* use rsync instead of lftp to download schemas and data

[don.git] / genetics / dbsnp_mirror.mdwn

diff --git a/genetics/dbsnp_mirror.mdwn b/genetics/dbsnp_mirror.mdwn
index addc10ea1c9dbebcb901e658c06b8e2bd9a7d829..9ffa841600d3419537e7ff20827362653508e408 100644 (file)
--- a/genetics/dbsnp_mirror.mdwn
+++ b/genetics/dbsnp_mirror.mdwn
@@ -8,10 +8,9 @@ download the databases and schemas for the current release of dbsnp.
 For humans, this is currently ≈60G, and takes a while to retrieve
 (about 24 hours or so).
 
-    for a in {organism,shared}_{data,schema}; do 
-        lftp -c "open ftp.ncbi.nlm.nih.gov; cd /snp/organisms/human_9606/database/; mirror $a";
-    done;
-
+   rsync -rvP --include 'organism_*' --exclude '**' rsync://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/ .
+   rsync -rvP rsync://ftp.ncbi.nlm.nih.gov/snp/database/shared_data .
+   rsync -rvP rsync://ftp.ncbi.nlm.nih.gov/snp/database/shared_schema .
 
 Preparing SQL Schemas
 ---------------------