How can I access the GSA public FTP server?

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin
edited September 2014 in FAQs

We make various files available for public download from the GSA FTP server, such as the GATK resource bundle and presentation slides. We also maintain a public upload feature for processing bug reports from users.

There are two logins to choose from depending on whether you want to upload or download something:

Downloading

location: ftp.broadinstitute.org
username: gsapubftp-anonymous
password: <blank>

Uploading

location: ftp.broadinstitute.org
username: gsapubftp
password: 5WvQWSfi

Using a browser as FTP client

If you use your browser as FTP client, make sure to include the login information in the address, otherwise you will access the general Broad Institute FTP instead of our team FTP. This should work as a direct link (for downloading only):

ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Questions and comments up to August 2014 have been moved to an archival thread here:

    http://gatkforums.broadinstitute.org/discussion/4559/questions-about-accessing-the-bundle-ftp-server

    Geraldine Van der Auwera, PhD

  • cpenkettcpenkett Cambridge, UKPosts: 1Member

    Hi there. Are you planning to upgrade the Broad Bundle to work with the GRCh38 genome and if so, do you know when the datasets will be available.
    Best wishes,
    Chris Penkett

  • SheilaSheila Broad InstitutePosts: 1,663Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @cpenkett

    Hi Chris,

    Have a look at this thread which may answer your questions: http://gatkforums.broadinstitute.org/discussion/3843/plans-to-update-the-gatk-bundle#latest

    -Sheila

  • yqyeyqye Posts: 1Member

    Hi,

    I wasn't able to login ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle. It always gave me login incorrect error message. Please help. Thanks.

    Yuanqing

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    @yqye‌ This looks like a temporary issue with the FTP server. I'll check with the server admin. Meanwhile, try connecting again later. Sorry for the inconvenience.

    Geraldine Van der Auwera, PhD

  • naymikmnaymikm Posts: 6Member

    anonymous

    works, is there a way to navigate to the bundle from there?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    @naymikm I don't understand your question. Do you have a problem accessing the bundle contents?

    Geraldine Van der Auwera, PhD

  • naymikmnaymikm Posts: 6Member

    Sorry the formatting turned out weird.. I can't access the ftp server with the login credentials. user:anonymous pass: blank> works. Can I access the bundle through the ftp from there?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    No, that will take you to the general Broad FTP server, not our group's. The link above worked for me when I tested it just now, does that not work for you?

    Geraldine Van der Auwera, PhD

  • naymikmnaymikm Posts: 6Member

    Hey it works now! It wasn't before... Thanks!

  • simonsanchezjsimonsanchezj GermanyPosts: 47Member

    Hello, I am trying to follow this link ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle but cannot access the bundle. Getting the following error message: "This webpage is not available".

    thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    If the direct link is not working for you, please try using an FTP client (such as FileZilla).

    Geraldine Van der Auwera, PhD

  • vincenzvincenz Ann ArborPosts: 1Member

    Your link
    ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle
    is not working. It does not accept my password and as a guest it's not working either. I there a problem at your end?

  • SheilaSheila Broad InstitutePosts: 1,663Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @vincenz
    Hi,

    It is working for me. Can you try one more time? Also, have you tried simply going to ftp.broadinstitute.org and using the username and password? https://www.broadinstitute.org/gatk/guide/article?id=1215

    I hope it works this time.

    -Sheila

  • bijuissacbijuissac Wash DCPosts: 1Member

    This was using FileZila, any suggestions
    I used
    adress: ftp.broadinstitute.org
    username: gsapubftp-anonymous
    passwd:

    Got back
    Status: Waiting to retry...
    Status: Resolving address of ftp.broadinstitute.org
    Status: Connecting to 69.173.80.251:21...
    Status: Connection attempt failed with "ECONNREFUSED - Connection refused by server".
    Error: Could not connect to server

  • SheilaSheila Broad InstitutePosts: 1,663Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @bijuissac
    Hi,

    You can try checking to see to see if your firewall is blocking FileZilla. Or, you can also talk to your IT department for help.

    -Sheila

  • marchoeppnermarchoeppner Kiel, GermanyPosts: 1Member
    edited July 28

    Hi,

    I can confirm that the FTP Login does not work. Connection refused when using the credentials provided above. Sheila, since you are at the Broad, I am guessing that this explains why it works for you. From Germany it really does not (the anonymous login to the public FTP works though, although of course I wasn't able to locate the bundle files there). Tried it via a browser, FileZilla and Linux CLI.

    Post edited by marchoeppner on

    Issue · Github
    by Sheila

    Issue Number
    84
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,171Administrator, GATK Dev admin

    Ack, FTP acting up again? We're getting closer to replacing it with a better solution, but in the meantime I'll have to run this through our IT helpdesk. Sorry for the inconvenience, folks. We'll notify you when this is resolved.

    Geraldine Van der Auwera, PhD

  • pandapanda beijingPosts: 2Member

    I am use filezilla.
    adress: ftp.broadinstitute.org
    username: gsapubftp-anonymous
    passwd:

    Status: USER gsapubftp-anonymous
    Status: 331 Password required for gsapubftp-anonymous
    Status: PASS
    Status: 530 Login incorrect.

    If this username has a password?

  • tkoyamatkoyama The University of TokyoPosts: 7Member

    Hi.
    I tried FTP connection to upload my data but failed.

    $ ftp
    ftp> open ftp.broadinstitute.org
    Connected to ftp.broadinstitute.org (69.173.80.251).
    220 ProFTPD 1.3.4a Server (Broad Institute of MIT and Harvard) [69.173.80.251]
    Name (ftp.broadinstitute.org:koyama): gsapubftp
    331 Password required for gsapubftp
    Password:
    530 Login incorrect.
    Login failed.
    Remote system type is UNIX.
    Using binary mode to transfer files.
    

    I also tried if I can login as anonymous user but still failed.

    ftp> open ftp.broadinstitute.org
    Connected to ftp.broadinstitute.org (69.173.80.251).
    220 ProFTPD 1.3.4a Server (Broad Institute of MIT and Harvard) [69.173.80.251]
    Name (ftp.broadinstitute.org:koyama): gsapubftp-anonymous
    331 Password required for gsapubftp-anonymous
    Password:
    530 Login incorrect.
    Login failed.
    Remote system type is UNIX.
    Using binary mode to transfer files.
    

    However, when I try with name 'anonymous', I can login.

    ftp> open ftp.broadinstitute.org
    Connected to ftp.broadinstitute.org (69.173.80.251).
    220 ProFTPD 1.3.4a Server (Broad Institute of MIT and Harvard) [69.173.80.251]
    Name (ftp.broadinstitute.org:koyama): anonymous
    331 Anonymous login ok, send your complete email address as your password
    Password:
    230-Welcome to the FTP server for the Broad Institute of MIT and Harvard 
     in Cambridge, Massachusetts, USA.
    
     All file transfers are logged.
    
     If you have problems, please contact the IT/Systems Group: 
     help@broadinstitute.org
    
     This information was last updated December 2011.
    230 Anonymous access granted, restrictions apply
    Remote system type is UNIX.
    Using binary mode to transfer files.
    

    Is this usual and how can I login as 'gsapubftp'?
    Thank you for your kind helps.

    tkoyama

  • SheilaSheila Broad InstitutePosts: 1,663Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @tkoyama @panda

    Hi,

    Yes, it looks like the FTP is still not working. I will let you know when it works again.

    -Sheila

  • tkoyamatkoyama The University of TokyoPosts: 7Member

    Hi, Shiela

    OK. Thanks!

    tkoyama

  • pandapanda beijingPosts: 2Member

    OK!Thanks!

  • d.aguilerad.aguilera AmsterdamPosts: 1Member

    Is the FTP already working? I have tried to connect and was no possible

  • SheilaSheila Broad InstitutePosts: 1,663Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @d.aguilera
    Hi,

    Sorry about that. I was told it should be back and up running smoothly again. I have emailed our IT department again.

    -Sheila

  • SheilaSheila Broad InstitutePosts: 1,663Member, GATK Dev, Broadie, Moderator, DSDE Dev admin

    @bijuissac @marchoeppner @panda @tkoyama @d.aguliera
    Hi,

    The FTP should be back up and running again. Please let me know if you are still having trouble.

    Thanks,
    Sheila

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