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How can I access the GSA public FTP server?

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,382Administrator, Dev admin
edited June 29 in FAQs

NOTE: This article will be deprecated in the near future as this information will be consolidated elsewhere.

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

Tagged:

Comments

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,382Administrator, 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: 3,739Member, Broadie, Moderator, 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: 10,382Administrator, 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: 10,382Administrator, 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: 10,382Administrator, 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: 10,382Administrator, 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: 3,739Member, Broadie, Moderator, 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: 3,739Member, Broadie, Moderator, 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: 2Member
    edited July 2015

    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: 10,382Administrator, 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: 9Member

    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: 3,739Member, Broadie, Moderator, 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: 9Member

    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: 3,739Member, Broadie, Moderator, 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: 3,739Member, Broadie, Moderator, 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

  • SehrishSehrish AustraliaPosts: 2Member

    @Sheila said:
    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

    Hi Sheila,

    I have tried accessing FTP server just now and it's not available?
    Any help would be appreciated

  • SehrishSehrish AustraliaPosts: 2Member

    Hi Sheila,

    I have tried accessing it again through Cyberduck and it says "530 Sorry, max 25 users --try again later".
    Not sure what does that mean?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,382Administrator, Dev admin

    Probably that many people were trying to use it at the same time. We're planning to upgrade to a better system, but I'm afraid that for now you'll have to try again later. Apologies for the inconvenience.

    Geraldine Van der Auwera, PhD

  • jjmmiijjmmii Posts: 4Member

    Hi Sheila and Geraldine,

    I too couldn't download the rest of the bundle after downloading some of the files and lost connection. I hope the max 25 users quota get increased soon. Thank you very much.

  • SheilaSheila Broad InstitutePosts: 3,739Member, Broadie, Moderator, Dev admin

    @jjmmii
    Hi,

    Sorry about that. Yes, the system will be upgraded, but unfortunately, not yet.

    -Sheila

  • lfallerlfaller boston maPosts: 1Member

    Hi all,

    I tried accessing the server today and it wasn't working for me. Has this been resolved for other users? Is there a workaround?

    Thanks a bunch!
    ~Lina

  • SheilaSheila Broad InstitutePosts: 3,739Member, Broadie, Moderator, Dev admin

    @lfaller
    Hi Lina,

    Perhaps try again? I know there were some issues that should be resolved now.

    -Sheila

  • matthewmatthew chinaPosts: 1Member
    edited February 25

    your username and password seems not work when i linked to ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle

    Post edited by matthew on
  • matthewmatthew chinaPosts: 1Member

    It works

  • kbanyaskbanyas Posts: 3Member

    I attempt to ftp in but get a Connection refused error.

  • SheilaSheila Broad InstitutePosts: 3,739Member, Broadie, Moderator, Dev admin

    @kbanyas
    Hi,

    Can you try again? It is working for me now.

    -Sheila

  • raman91raman91 SingaporePosts: 3Member

    Hi, i tried to log in the GSA public FTP server. It says - Sorry, max 25 users -- try again later

  • raman91raman91 SingaporePosts: 3Member

    maximum 25 users. Why so less? Is there any link to download the db snp vcf file to run for muTect2? Thanks

    Issue · Github
    by Sheila

    Issue Number
    790
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,382Administrator, Dev admin

    Hi @raman91, I'm sorry you ran into this limitation. We share the FTP server with the rest of our institute so we cannot offer unlimited download bandwidth. We have a project to move the bundle to a cloud platform to make it easier for people to access the data quickly and reliably from wherever they are in the world, but we are still figuring out some details (such as how to keep this service completely free for everyone).

    Geraldine Van der Auwera, PhD

  • slamentslament SwedenPosts: 25Member

    Sorry guys, but I'm new to this. I tried to connect to the server through Finder in Mac OSX to upload files for a bug report, typing ftp://gsapubftp@ftp.broadinstitute.org and the password in the instructions above. I seem to access a folder but I have no rights to write anything in it. Help!

  • SheilaSheila Broad InstitutePosts: 3,739Member, Broadie, Moderator, Dev admin

    @slament
    Hi,

    Can you try this link: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle

    Also have a look at this page.

    -Sheila

  • slamentslament SwedenPosts: 25Member

    Hi @Sheila, thank you for your answer. However I'm trying to upload stuff (not download), so I think that link is not useful to me. Is that correct?

    Thanks!

  • SheilaSheila Broad InstitutePosts: 3,739Member, Broadie, Moderator, Dev admin

    @slament
    Hi,

    The webpage I linked you to has instructions for uploading as well. I just tried it away from the Broad and it works for me.

    I hope it works when you try again! :smile:

    -Sheila

  • slamentslament SwedenPosts: 25Member

    Hi again @Sheila. The instructions in the link weren't working for me as I mention in my original question, when trying to connect just from Finder. I gave up and I ended up downloading FileZilla. It seems now I can upload stuff with it :)

  • tllepptllepp slcPosts: 1Member

    I've tried this link: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle
    and this ftp://ftp.broadinstitute.org/pub/ExAC_release

    I get messages that this site cannot be reached. Help!

  • SheilaSheila Broad InstitutePosts: 3,739Member, Broadie, Moderator, Dev admin

    @tllepp
    Hi,

    Have you tried using FileZilla or trying the other options given in this document? Hopefully one of those works for you!

    -Sheila

  • HeidiLingHeidiLing Posts: 22Member

    @Sheila said:
    @tllepp
    Hi,

    Have you tried using FileZilla or trying the other options given in this document? Hopefully one of those works for you!

    -Sheila

    FileZilla doesn't work either. Below is the error message we got from FileZilla.

    Status: Insecure server, it does not support FTP over TLS.
    Command: USER gsapubftp
    Response: 331 Password required for gsapubftp
    Command: PASS ********
    Response: 530 Sorry, max 20 users -- try again later
    Error: Critical error: Could not connect to server

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,382Administrator, Dev admin

    It looks like the FTP has been having some stability issues again. We're looking into replacing it by a better solution. In the meantime, please try again after an hour or two. Apologies for the inconvenience!

    Geraldine Van der Auwera, PhD

  • SungSung CambridgePosts: 1Member

    @Geraldine_VdAuwera said:
    It looks like the FTP has been having some stability issues again. We're looking into replacing it by a better solution. In the meantime, please try again after an hour or two. Apologies for the inconvenience!

    Is it back?
    It keeps asking user/pwd:
    ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg38/hg38bundle/

  • SheilaSheila Broad InstitutePosts: 3,739Member, Broadie, Moderator, Dev admin

    @Sung
    Hi,

    We are sorry for the inconvenience. I tried a few times myelf, and sometimes I am able to access the page you linked to, and sometimes I am not. I think the best recommendation is to try again :neutral:

    -Sheila

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