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.commailto:shenwiyn@gmail.com> Date: Wednesday, September 11, 2013 2:41 AM To: galaxy-dev <galaxy-dev@bx.psu.edumailto: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： shenwiynmailto:shenwiyn@gmail.com 发送时间： 2013-09-05 10:03 收件人： galaxy-devmailto: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

---

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/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

-- Jennifer Hillman-Jackson http://galaxyproject.org

---

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/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/