iGenome ftp site

[JQL]

Hi,

Sorry for this naive question. I would like to get the GTF files from Illumina's iGenome ftp site, but don't have access. I can download from http://cufflinks.cbcb.umd.edu/igenomes.html

but how to access from a linux server? It prompted for user name and pwd which were denied.

thanks!

[Richard Finney]

Worked for me:
ftp ftp://igenome:[email protected]

I did this ...
-bash-3.00$ ftp
ftp> open ussd-ftp.illumina.com
Connected to ussd-ftp.illumina.com.
220 EFT Server 6.4.1 Build 12.19.2011.1
500 Protocol not supported.
500 Protocol not supported.
KERBEROS_V4 rejected as an authentication type
Name (ussd-ftp.illumina.com:finneyr): igenome
331 Password required for igenome.
Password: (note, enter G3nom3s4u )
230 Login OK. Proceed.
Remote system type is UNIX.
Using binary mode to transfer files.
ftp> pwd
257 "/" is current folder.
ftp> cd Homo_sapiens
250 Folder changed to "/Homo_sapiens".
ftp> cd NCBI/build37.1
250 Folder changed to "/Homo_sapiens/NCBI/build37.1".
ftp> ls
227 Entering Passive Mode (66,192,10,36,216,48).
150 Opening ASCII mode data connection for file list.
-r--r--r-- 1 user group 16620139308 May 14 19:04 Homo_sapiens_NCBI_build37.1.tar.gz
226 Transfer complete. 91 bytes transferred. 91 bps.
ftp>
....

Better yet just use "wget".

Search for wget for more info.

[JQL]

Thank you. I thought that was what I entered. I will try again tomorrow.

[JQL]

Both wget and get worked.

is wget generally preferred becaused it downloads faster?

[Richard Finney]

wget is very convenient for scripting.
For instance you can scrape the page, filter out the URLs, pick the ones you want and slap a "wget " in front and pipe it to a shell. Tricky but easily do-able with with a little experience.

ftp and (sftp with -b parameter) is scriptable, too.

They are both the same speed as they're written in C and implement the same protocol (though wget does support other protocols, notably the http protocol). Any difference you see are probably network congestion or the result of I/O caching.

[JQL]

thanks Richard.

[Etherella]

Sorry for reviving this old topic, but I cannot connect to ussd-ftp.illumina.com. It says : connection reset by peer.

How can I download the human genome hg19?

[GenoMax]

Sorry for reviving this old topic, but I cannot connect to ussd-ftp.illumina.com. It says : connection reset by peer.

How can I download the human genome hg19?

Are you behind an institutional firewall that is preventing you from downloading?
The iGenomes/Illumina server is up and available.

If you only need the hg19 sequence then you can get it from other locations:

UCSC: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/
Ensembl: ftp://ftp.ensembl.org/pub/release-73...o_sapiens/dna/
NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/

[Etherella]

Thanks a lot!

[lucas81]

Dear all, I cannot access the iGenome ftp server too. Is there some problem?

Thanks
Luca

[GenoMax]

Dear all, I cannot access the iGenome ftp server too. Is there some problem?

Thanks
Luca

Server is up and available. Local firewall may be preventing you from reaching the site.

[lucas81]

Dear GenoMax I tried from different computers in different institution, so I don't think is a problem of firewall... have you tried to download this? ftp://ussd-ftp.illumina.com/Mus_musc..._GRCm38.tar.gz

Best and thanks for your prompt reply

Luca

[GenoMax]

Dear GenoMax I tried from different computers in different institution, so I don't think is a problem of firewall... have you tried to download this? ftp://ussd-ftp.illumina.com/Mus_musc..._GRCm38.tar.gz

Best and thanks for your prompt reply

Luca

The link you posted is working for me (with right login/password, see below).

You are trying to download a genome that is not listed on the iGenomes site (http://cufflinks.cbcb.umd.edu/igenomes.html). If you look at one of the existing download links at the igenomes site you will see the account name/password (embedded in the link) that you need to use for the FTP site (which will work for the link above).

Post #2 in this thread has the login information you need.

[lucas81]

solved (I hope)

The link you posted is working for me (with right login/password, see below).

You are trying to download a genome that is not listed on the iGenomes site (http://cufflinks.cbcb.umd.edu/igenomes.html). If you look at one of the existing download links at the igenomes site you will see the account name/password (embedded in the link) that you need to use for the FTP site (which will work for the link above).

Post #2 in this thread has the login information you need.

Many thanks for your advice. We have some IP problem apparently. We managed accessing a computer in another city(!). Many thanks again!

Luca