How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?
Dear All, I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/. <http://bioopenergalaxy.insight-centre.org/> However, I'm wondering how to FTP files on it. Please note that I have the following configuration on the galaxy.ini file: # This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp # This should be the hostname of your FTP server, which will be provided to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org Any help or pointer would be highly appreciated. Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>
Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container. Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Dear All,
I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/.
However, I'm wondering how to FTP files on it. Please note that I have the following configuration on the galaxy.ini file:
# This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp
# This should be the hostname of your FTP server, which will be provided to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org
Any help or pointer would be highly appreciated.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Hi Devon, Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy <http://bioopenergalaxy.insight-centre.org/>is built on top of it (version 17.05). My system admin has provided me with the IP address of this DNS and when I issue the FTP command as follows: asif@ubuntu:~$ ftp 10.196.106.60 8021 It shows: Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif): It seems ProFTPD is already configured. While running the container, port 8021 was mapped to 21. Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html> On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote:
Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
Dear All,
I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/.
However, I'm wondering how to FTP files on it. Please note that I have
On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote: the
following configuration on the galaxy.ini file:
# This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp
# This should be the hostname of your FTP server, which will be provided to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org
Any help or pointer would be highly appreciated.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Hi Devon,
Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy is built on top of it (version 17.05). My system admin has provided me with the IP address of this DNS and when I issue the FTP command as follows:
asif@ubuntu:~$ ftp 10.196.106.60 8021
It shows:
Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif):
It seems ProFTPD is already configured. While running the container, port 8021 was mapped to 21.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote:
Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Dear All,
I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/.
However, I'm wondering how to FTP files on it. Please note that I have the following configuration on the galaxy.ini file:
# This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp
# This should be the hostname of your FTP server, which will be provided to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org
Any help or pointer would be highly appreciated.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Did you mean using the admin user email id and the password? Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html> On 23 June 2017 at 10:44, Devon Ryan <dpryan@dpryan.com> wrote:
You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
Hi Devon,
Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy is built on top of it (version 17.05). My system admin has provided me with
IP address of this DNS and when I issue the FTP command as follows:
asif@ubuntu:~$ ftp 10.196.106.60 8021
It shows:
Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif):
It seems ProFTPD is already configured. While running the container, port 8021 was mapped to 21.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote:
Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Dear All,
I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/.
However, I'm wondering how to FTP files on it. Please note that I have the following configuration on the galaxy.ini file:
# This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp
# This should be the hostname of your FTP server, which will be
On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote: the provided
to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org
Any help or pointer would be highly appreciated.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
If your user is an admin then yes. Each user can use their normal login credentials. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Did you mean using the admin user email id and the password?
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:44, Devon Ryan <dpryan@dpryan.com> wrote:
You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Hi Devon,
Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy is built on top of it (version 17.05). My system admin has provided me with the IP address of this DNS and when I issue the FTP command as follows:
asif@ubuntu:~$ ftp 10.196.106.60 8021
It shows:
Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif):
It seems ProFTPD is already configured. While running the container, port 8021 was mapped to 21.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote:
Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Dear All,
I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/.
However, I'm wondering how to FTP files on it. Please note that I have the following configuration on the galaxy.ini file:
# This should point to a directory containing subdirectories matching users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp
# This should be the hostname of your FTP server, which will be provided to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org
Any help or pointer would be highly appreciated.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Ok, thanks for the clarification. I will try again and get back to you. On Jun 23, 2017 11:03 AM, "Devon Ryan" <dpryan@dpryan.com> wrote:
If your user is an admin then yes. Each user can use their normal login credentials. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Did you mean using the admin user email id and the password?
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:44, Devon Ryan <dpryan@dpryan.com> wrote:
You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Hi Devon,
Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy is built on top of it (version 17.05). My system admin has provided me
with
the IP address of this DNS and when I issue the FTP command as follows:
asif@ubuntu:~$ ftp 10.196.106.60 8021
It shows:
Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif):
It seems ProFTPD is already configured. While running the container, port 8021 was mapped to 21.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote:
Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Dear All,
I have Dockerized the Galaxy and it's running as a containerized application on the DC/OS server. It can be accessed at http://bioopenergalaxy.insight-centre.org/.
However, I'm wondering how to FTP files on it. Please note that I have the following configuration on the galaxy.ini file:
# This should point to a directory containing subdirectories
matching
users' identifier (defaults to e-mail), where Galaxy will look for files. ftp_upload_dir = /export/ftp
# This should be the hostname of your FTP server, which will be provided to users in the help text. ftp_upload_site = bioopenergalaxy.insight-centre.org
Any help or pointer would be highly appreciated.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
Hi Devon, I tried to connect to Galaxy instance with FTP client WinSCP as follows: [image: Inline images 1] But no luck. Even I tried with the DNS (i.e. http://bioopenergalaxy.insight-centre.org/) and changing SFTP to FTP and tried with port number 21 and 8021 too. Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html> On 23 June 2017 at 11:05, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Ok, thanks for the clarification. I will try again and get back to you.
On Jun 23, 2017 11:03 AM, "Devon Ryan" <dpryan@dpryan.com> wrote:
If your user is an admin then yes. Each user can use their normal login credentials. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Did you mean using the admin user email id and the password?
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:44, Devon Ryan <dpryan@dpryan.com> wrote:
You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Hi Devon,
Yes, I'm running the galaxy-docker-stable from Björn and my
RiboGalaxy
is built on top of it (version 17.05). My system admin has provided me with the IP address of this DNS and when I issue the FTP command as follows:
asif@ubuntu:~$ ftp 10.196.106.60 8021
It shows:
Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif):
It seems ProFTPD is already configured. While running the container, port 8021 was mapped to 21.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote:
Are you using galaxy-docker-stable from Björn (https://github.com/bgruening/docker-galaxy-stable) or did you make your own dockerized-Galaxy version? Björn's runs proFTPd by default, so if you're using it then ensure that's running in the container.
Devon -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote: > Dear All, > > I have Dockerized the Galaxy and it's running as a containerized > application > on the DC/OS server. It can be accessed at > http://bioopenergalaxy.insight-centre.org/. > > However, I'm wondering how to FTP files on it. Please note that I > have > the > following configuration on the galaxy.ini file: > > # This should point to a directory containing subdirectories
matching
> users' > identifier (defaults to e-mail), where Galaxy will look for files. > ftp_upload_dir = /export/ftp > > # This should be the hostname of your FTP server, which will be > provided > to > users in the help text. > ftp_upload_site = bioopenergalaxy.insight-centre.org > > > Any help or pointer would be highly appreciated. > > > > > Regards, > _________________________________ > Md. Rezaul Karim, BSc, MSc > Researcher, INSIGHT Centre for Data Analytics > National University of Ireland, Galway > IDA Business Park, Dangan, Galway, Ireland > Web: http://www.reza-analytics.eu/index.html > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/
Do you get an error of some sort? -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany <devon.ryan@dzne.de> On Fri, Jun 23, 2017 at 12:33 PM, Md. Rezaul Karim < rezaul.karim@insight-centre.org> wrote:
Hi Devon,
I tried to connect to Galaxy instance with FTP client WinSCP as follows:
[image: Inline images 1]
But no luck. Even I tried with the DNS (i.e. http://bioopenergalaxy. insight-centre.org/) and changing SFTP to FTP and tried with port number 21 and 8021 too.
Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>
On 23 June 2017 at 11:05, Md. Rezaul Karim <rezaul.karim@insight-centre. org> wrote:
Ok, thanks for the clarification. I will try again and get back to you.
On Jun 23, 2017 11:03 AM, "Devon Ryan" <dpryan@dpryan.com> wrote:
If your user is an admin then yes. Each user can use their normal login credentials. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Did you mean using the admin user email id and the password?
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:44, Devon Ryan <dpryan@dpryan.com> wrote:
You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Hi Devon,
Yes, I'm running the galaxy-docker-stable from Björn and my
RiboGalaxy
is built on top of it (version 17.05). My system admin has provided me with the IP address of this DNS and when I issue the FTP command as follows:
asif@ubuntu:~$ ftp 10.196.106.60 8021
It shows:
Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif):
It seems ProFTPD is already configured. While running the container, port 8021 was mapped to 21.
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote: > > Are you using galaxy-docker-stable from Björn > (https://github.com/bgruening/docker-galaxy-stable) or did you make > your own dockerized-Galaxy version? Björn's runs proFTPd by default, > so if you're using it then ensure that's running in the container. > > Devon > -- > Devon Ryan, Ph.D. > Email: dpryan@dpryan.com > Data Manager/Bioinformatician > Max Planck Institute of Immunobiology and Epigenetics > Stübeweg 51 > 79108 Freiburg > Germany > > > On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim > <rezaul.karim@insight-centre.org> wrote: > > Dear All, > > > > I have Dockerized the Galaxy and it's running as a containerized > > application > > on the DC/OS server. It can be accessed at > > http://bioopenergalaxy.insight-centre.org/. > > > > However, I'm wondering how to FTP files on it. Please note that I > > have > > the > > following configuration on the galaxy.ini file: > > > > # This should point to a directory containing subdirectories matching > > users' > > identifier (defaults to e-mail), where Galaxy will look for files. > > ftp_upload_dir = /export/ftp > > > > # This should be the hostname of your FTP server, which will be > > provided > > to > > users in the help text. > > ftp_upload_site = bioopenergalaxy.insight-centre.org > > > > > > Any help or pointer would be highly appreciated. > > > > > > > > > > Regards, > > _________________________________ > > Md. Rezaul Karim, BSc, MSc > > Researcher, INSIGHT Centre for Data Analytics > > National University of Ireland, Galway > > IDA Business Park, Dangan, Galway, Ireland > > Web: http://www.reza-analytics.eu/index.html > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/
Timeout detected. (data connection) Could not retrieve directory listing Error listing directory '/'. However, when I tried from Ubuntu terminal it gets connected. However, I am getting below error: asif@ubuntu:~$ ftp 10.196.106.60 8021 Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif): rezaul.karim@insight-centre.org 331 Password required for rezaul.karim@insight-centre.org Password: 230 User rezaul.karim@insight-centre.org logged in Remote system type is UNIX. Using binary mode to transfer files. ftp> ls 500 Illegal PORT command ftp: bind: Address already in use ftp> quit 221 Goodbye. Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html> On 23 June 2017 at 12:01, Devon Ryan <dpryan@dpryan.com> wrote:
Do you get an error of some sort?
-- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany <devon.ryan@dzne.de>
On Fri, Jun 23, 2017 at 12:33 PM, Md. Rezaul Karim < rezaul.karim@insight-centre.org> wrote:
Hi Devon,
I tried to connect to Galaxy instance with FTP client WinSCP as follows:
[image: Inline images 1]
But no luck. Even I tried with the DNS (i.e. http://bioopenergalaxy.insight-centre.org/) and changing SFTP to FTP and tried with port number 21 and 8021 too.
Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>
On 23 June 2017 at 11:05, Md. Rezaul Karim <rezaul.karim@insight-centre.o rg> wrote:
Ok, thanks for the clarification. I will try again and get back to you.
On Jun 23, 2017 11:03 AM, "Devon Ryan" <dpryan@dpryan.com> wrote:
If your user is an admin then yes. Each user can use their normal login credentials. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote:
Did you mean using the admin user email id and the password?
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:44, Devon Ryan <dpryan@dpryan.com> wrote:
You should be able to login with the email address and password that you use for Galaxy then. That works for my instances at least. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote: > Hi Devon, > > Yes, I'm running the galaxy-docker-stable from Björn and my
RiboGalaxy
> is > built on top of it (version 17.05). My system admin has provided me with > the > IP address of this DNS and when I issue the FTP command as follows: > > asif@ubuntu:~$ ftp 10.196.106.60 8021 > > It shows: > > Connected to 10.196.106.60. > 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] > Name (10.196.106.60:asif): > > It seems ProFTPD is already configured. While running the container, > port > 8021 was mapped to 21. > > > Regards, > _________________________________ > Md. Rezaul Karim, BSc, MSc > Researcher, INSIGHT Centre for Data Analytics > National University of Ireland, Galway > IDA Business Park, Dangan, Galway, Ireland > Web: http://www.reza-analytics.eu/index.html > > On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote: >> >> Are you using galaxy-docker-stable from Björn >> (https://github.com/bgruening/docker-galaxy-stable) or did you make >> your own dockerized-Galaxy version? Björn's runs proFTPd by default, >> so if you're using it then ensure that's running in the container. >> >> Devon >> -- >> Devon Ryan, Ph.D. >> Email: dpryan@dpryan.com >> Data Manager/Bioinformatician >> Max Planck Institute of Immunobiology and Epigenetics >> Stübeweg 51 >> 79108 Freiburg >> Germany >> >> >> On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim >> <rezaul.karim@insight-centre.org> wrote: >> > Dear All, >> > >> > I have Dockerized the Galaxy and it's running as a containerized >> > application >> > on the DC/OS server. It can be accessed at >> > http://bioopenergalaxy.insight-centre.org/. >> > >> > However, I'm wondering how to FTP files on it. Please note that I >> > have >> > the >> > following configuration on the galaxy.ini file: >> > >> > # This should point to a directory containing subdirectories matching >> > users' >> > identifier (defaults to e-mail), where Galaxy will look for files. >> > ftp_upload_dir = /export/ftp >> > >> > # This should be the hostname of your FTP server, which will be >> > provided >> > to >> > users in the help text. >> > ftp_upload_site = bioopenergalaxy.insight-centre.org >> > >> > >> > Any help or pointer would be highly appreciated. >> > >> > >> > >> > >> > Regards, >> > _________________________________ >> > Md. Rezaul Karim, BSc, MSc >> > Researcher, INSIGHT Centre for Data Analytics >> > National University of Ireland, Galway >> > IDA Business Park, Dangan, Galway, Ireland >> > Web: http://www.reza-analytics.eu/index.html >> > >> > ___________________________________________________________ >> > 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: >> > https://lists.galaxyproject.org/ >> > >> > To search Galaxy mailing lists use the unified search at: >> > http://galaxyproject.org/search/ > >
This is likely an issue with using active vs. passive FTP. Unfortunately since you're not using `--net=host` you can't use passive ftp (at least it's never worked for me). Perhaps sftp on port 8022 will work better. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany <devon.ryan@dzne.de> On Fri, Jun 23, 2017 at 1:06 PM, Md. Rezaul Karim < rezaul.karim@insight-centre.org> wrote:
Timeout detected. (data connection) Could not retrieve directory listing Error listing directory '/'.
However, when I tried from Ubuntu terminal it gets connected. However, I am getting below error:
asif@ubuntu:~$ ftp 10.196.106.60 8021 Connected to 10.196.106.60. 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] Name (10.196.106.60:asif): rezaul.karim@insight-centre.org 331 Password required for rezaul.karim@insight-centre.org Password: 230 User rezaul.karim@insight-centre.org logged in Remote system type is UNIX. Using binary mode to transfer files. ftp> ls 500 Illegal PORT command ftp: bind: Address already in use ftp> quit 221 Goodbye.
Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>
On 23 June 2017 at 12:01, Devon Ryan <dpryan@dpryan.com> wrote:
Do you get an error of some sort?
-- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany <devon.ryan@dzne.de>
On Fri, Jun 23, 2017 at 12:33 PM, Md. Rezaul Karim < rezaul.karim@insight-centre.org> wrote:
Hi Devon,
I tried to connect to Galaxy instance with FTP client WinSCP as follows:
[image: Inline images 1]
But no luck. Even I tried with the DNS (i.e. http://bioopenergalaxy.insight-centre.org/) and changing SFTP to FTP and tried with port number 21 and 8021 too.
Regards, _________________________________ *Md. Rezaul Karim*, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html <http://139.59.184.114/index.html>
On 23 June 2017 at 11:05, Md. Rezaul Karim < rezaul.karim@insight-centre.org> wrote:
Ok, thanks for the clarification. I will try again and get back to you.
On Jun 23, 2017 11:03 AM, "Devon Ryan" <dpryan@dpryan.com> wrote:
If your user is an admin then yes. Each user can use their normal login credentials. -- Devon Ryan, Ph.D. Email: dpryan@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
Did you mean using the admin user email id and the password?
Regards, _________________________________ Md. Rezaul Karim, BSc, MSc Researcher, INSIGHT Centre for Data Analytics National University of Ireland, Galway IDA Business Park, Dangan, Galway, Ireland Web: http://www.reza-analytics.eu/index.html
On 23 June 2017 at 10:44, Devon Ryan <dpryan@dpryan.com> wrote: > > You should be able to login with the email address and password that > you use for Galaxy then. That works for my instances at least. > -- > Devon Ryan, Ph.D. > Email: dpryan@dpryan.com > Data Manager/Bioinformatician > Max Planck Institute of Immunobiology and Epigenetics > Stübeweg 51 > 79108 Freiburg > Germany > > > On Fri, Jun 23, 2017 at 11:38 AM, Md. Rezaul Karim > <rezaul.karim@insight-centre.org> wrote: > > Hi Devon, > > > > Yes, I'm running the galaxy-docker-stable from Björn and my RiboGalaxy > > is > > built on top of it (version 17.05). My system admin has provided me with > > the > > IP address of this DNS and when I issue the FTP command as follows: > > > > asif@ubuntu:~$ ftp 10.196.106.60 8021 > > > > It shows: > > > > Connected to 10.196.106.60. > > 220 ProFTPD 1.3.5rc3 Server (Public Galaxy FTP) [::ffff:172.17.0.2] > > Name (10.196.106.60:asif): > > > > It seems ProFTPD is already configured. While running the container, > > port > > 8021 was mapped to 21. > > > > > > Regards, > > _________________________________ > > Md. Rezaul Karim, BSc, MSc > > Researcher, INSIGHT Centre for Data Analytics > > National University of Ireland, Galway > > IDA Business Park, Dangan, Galway, Ireland > > Web: http://www.reza-analytics.eu/index.html > > > > On 23 June 2017 at 10:30, Devon Ryan <dpryan@dpryan.com> wrote: > >> > >> Are you using galaxy-docker-stable from Björn > >> (https://github.com/bgruening/docker-galaxy-stable) or did you make > >> your own dockerized-Galaxy version? Björn's runs proFTPd by default, > >> so if you're using it then ensure that's running in the container. > >> > >> Devon > >> -- > >> Devon Ryan, Ph.D. > >> Email: dpryan@dpryan.com > >> Data Manager/Bioinformatician > >> Max Planck Institute of Immunobiology and Epigenetics > >> Stübeweg 51 > >> 79108 Freiburg > >> Germany > >> > >> > >> On Fri, Jun 23, 2017 at 11:17 AM, Md. Rezaul Karim > >> <rezaul.karim@insight-centre.org> wrote: > >> > Dear All, > >> > > >> > I have Dockerized the Galaxy and it's running as a containerized > >> > application > >> > on the DC/OS server. It can be accessed at > >> > http://bioopenergalaxy.insight-centre.org/. > >> > > >> > However, I'm wondering how to FTP files on it. Please note
On Fri, Jun 23, 2017 at 11:45 AM, Md. Rezaul Karim <rezaul.karim@insight-centre.org> wrote: that I
> >> > have > >> > the > >> > following configuration on the galaxy.ini file: > >> > > >> > # This should point to a directory containing subdirectories matching > >> > users' > >> > identifier (defaults to e-mail), where Galaxy will look for files. > >> > ftp_upload_dir = /export/ftp > >> > > >> > # This should be the hostname of your FTP server, which will be > >> > provided > >> > to > >> > users in the help text. > >> > ftp_upload_site = bioopenergalaxy.insight-centre.org > >> > > >> > > >> > Any help or pointer would be highly appreciated. > >> > > >> > > >> > > >> > > >> > Regards, > >> > _________________________________ > >> > Md. Rezaul Karim, BSc, MSc > >> > Researcher, INSIGHT Centre for Data Analytics > >> > National University of Ireland, Galway > >> > IDA Business Park, Dangan, Galway, Ireland > >> > Web: http://www.reza-analytics.eu/index.html > >> > > >> > ___________________________________________________________ > >> > 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: > >> > https://lists.galaxyproject.org/ > >> > > >> > To search Galaxy mailing lists use the unified search at: > >> > http://galaxyproject.org/search/ > > > >
participants (2)
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Md. Rezaul Karim