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  • iGenome ftp site

    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!

  • #2
    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.

    Comment


    • #3
      Thank you. I thought that was what I entered. I will try again tomorrow.

      Comment


      • #4
        Both wget and get worked.

        is wget generally preferred becaused it downloads faster?

        Comment


        • #5
          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.
          Last edited by Richard Finney; 09-20-2012, 06:54 AM.

          Comment


          • #6
            thanks Richard.

            Comment


            • #7
              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?

              Comment


              • #8
                Originally posted by Etherella View Post
                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/

                Comment


                • #9
                  Thanks a lot!

                  Comment


                  • #10
                    Dear all, I cannot access the iGenome ftp server too. Is there some problem?

                    Thanks
                    Luca

                    Comment


                    • #11
                      Originally posted by lucas81 View Post
                      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.

                      Comment


                      • #12
                        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

                        Comment


                        • #13
                          Originally posted by lucas81 View Post
                          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.
                          Last edited by GenoMax; 09-18-2013, 05:35 AM.

                          Comment


                          • #14
                            solved (I hope)

                            Originally posted by GenoMax View Post
                            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

                            Comment

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