] <list of db names>

       getData --list

DESCRIPTION

       Bioinformatics has the intrinsic problem to bring the biological data to the end user. Astronomers have
       the equivalent problem and particle physicists, well, they haven come up with (first) the web and
       (second) the computational grids to address their problems. Debian helps with the programs but will not
       provide such huge datasets that are even frequently updated - not even in volatile.debian.org. Most
       bioinformatics researchers will not need too many of such databases. And even more so will gladly
       continue in using public services remotely.

       For those who need a set of databases on a regular basis, this script shall be a start to automate the
       burden to download the data and update indices and the like. The world has seen such magic before with
       the Lion Biosciences Prisma tool (http://bib.oxfordjournals.org/cgi/reprint/3/4/389.pdf) but how about
       something simpler (as a start) that at least gets close to what we desire and is Free. The aim must be to
       address the needs of all (most) communities, not only of the bioinformatics world. The seed was hence
       made with databases from astronomy.

       Please contact the Debian-Med community if you consider this program to be almost ready for your needs
       and explain what still needs to be added. Public databases that you managed to integrate with this system
       are also very warmly welcomed as feedback.

OPTIONS

--help
this help

--man
Present a more detailed description in form of a man page.

--verbose
Say one or two words more than required.

--mirrordir <path>
Specifies destination directory. The data will be mirrored to the folder $mirrordir/$dbname/. Please
be aware that this mirrordir is nowhere stored. The directory can consequently be moved to arbitrary
locations at any time, if the users of the data are only informed about that moving.

--list
Lists all databases that may be requested to be installed.

<list of db names>
Only those databases that are explicitly requested to be downloaded will be downloaded. Such
databases may require considerable bandwidth, so please make sure you know you are doing the right
thing.

--post
Perform only the unpacking/indexing, but do not retrieve/update the databases. This option is
considered useful when adding a new database management system to the system, e.g. after installing
EMBOSS.

--source
Perform only the unpacking/indexing, but do not retrieve/update the databases. This option may be
beneficial when the site administator is aware of current analyses that should not be disturbed by
the indexing process but the downloading from the net can already be started.

--confd <directory>
Allows for the specification of a directory in which multiple files can be stored that will be read
by getData upon its invocation. These may add values to the global variable %toBeMirrored that
specifies the databases and their download scripts.

--config <system>
Preparation of the configuration file that would be reuired for a particular system that deals with
the database. The configuration is printed to stdout and is expected to be copied manually to the
proper file or folder. One could imagine this process to be automated, though this is not yet
implemented. Currently available is support for two systems:

emboss This specifies the EMBOSS suite of tools for bioinformatics (www.emboss.org) that is also
available as a Debian package. The configuration for the Uniprot databases will allow the
sequence retrieval with the seqret tool.

dre - ARC Grid Runtime Environment
Runtime environments (REs) are a concept of the ARC grid middleware of which more can be
learned on http://www.nordugrid.org. A script is needed to indicate the presence of a
runtime environment. Here, the name of the script is important, which is not definable by
getData though since it only writes to stdout.

Unfortunately, the configuration was not yet be found to be modularised. It all needs to happen
within the getData script itself.

--remove <list of dbnames>
This command removes folders that store the data. In principle this could be performed manually,
though some databases may have special requirements pre- or post-removal, which can be specified
individually for every database.

SPECIFICATION OF DATABASES

Databases for download and their post-processing are specified at two different locations. One is the
getData script itself, the other are files stored in /etc/getData.d. Either will define elements of a
considerably large hash. The key is the identifier which is also shown by the 'getData --list' directive.
The value is a reference to another hash, which assigns values to all the properties that a database has
for its download and post-processing:

name - a human-readable pretty-printed name or short description that makes clear to the world what this
database is about.
A bad example is the mere assignment of "DE405", which few people understand. A better example is
"Pfam-A : Manually curated protein families and domains, only the seed is presented.". One could
argue that one should have that field renamed to "description".

source - shell commands to perform the initial download and subsequent updates
Commonly the wget tool is used for download. The such presented little script is executed underneath
the mirrordir directory. One simple example is "wget --mirror
ftp://ssd.jpl.nasa.gov/pub/eph/export/unix/unxp2[01]*.405". With increasing proficiency in using
wget, one is tempted to substitute "--mirror" with "--recursive --no-host-directories
--no-directories --level 1 --no-parent".

post-download - shell commands to perform after the data has been downloaded.
A simple (and unnecessary when used the right flags to wget) example is the mere setting of a
symbolic link:

"post-download" => "ln -s ssd.jpl.nasa.gov/pub/eph/export/unix/unxp*.405 ."

Some more effort has been put into TrEMBL for the merging of releases with subsequent updates and the
indexing for EMBOSS:

"d=uncompressed; if [ ! -d \$d ]; then mkdir \$d; fi; "
."rm -rf \$d/trembl.dat; "
."(find ftp.ebi.ac.uk -name '*.dat.gz' | xargs -r zcat ) > \$d/trembl.dat; "
."[ -x /usr/bin/dbxflat ] "
. "&& cd \$d && "
. "dbxflat -dbresource embl -dbname trembllocal -idformat swiss -filenames=trembl.dat -fields id,acc -auto",

The dots are connecting strings in Perl. This helps the readability of the code. When writing these
scripts, please be aware the newlines don't separate the individual commands here. Semicolon are
required.

recommends - suggests a series of packages to be present for the use of the database or the performance
of the indexing.
This information is not used at the moment, also to render this script more useful for other Linux
distributions than Debian.

getWgetOptions - private command to get wget options
This is used at download time by makefiles, is not intended to be used interactively, and could be
removed anytime.

EXAMPLES

       The following will list the identifiers and the descriptions of the first 4 databases that area available
       via getData on your system.

            ./getData --mirrordir=/local/databases/mirrored --list | head 4

       To install any particular database, only give its name as an argument. If the installation is performed
       at another directory than the default, then the --mirrordir needs again to be set.

            ./getData swiss.dat

       To remove the database again, give the script a hint with the --remove flag

            ./getData --remove swiss.dat

       To perform the indexing only and circumvent the download (attention, this is dangerous since the index
       files will look newer than the database is), do

            ./getData --post swiss.dat

       A special exception to these extra scripts is the --config flag in that it takes a list of extra
       arguments. Each shall denote a particular system that this database may be of interest for. There are
       today two systems supported:

TODO

       We now need a mechanism with which packages can specify hooks that shall be called upon an update of a
       database. But we cannot assume that every indexing that can be performed because of the installation of
       some package is also desired by the user. How to configure this properly is left to be decided.

AUTHORS

       This script was prepared by Steffen Moeller <moeller@debian.org> and Charles Plessy
       <debian-no-spam@plessy.org> and is distributed under the terms of the GNU Public License (GPL). On Debian
       systems, this license can be found under /usr/share/common-licenses/GPL.