Update:

We are hosting .2bit files as a standard on the rsync server, so this is how to retrieve sequence data. No .fa files will be served.

The advantages are that the files are 25% smaller, the rsyncs are quicker, and local/cloud users can easily convert to fasta format anytime.

I will be adding in these notes to our rsync wiki to avoid confusion going forward.

Thanks Shenwiyn, I am sure that this helped many other readers.

Jen
Galaxy team

On 10/16/13 12:39 PM, Jennifer Jackson wrote:

Hello Shenwiyn,

We can confirm that the hg_g1k_v37.fa is currently unavailable. We are working to correct this.

Meanwhile, the hg_g1k_v37.2bit files is available. This can be convert to fasta using the tool "twoBitToFa" available from UCSC in the downloads area, under source code, pre-compiled for several platforms: http://genome.ucsc.edu

You will likely want both files version anyway, as several tools rely on the .2bit file for input/reference.

Very sorry for the current inconvenience,

Jen
Galaxy team

On 9/4/13 7:03 PM, shenwiyn wrote:
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
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