man getData (1): 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 perfomed 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 <[email protected]> and Charles Plessy <[email protected]> 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.