Hey Jennifer, I was using email/password, just tried again and I got in. Weird. Thanks for the quick response! Danny On Mon, Feb 7, 2011 at 3:21 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hello Danny,

Are you connecting to main.g2.bx.psu.edu and using your Galaxy credentials "email/password"?

Maybe you were trying "anonymous/email" - which will not work?

Please double check and let us know if you continue to have issues,

Thanks! jen

On 2/7/11 8:58 AM, Danny Park wrote:

...

Hey guys,

I was trying to connect to the public instance of galaxy via FTP but was not able to do so successfully. I tried both FTP and SFTP. Is there something I am missing?

Thanks,

Danny

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Florent, maybe your questions better reside in the dev-list but anyway we have encounter similar things for various reasons. When plugging binaries/tools outside galaxy it works setting paths and such.... but PATH environments and other ENVironmental variables are usually not directly set for the running galaxy user (since it phusically doesn't get into shell. We therefore source the /etc/profile in the galaxy server startup script to be sure to have the correct environmentals set as is for the other users. What I do not understand is that the tools seem to work when logged in fysically as galaxy user....in our case the tools wouldn't have worked. Are you sure (I think you are but you never know) that its a perl script? Ocassionally we have seen something like this but was solved by omitting the interpreter part in the tool config xml or setting it to bash. Good luck. Alex ________________________________________ Van: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Florent Angly [florent.angly@gmail.com] Verzonden: zondag 13 februari 2011 9:03 Aan: galaxy-user@lists.bx.psu.edu Onderwerp: [galaxy-user] Galaxy does not find my executables Hi list, I am writing a wrapper for a Grinder, a Perl program installed globally on my Galaxy server. Galaxy runs as user 'galaxy': $ ps aux | grep paster galaxy 26807 0.0 0.8 2636308 136364 ?? S 2:52PM 0:19.15 python ./scripts/paster.py serve universe_wsgi.ini When logged in as user galaxy, I can run Grinder: $ Grinder --help Usage: Grinder [options] Grinder --help Grinder --version ... Grinder's location is: $ which Grinder /opt/local/bin/Grinder In grinder.xml: If I put: <command interpreter="perl"> In the Galaxy webinterface, I get the error: Can't open perl script "/Users/galaxy/galaxy_dist/tools/ngs_simulation/Grinder": No such file or directory Obviously, here, Galaxy assumes wrongly that tool is installed under the Galaxy ~/tools/ngs_simulation/ folder. So I tried to omit the interpreter: <command> And I got the error: /bin/sh: Grinder: command not found This is surprising, since Grinder is found if I run it on the command-line as user galaxy I noticed that I have the same issue with the Velvet wrapper (also located in /opt/local/bin) and thought that this could be an environment issue. And indeed the environment within a wrapper is: PERL=/usr/bin/perl PATH=/usr/bin:/bin:/usr/sbin:/sbin While on the command line, the environment is: PERL=/opt/local/bin/perl PATH=/opt/local/bin:/opt/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/sw/bin This difference in environment explains why Galaxy cannot find Grinder or Velvet. Does this make any sense? Does Galaxy modify the environment? Why would the environment be different? Thanks for your help, Florent _______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

On Mon, Feb 14, 2011 at 7:17 AM, Florent Angly <florent.angly@gmail.com> wrote:

Hi Alex,

Thanks for the pointers! The fact that Galaxy only reads /etc/profile and not the profile of the user that runs it, ~/.profile, entirely explains why it cannot find Grinder or Velvet: I run Galaxy on a Mac OS X and I have many programs installed from MacPorts. All these programs get installed under /opt/local/bin/, which is outside of the usual Mac paths (to avoid any conflict). So, every user on this Mac has to have /opt/local/bin added to its path in its ~/.profile to be able to use MacPorts program. I did this for my galaxy user, but if Galaxy does not read ~/.profile, then it won't find the programs I installed.

I am surprised that you report that Galaxy does not read ~/.profile in fact, because on this wiki page, https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer, it is advised to set up the $TEMP environment variable for Galaxy. How is one supposed to do that? I don't think that it would be advisable to ask people to edit their system-wide /etc/profile...

So, how do I have to setup environment variables so that they will be used by Galaxy?

We do it in run.sh but this is partly because we're running Galaxy under a non-login account, so there is no home directory. Peter

Florent, Maybe obsolete already. You could also source the user specific .profile in the galaxy startup script. We have chosen for maybe the unsafe manner sourcing etc/profile...but to that only developers (a few) have access anyway for installing system wide commands/utils... I never checked the ~/.profile whether its sourced. We directly put etc/profile there! Cheers, Alex -----Oorspronkelijk bericht----- Van: Florent Angly [mailto:florent.angly@gmail.com] Verzonden: maandag 14 februari 2011 8:18 Aan: Bossers, Alex CC: galaxy-user@lists.bx.psu.edu Onderwerp: Re: [galaxy-user] Galaxy does not find my executables Hi Alex, Thanks for the pointers! The fact that Galaxy only reads /etc/profile and not the profile of the user that runs it, ~/.profile, entirely explains why it cannot find Grinder or Velvet: I run Galaxy on a Mac OS X and I have many programs installed from MacPorts. All these programs get installed under /opt/local/bin/, which is outside of the usual Mac paths (to avoid any conflict). So, every user on this Mac has to have /opt/local/bin added to its path in its ~/.profile to be able to use MacPorts program. I did this for my galaxy user, but if Galaxy does not read ~/.profile, then it won't find the programs I installed. I am surprised that you report that Galaxy does not read ~/.profile in fact, because on this wiki page, https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer, it is advised to set up the $TEMP environment variable for Galaxy. How is one supposed to do that? I don't think that it would be advisable to ask people to edit their system-wide /etc/profile... So, how do I have to setup environment variables so that they will be used by Galaxy? Best, Florent On 14/02/11 06:01, Bossers, Alex wrote:

Florent, maybe your questions better reside in the dev-list but anyway we have encounter similar things for various reasons. When plugging binaries/tools outside galaxy it works setting paths and such.... but PATH environments and other ENVironmental variables are usually not directly set for the running galaxy user (since it phusically doesn't get into shell. We therefore source the /etc/profile in the galaxy server startup script to be sure to have the correct environmentals set as is for the other users. What I do not understand is that the tools seem to work when logged in fysically as galaxy user....in our case the tools wouldn't have worked. Are you sure (I think you are but you never know) that its a perl script? Ocassionally we have seen something like this but was solved by omitting the interpreter part in the tool config xml or setting it to bash. Good luck. Alex

________________________________________ Van: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] namens Florent Angly [florent.angly@gmail.com] Verzonden: zondag 13 februari 2011 9:03 Aan: galaxy-user@lists.bx.psu.edu Onderwerp: [galaxy-user] Galaxy does not find my executables

Hi list,

I am writing a wrapper for a Grinder, a Perl program installed globally on my Galaxy server.

Galaxy runs as user 'galaxy': $ ps aux | grep paster galaxy 26807 0.0 0.8 2636308 136364 ?? S 2:52PM 0:19.15 python ./scripts/paster.py serve universe_wsgi.ini

When logged in as user galaxy, I can run Grinder: $ Grinder --help Usage: Grinder [options] Grinder --help Grinder --version ...

Grinder's location is: $ which Grinder /opt/local/bin/Grinder

In grinder.xml: If I put:<command interpreter="perl"> In the Galaxy webinterface, I get the error: Can't open perl script "/Users/galaxy/galaxy_dist/tools/ngs_simulation/Grinder": No such file or directory Obviously, here, Galaxy assumes wrongly that tool is installed under the Galaxy ~/tools/ngs_simulation/ folder.

So I tried to omit the interpreter:<command> And I got the error: /bin/sh: Grinder: command not found This is surprising, since Grinder is found if I run it on the command-line as user galaxy

I noticed that I have the same issue with the Velvet wrapper (also located in /opt/local/bin) and thought that this could be an environment issue. And indeed the environment within a wrapper is: PERL=/usr/bin/perl PATH=/usr/bin:/bin:/usr/sbin:/sbin

While on the command line, the environment is: PERL=/opt/local/bin/perl PATH=/opt/local/bin:/opt/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/sw/ bin

This difference in environment explains why Galaxy cannot find Grinder or Velvet.

Does this make any sense? Does Galaxy modify the environment? Why would the environment be different?

Thanks for your help,

Florent

_______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/