Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
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: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Fri, Jun 23, 2017 at 1:06 PM, Md. Rezaul Karim <
rezaul.ka...@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) [:::172.17.0.2]
> Name (10.196.106.60:asif): rezaul.ka...@insight-centre.org
> 331 Password required for rezaul.ka...@insight-centre.org
> Password:
> 230 User rezaul.ka...@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
> 
>
> On 23 June 2017 at 12:01, Devon Ryan  wrote:
>
>> Do you get an error of some sort?
>>
>> --
>> Devon Ryan, Ph.D.
>> Email: dpr...@dpryan.com
>> Data Manager/Bioinformatician
>> Max Planck Institute of Immunobiology and Epigenetics
>> Stübeweg 51
>> 79108 Freiburg
>> Germany
>> 
>>
>> On Fri, Jun 23, 2017 at 12:33 PM, Md. Rezaul Karim <
>> rezaul.ka...@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
>>> 
>>>
>>> On 23 June 2017 at 11:05, Md. Rezaul Karim <
>>> rezaul.ka...@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"  wrote:

> If your user is an admin then yes. Each user can use their normal
> login credentials.
> --
> Devon Ryan, Ph.D.
> Email: dpr...@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
>  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  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: dpr...@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
> >>  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)
> [:::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.
> >> >
> >> >

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Md. Rezaul Karim 
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) [:::172.17.0.2]
Name (10.196.106.60:asif): rezaul.ka...@insight-centre.org
331 Password required for rezaul.ka...@insight-centre.org
Password:
230 User rezaul.ka...@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


On 23 June 2017 at 12:01, Devon Ryan  wrote:

> Do you get an error of some sort?
>
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
> 
>
> On Fri, Jun 23, 2017 at 12:33 PM, Md. Rezaul Karim <
> rezaul.ka...@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
>> 
>>
>> On 23 June 2017 at 11:05, Md. Rezaul Karim > 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"  wrote:
>>>
 If your user is an admin then yes. Each user can use their normal
 login credentials.
 --
 Devon Ryan, Ph.D.
 Email: dpr...@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
  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  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: dpr...@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
 >>  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) [:::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  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

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Md. Rezaul Karim 
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


On 23 June 2017 at 11:05, Md. Rezaul Karim 
wrote:

> Ok, thanks for the clarification. I will try again and get back to you.
>
>
>
> On Jun 23, 2017 11:03 AM, "Devon Ryan"  wrote:
>
>> If your user is an admin then yes. Each user can use their normal
>> login credentials.
>> --
>> Devon Ryan, Ph.D.
>> Email: dpr...@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
>>  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  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: dpr...@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
>> >>  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) [:::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  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: dpr...@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
>> >> >>  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

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Md. Rezaul Karim 
Ok, thanks for the clarification. I will try again and get back to you.



On Jun 23, 2017 11:03 AM, "Devon Ryan"  wrote:

> If your user is an admin then yes. Each user can use their normal
> login credentials.
> --
> Devon Ryan, Ph.D.
> Email: dpr...@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
>  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  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: dpr...@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
> >>  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) [:::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  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: dpr...@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
> >> >>  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/
> >> >
> >> >
> >
> >
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
If your user is an admin then yes. Each user can use their normal
login credentials.
--
Devon Ryan, Ph.D.
Email: dpr...@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
 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  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: dpr...@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
>>  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) [:::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  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: dpr...@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
>> >>  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/
>> >
>> >
>
>
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Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Md. Rezaul Karim 
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  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: dpr...@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
>  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) [:::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  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: dpr...@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
> >>  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/
> >
> >
>
___
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in your mail client.  To manage your subscriptions to this
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To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
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: dpr...@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
 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) [:::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  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: dpr...@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
>>  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/
>
>
___
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/

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Md. Rezaul Karim 
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) [:::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  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: dpr...@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
>  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/
>
___
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/

Re: [galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Devon Ryan 
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: dpr...@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
 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/
___
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/

[galaxy-dev] How to FTP files on Dockerized version of Galaxy instance running on DC/OS server?

2017-06-23 Thread Md. Rezaul Karim 
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

___
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/