IE setup problem
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command: node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose Thank you in advance Mic
... or is there is another way to start automatically nodejs without to use Supervisord? On Fri, Dec 18, 2015 at 3:58 PM, Mic <mictadlo@gmail.com> wrote:
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command:
node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
Thank you in advance
Mic
Hi, you need to have node installed. And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose from your Galaxy root dir. Cheers, Bjoern Am 18.12.2015 um 06:58 schrieb Mic:
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command:
node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
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/
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Hi Mic, Since you asked for the supervisord config... it would look something like this:] [program:galaxy_proxy] command=/usr/local/bin/node /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port 8800 --sessions /path/to/galaxy/database/session_map.sqlite --cookie galaxysession --verbose numprocs=1 autostart=true autorestart=true startsecs=10 user=galaxy-user directory=/galaxy/home/directory umask=022 Galaxy can also automatically manage the proxy for you, if you set "dynamic_proxy_manage_proxy=True" in your galaxy.ini On 12/18/2015 01:23 AM, Björn Grüning wrote:
Hi,
you need to have node installed.
And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
from your Galaxy root dir.
Cheers, Bjoern
Am 18.12.2015 um 06:58 schrieb Mic:
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command:
node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
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/
___________________________________________________________ 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/
-- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
Hi all, Thank you for the responses. If I would use "dynamic_proxy_manage_proxy=True" than Galaxy would execute automatically: /lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose without the need to use supervisors config? Thank you in advance. Mic On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche <esr@tamu.edu> wrote:
Hi Mic,
Since you asked for the supervisord config... it would look something like this:]
[program:galaxy_proxy] command=/usr/local/bin/node /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port 8800 --sessions /path/to/galaxy/database/session_map.sqlite --cookie galaxysession --verbose numprocs=1 autostart=true autorestart=true startsecs=10 user=galaxy-user directory=/galaxy/home/directory umask=022
Galaxy can also automatically manage the proxy for you, if you set "dynamic_proxy_manage_proxy=True" in your galaxy.ini
On 12/18/2015 01:23 AM, Björn Grüning wrote:
Hi,
you need to have node installed.
And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
from your Galaxy root dir.
Cheers, Bjoern
Am 18.12.2015 um 06:58 schrieb Mic:
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction
http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command:
node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
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/
___________________________________________________________ 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/
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
19. des. 2015 1.17 a.m. skrev "Mic" <mictadlo@gmail.com>:
Hi all, Thank you for the responses. If I would
use "dynamic_proxy_manage_proxy=True" than Galaxy would execute automatically:
/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
without the need to use supervisors config?
Yes. That's the idea. I'm not sure I trust it quite as much as supervisord, but it has worked quite well for us so far :-)
Thank you in advance.
Mic
On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche <esr@tamu.edu> wrote:
Hi Mic,
Since you asked for the supervisord config... it would look something like this:]
[program:galaxy_proxy] command=/usr/local/bin/node /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port 8800 --sessions /path/to/galaxy/database/session_map.sqlite --cookie galaxysession --verbose numprocs=1 autostart=true autorestart=true startsecs=10 user=galaxy-user directory=/galaxy/home/directory umask=022
Galaxy can also automatically manage the proxy for you, if you set "dynamic_proxy_manage_proxy=True" in your galaxy.ini
On 12/18/2015 01:23 AM, Björn Grüning wrote:
Hi,
you need to have node installed.
And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
from your Galaxy root dir.
Cheers, Bjoern
Am 18.12.2015 um 06:58 schrieb Mic:
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy.
I am
trying to follow this instruction
http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command:
node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
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/
___________________________________________________________ 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/
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
dynamic_proxy_manage_proxy=True is a terrible hack, I would set it to False and use supervisord if you have any inclination to at all. Like sqlite or the local job runner, it is just an attempt to make sure things work out of the box but it isn't that robust. -John On Sat, Dec 19, 2015 at 1:20 AM, Eric Rasche <esr@tamu.edu> wrote:
19. des. 2015 1.17 a.m. skrev "Mic" <mictadlo@gmail.com>:
Hi all, Thank you for the responses. If I would use "dynamic_proxy_manage_proxy=True" than Galaxy would execute automatically:
/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
without the need to use supervisors config?
Yes. That's the idea. I'm not sure I trust it quite as much as supervisord, but it has worked quite well for us so far :-)
Thank you in advance.
Mic
On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche <esr@tamu.edu> wrote:
Hi Mic,
Since you asked for the supervisord config... it would look something like this:]
[program:galaxy_proxy] command=/usr/local/bin/node /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port 8800 --sessions /path/to/galaxy/database/session_map.sqlite --cookie galaxysession --verbose numprocs=1 autostart=true autorestart=true startsecs=10 user=galaxy-user directory=/galaxy/home/directory umask=022
Galaxy can also automatically manage the proxy for you, if you set "dynamic_proxy_manage_proxy=True" in your galaxy.ini
On 12/18/2015 01:23 AM, Björn Grüning wrote:
Hi,
you need to have node installed.
And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
from your Galaxy root dir.
Cheers, Bjoern
Am 18.12.2015 um 06:58 schrieb Mic:
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction
http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command:
node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
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/
___________________________________________________________ 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/
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
___________________________________________________________ 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 all, I tried with *dynamic_proxy_manage=True* and *dynamic_proxy_manage=False*, but IE does not start inside Galaxy on a Annovar tab separated file (see attached). I also tried the following commands, but without any luck: $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip 0.0.0.0 --port 8800 --sessions /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession --verbose Watching path /home/galaxy/galaxy/database/session_map.sqlite Listening on 0.0.0.0:8800 $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip 127.0.0.1 --port 8800 --sessions /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession --verbose Watching path /home/galaxy/galaxy/database/session_map.sqlite Listening on 127.0.0.1:8800 $ node /home/galaxy/galaxy/lib/galaxy/web/proxy/js/lib/main.js --ip localhost --port 8800 --sessions /home/galaxy/galaxy/database/session_map.sqlite --cookie galaxysession --verbose Watching path /home/galaxy/galaxy/database/session_map.sqlite Listening on localhost:8800 My Galaxy is running on *0.0.0.0:8080 <http://0.0.0.0:8080>* view at *http://127.0.0.1:8080 <http://127.0.0.1:8080>*. I use Docker version 1.9.1, build a34a1d5. Please find attached my *galaxy.ini* and apache proxy config file ( *000-default.conf*). The following Apache modules I have enabled (*sudo a2enmod rewrite deflate expires proxy proxy_html xsendfile xml2enc proxy_wstunnel*) What did I do wrong so I can not start Rstudio and IPython inside Galaxy? Thank you in advance. Mic On Sat, Dec 19, 2015 at 1:12 PM, John Chilton <jmchilton@gmail.com> wrote:
dynamic_proxy_manage_proxy=True is a terrible hack, I would set it to False and use supervisord if you have any inclination to at all. Like sqlite or the local job runner, it is just an attempt to make sure things work out of the box but it isn't that robust.
-John
On Sat, Dec 19, 2015 at 1:20 AM, Eric Rasche <esr@tamu.edu> wrote:
19. des. 2015 1.17 a.m. skrev "Mic" <mictadlo@gmail.com>:
Hi all, Thank you for the responses. If I would use "dynamic_proxy_manage_proxy=True" than Galaxy would execute
automatically:
/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
without the need to use supervisors config?
Yes. That's the idea. I'm not sure I trust it quite as much as supervisord, but it has worked quite well for us so far :-)
Thank you in advance.
Mic
On Sat, Dec 19, 2015 at 12:26 AM, Eric Rasche <esr@tamu.edu> wrote:
Hi Mic,
Since you asked for the supervisord config... it would look something like this:]
[program:galaxy_proxy] command=/usr/local/bin/node /path/to/galaxy/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 --port
8800
--sessions /path/to/galaxy/database/session_map.sqlite --cookie galaxysession --verbose numprocs=1 autostart=true autorestart=true startsecs=10 user=galaxy-user directory=/galaxy/home/directory umask=022
Galaxy can also automatically manage the proxy for you, if you set "dynamic_proxy_manage_proxy=True" in your galaxy.ini
On 12/18/2015 01:23 AM, Björn Grüning wrote:
Hi,
you need to have node installed.
And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
from your Galaxy root dir.
Cheers, Bjoern
Am 18.12.2015 um 06:58 schrieb Mic:
Hello, I am using the latest stable Galaxy with PostgreSQL and Apache Proxy. I am trying to follow this instruction
http://galaxy.readthedocs.org/en/master/admin/interactive_environments.html
in order to be able to setup IE (Rstudio and Ipython). However, I do not know how to setup automatically Supervisord for this command:
node $GALAXY_ROOT/lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose
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/
___________________________________________________________ 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/
-- Eric Rasche Programmer II
Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu
___________________________________________________________ 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 (4)
-
Björn Grüning -
Eric Rasche -
John Chilton -
Mic