I am having the same issue. Has this question ever been answered?? Should hg_g1k_v37.fa be pulled down when you rsync?? -- From: shenwiyn <shenwiyn@gmail.com<mailto:shenwiyn@gmail.com>> Date: Wednesday, September 11, 2013 2:41 AM To: galaxy-dev <galaxy-dev@bx.psu.edu<mailto: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<mailto:shenwiyn@gmail.com> 发送时间： 2013-09-05 10:03 收件人： galaxy-dev<mailto:galaxy-dev@bx.psu.edu> 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

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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___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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