[med-svn] r2109 - trunk/community/infrastructure/getData

[smoe-guest at alioth.debian.org]

Author: smoe-guest
Date: 2008-06-30 13:48:22 +0000 (Mon, 30 Jun 2008)
New Revision: 2109

Modified:
   trunk/community/infrastructure/getData/getData
Log:
Added TrEMBL (protein sequence data maintained at the European Bioinformatics Institute)
to the list of available databases.


Modified: trunk/community/infrastructure/getData/getData
===================================================================
--- trunk/community/infrastructure/getData/getData	2008-06-30 00:18:13 UTC (rev 2108)
+++ trunk/community/infrastructure/getData/getData	2008-06-30 13:48:22 UTC (rev 2109)
@@ -2,7 +2,7 @@
 
 =head1 NAME
 
-getData.pl - retrieves databases from the Internet
+getData - retrieves databases from the Internet
 
 =cut
 
@@ -50,9 +50,10 @@
 
 =head1 SYNOPSIS
 
-getData.pl [ --mirrordir <path> ] <list of db names>
-getData.pl --list
+getData [ --mirrordir <path> ] <list of db names>
 
+getData --list
+
 =head1 DESCRIPTION
 
 Bioinformatics has the intrinsic problem to bring the biological data
@@ -92,7 +93,10 @@
 
 =item --mirrordir <path>
 
-    Specifies destination directory. The data will be mirrored to $mirrordir/$dbname/
+    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.
 
 =item --list
 
@@ -106,7 +110,7 @@
 
 =head1 EXAMPLES
 
-./getData.pl --list | head 4
+./getData --mirrordir=/local/databases/mirrored --list | head 4
 
 =head1 TODO
 
@@ -205,11 +209,18 @@
 	},
 
 
-#	"swiss.dat" => {
-#		name => "UniProt - SwissProt in EMBL format",
-#		source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_sprot.dat.gz ftp://ftp.ebi.ac.uk/pub/databases/swissprot/updates_compressed/*.dat.gz"
-#	},
-#
+	"trembl.dat" => {
+		name => "UniProt - TrEMBL in EMBL format",
+		source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_trembl.dat.gz"
+	#	source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_sprot.dat.gz"
+	},
+
+	"swiss.dat" => {
+		name => "UniProt - SwissProt in EMBL format",
+		source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_sprot.dat.gz ftp://ftp.ebi.ac.uk/pub/databases/swissprot/updates_compressed/*.dat.gz"
+	#	source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_sprot.dat.gz"
+	},
+
 	"swiss.fasta" => {
 		name => "UniProt - SWISS-PROT in FASTA format",
 		source => "wget --mirror ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz"