GETDATA(1)

🦋 GETDATA 💅

okay bestie, so this is the getData page from section 1 of the manual — the User Contributed Perl Documentation corner of the universe. she's a Perl script. she's a little unhinged. she downloads giant scientific databases off the internet for you and does your indexing. sit down, hydrate, let's go ✨

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🌸 NAME 🌸

getData — retrieves databases from the Internet. that's it. that's the whole personality. iconic behavior honestly 🫶

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✨ SYNOPSIS ✨

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

getData --list

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💖 DESCRIPTION 💖

so here's the tea, bestie. bioinformatics has this intrinsic problem: you gotta bring the biological data to the end user. astronomers have the exact same problem. particle physicists? well, they came up with (first) the web and (second) the computational grids to deal with their stuff. no cap.

Debian helps with the programs but will NOT hand you these huge datasets — not even the ones that get updated constantly, and not even in volatile.debian.org. and honestly? most bioinformatics researchers don't need that many of these databases anyway. and even more so, they'll happily keep using public services remotely. periodt.

so for the people who do need a set of databases on a regular basis, this script is meant to be a start — a way to automate the burden of downloading the data and updating indices and the like. the world has seen this kind of magic before with the Lion Biosciences Prisma tool (http://bib.oxfordjournals.org/cgi/reprint/3/4/389.pdf), but like… how about something simpler as a start? something that at least gets close to what we desire and is Free? 👑

the aim has to be addressing the needs of all (most) communities — not just the bioinformatics world. so the seed was made with databases from astronomy. plot twist, slay.

please contact the Debian-Med community if you think this program is almost ready for your needs, and explain what still needs to be added. public databases you managed to integrate with this system are also very warmly welcomed as feedback. we love feedback. we eat feedback for breakfast 🍓

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🎀 OPTIONS 🎀

• --help — this help. short king energy.
• --man — present a more detailed description in the form of a man page.
• --verbose — say one or two words more than required.
• --mirrordir <path> — specifies the 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. so like, tell your friends before you move the folder, okay? communication is key 💅
• --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. this is not a drill, bestie 😭
• --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 required 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.

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🌈 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. (yes, "semicolon are required." we're keeping that. it's a vibe.)

• 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. 💀

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⭐ 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

🚨 bestie, genuinely — that --post one is dangerous. index files looking newer than the actual database is a whole mess. do not play.

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. (see --config above, iykyk ✨)

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🔥 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. (main character problem, honestly 💜)

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🫶 SEE ALSO 🫶

http://debian-med.alioth.debian.org, http://wiki.debian.org/DebianMed, /etc/getData.conf

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👑 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.

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and that's the whole page, babe 💖 this one was written against perl v5.32.0 and dated 2020-11-29 — so go forth, mirror your databases, and remember: --list before you wreck yourself 🌸🦋💅