I am having the same issue. Has this question ever been answered?? Should hg_g1k_v37.fa be pulled down when you rsync?? 

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From: shenwiyn <shenwiyn@gmail.com>
Date: Wednesday, September 11, 2013 2:41 AM
To: galaxy-dev <galaxy-dev@bx.psu.edu>
Subject: [galaxy-dev] 回复: Can not find hg_g1k_v37.fa.

Hi,
Fortunately,I get the human_g1k_v37.fasta.gz in ftp://ftp.ncbi.nih.gov/1000genomes/ftp/technical/reference/ .
 
shenwiyn
 
发件人： shenwiyn
发送时间： 2013-09-05 10:03
收件人： galaxy-dev
主题： Can not find hg_g1k_v37.fa.
Hi everyone,
I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find this data.When I use the command :
rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/hg_g1k_v37/seq/hg_g1k_v37.fa 
the error occurred:
receiving incremental file list
rsync: link_stat "/hg_g1k_v37/seq/hg_g1k_v37.fa" (in indexes) failed: No such file or directory (2)
 
sent 4 bytes  received 6 bytes  4.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1532) [receiver=3.0.6]

Please any suggestions would be most welcome. 

Thanks.

shenwiyn