Hello, I installed all tools from the toolshed which I needed for Galaxy (15.10) and noticed that I can not upload bigger files than 2 GB to Galaxy without a FTP server. I installed on Ubuntu 14.04 ProFTPD in the following way: *sudo aptitude install ProFTPD proftpd-mod-sqlite sqlite3* Unfortunately, I do not know how to connect the ProFTPD with Galaxy's SQLite. Thank you in advance. Mic
Hi Mic, Am 12.11.2015 um 01:22 schrieb Mic:
Hello, I installed all tools from the toolshed which I needed for Galaxy (15.10) and noticed that I can not upload bigger files than 2 GB to Galaxy without a FTP server.
I installed on Ubuntu 14.04 ProFTPD in the following way:
*sudo aptitude install ProFTPD proftpd-mod-sqlite sqlite3*
Unfortunately, I do not know how to connect the ProFTPD with Galaxy's SQLite.
ProFTP is an FTP Server and SQLite is a database you cannot connect from the one the the other. Are you still using the Galaxy Docker? If so we have already installed a FTP Server for you and configured it so Galaxy can talk to the FTP server. Please see the documentation about the Docker FTP server: https://github.com/bgruening/docker-galaxy-stable To transfer data from your client to Galaxy you only need an FTP cient. Have a look at Filezilla as FTP-client. Cheers, Bjoern
Thank you in advance.
Mic
___________________________________________________________ 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/mailinglists/
HI Bjoern, Thank you for your email. I have just started to build a new docker container based on bgruening/galaxy-stable:15.07 . It seems that 15.10 has not been yet included. The problem which I have with Docker container is that if a tool from the toolshed failed to install then I can not get access to INSTALLATION.log. If I press repair repository button then NGINX complain with an error 400. Therefore, I also started to try to convert you Dockerfiles to a VM image. How do you handle broken tools and how do you repair them in a Docker container. I really like your Dockerfiles. Thank you in advance. Mic On Thu, Nov 12, 2015 at 9:42 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Mic,
Am 12.11.2015 um 01:22 schrieb Mic:
Hello, I installed all tools from the toolshed which I needed for Galaxy (15.10) and noticed that I can not upload bigger files than 2 GB to Galaxy without a FTP server.
I installed on Ubuntu 14.04 ProFTPD in the following way:
*sudo aptitude install ProFTPD proftpd-mod-sqlite sqlite3*
Unfortunately, I do not know how to connect the ProFTPD with Galaxy's SQLite.
ProFTP is an FTP Server and SQLite is a database you cannot connect from the one the the other.
Are you still using the Galaxy Docker? If so we have already installed a FTP Server for you and configured it so Galaxy can talk to the FTP server.
Please see the documentation about the Docker FTP server: https://github.com/bgruening/docker-galaxy-stable
To transfer data from your client to Galaxy you only need an FTP cient. Have a look at Filezilla as FTP-client.
Cheers, Bjoern
Thank you in advance.
Mic
___________________________________________________________ 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/mailinglists/
Hi Mic, you can always dive into a container and get access to everything. Please read about `docker exec`, also described in our readme file. cheers, Bjoern Am 12.11.2015 um 15:24 schrieb Mic:
HI Bjoern, Thank you for your email. I have just started to build a new docker container based on bgruening/galaxy-stable:15.07 . It seems that 15.10 has not been yet included.
The problem which I have with Docker container is that if a tool from the toolshed failed to install then I can not get access to INSTALLATION.log. If I press repair repository button then NGINX complain with an error 400. Therefore, I also started to try to convert you Dockerfiles to a VM image.
How do you handle broken tools and how do you repair them in a Docker container. I really like your Dockerfiles.
Thank you in advance.
Mic
On Thu, Nov 12, 2015 at 9:42 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Mic,
Am 12.11.2015 um 01:22 schrieb Mic:
Hello, I installed all tools from the toolshed which I needed for Galaxy (15.10) and noticed that I can not upload bigger files than 2 GB to Galaxy without a FTP server.
I installed on Ubuntu 14.04 ProFTPD in the following way:
*sudo aptitude install ProFTPD proftpd-mod-sqlite sqlite3*
Unfortunately, I do not know how to connect the ProFTPD with Galaxy's SQLite.
ProFTP is an FTP Server and SQLite is a database you cannot connect from the one the the other.
Are you still using the Galaxy Docker? If so we have already installed a FTP Server for you and configured it so Galaxy can talk to the FTP server.
Please see the documentation about the Docker FTP server: https://github.com/bgruening/docker-galaxy-stable
To transfer data from your client to Galaxy you only need an FTP cient. Have a look at Filezilla as FTP-client.
Cheers, Bjoern
Thank you in advance.
Mic
___________________________________________________________ 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/mailinglists/
Hi Boern, Thank you. I changed to Postgresql and proFTPd and it works. Cheers, Mic On Fri, Nov 13, 2015 at 12:57 AM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Mic,
you can always dive into a container and get access to everything. Please read about `docker exec`, also described in our readme file.
cheers, Bjoern
HI Bjoern, Thank you for your email. I have just started to build a new docker container based on bgruening/galaxy-stable:15.07 . It seems that 15.10 has not been yet included.
The problem which I have with Docker container is that if a tool from the toolshed failed to install then I can not get access to INSTALLATION.log. If I press repair repository button then NGINX complain with an error
Am 12.11.2015 um 15:24 schrieb Mic: 400.
Therefore, I also started to try to convert you Dockerfiles to a VM image.
How do you handle broken tools and how do you repair them in a Docker container. I really like your Dockerfiles.
Thank you in advance.
Mic
On Thu, Nov 12, 2015 at 9:42 PM, Björn Grüning < bjoern.gruening@gmail.com> wrote:
Hi Mic,
Am 12.11.2015 um 01:22 schrieb Mic:
Hello, I installed all tools from the toolshed which I needed for Galaxy (15.10) and noticed that I can not upload bigger files than 2 GB to Galaxy without a FTP server.
I installed on Ubuntu 14.04 ProFTPD in the following way:
*sudo aptitude install ProFTPD proftpd-mod-sqlite sqlite3*
Unfortunately, I do not know how to connect the ProFTPD with Galaxy's SQLite.
ProFTP is an FTP Server and SQLite is a database you cannot connect from the one the the other.
Are you still using the Galaxy Docker? If so we have already installed a FTP Server for you and configured it so Galaxy can talk to the FTP server.
Please see the documentation about the Docker FTP server: https://github.com/bgruening/docker-galaxy-stable
To transfer data from your client to Galaxy you only need an FTP cient. Have a look at Filezilla as FTP-client.
Cheers, Bjoern
Thank you in advance.
Mic
___________________________________________________________ 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/mailinglists/
participants (2)
-
Björn Grüning -
Mic