Author: plessy
Date: 2008-08-31 10:41:47 +0000 (Sun, 31 Aug 2008)
New Revision: 2440
Modified:
trunk/community/infrastructure/getData/getData
Log:
Since $sharedWgetOptions has --no-host-directories, the script should not look
in ftp.ebi.ac.uk.
Modified: trunk/community/infrastructure/getData/getData
===================================================================
--- trunk/community/infrastructure/getData/getData 2008-08-31 09:07:42 UTC
(rev 2439)
+++ trunk/community/infrastructure/getData/getData 2008-08-31 10:41:47 UTC
(rev 2440)
@@ -415,7 +415,7 @@
source => "wget $sharedWgetOptions
ftp://ftp.ebi.ac.uk/pub/databases/swissprot/release_compressed/uniprot_trembl.dat.gz";,
"post-download" => "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; "
+ ."(find . -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",
@@ -428,7 +428,7 @@
source => "wget $sharedWgetOptions
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";,
"post-download" => "d=uncompressed; if [ ! -d \$d ]; then mkdir
\$d; fi; "
."rm -rf \$d/swissprot.dat; "
- ."(find ftp.ebi.ac.uk -name '*.dat.gz' |
xargs -r zcat ) > \$d/swissprot.dat; "
+ ."(find . -name '*.dat.gz' | xargs -r zcat )
> \$d/swissprot.dat; "
."[ -x /usr/bin/dbiflat ] && "
. "cd \$d && "
. "dbiflat -dbname swisslocal -fields
acc,des -idformat swiss -auto",
_______________________________________________
debian-med-commit mailing list
[email protected]
http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
