Question About Ftp

7.8 years ago by

Florent Angly • 370 wrote:

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

ADD COMMENT • link written 7.8 years ago by Florent Angly • 370

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: 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: 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/

ADD REPLY • link written 7.8 years ago by Bossers, Alex • 240

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

ADD REPLY • link written 7.8 years ago by Florent Angly • 370

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

ADD REPLY • link written 7.8 years ago by Peter Cock • 1.4k

Indeed, this workaround works! Thank you. I added these lines to the beginning of my run.sh: PATH="/opt/local/bin:/opt/local/sbin:$PATH" export $PATH Now, Galaxy can find Grinder, Velvet, etc.... Could Galaxy detect and use ~/.profile automatically if it exists? Alternatively, maybe there should be a place in the configuration file universe_wsgi.ini to specify which file to read environment variables from? Is it worth filing an enhancement request in the bug tracker? Again, thanks for the help. Florent

ADD REPLY • link written 7.8 years ago by Florent Angly • 370

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 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

ADD REPLY • link written 7.8 years ago by Bossers, Alex • 240

7.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Luciano, This was a bug, fixed in galaxy-central yesterday: changeset 4212f675f95b . You can either pull the changeset into your local instance or wait for it to be incorporated into the next distribution (within the next few weeks). Next time, it would be great if you would send questions like this directly to the mailing lists: - galaxy-user@bx.psu.edu for data/tool questions like this one - galaxy-dev@bx.psu.edu local install/technical questions Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

ADD COMMENT • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k

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