Re: [galaxy-dev] Issues with local instance of toolshed?
Hi Amanda, > I've recently been trying to implement a local instance of the tool > shed, and have followed the tutorials on the wiki, but when I run sh > run_community.sh, it doesn't do anything. I have mercurial installed, > so that shouldn't be a problem, and I've used the example > community_wsgi.ini and run_community.sh. I can pastebin what I have if > it would help. Thank you in advance. Greg will probably have this fixed by the time I reply, but I had a similar problem, which resulted from me minsunderstanding or missing what had to be configured in the toolshed ini file. From my notes, set these vars, in a similar manner to the main Galaxy: - port & host: should be set to where you want the toolshed to be available from - database_file: use this is if you want to use the sqlite3 db. I had some problems with this, which were eventually solved by setting the path correctly for insertion in an sqlite protocol string (e.g. /database/community.sqlite for a relative path that puts the file in the database folder) - file_path: again, had some problems with this, which were solved by creating the directory for the file (e.g. /database/community_files) explicitly - admin_users: like the main Galaxy installation, for setting the admins Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Issues with local instance of toolshed?
Greg, Thank you for your offer of assistance. However, I have decided not to use an internal toolshed instance and use the public instead. 2012/4/16 Greg Von Kuster : > Hi Amanda, > > I'll need to see your paster log to be able to help on this one. You can > view it using "tail -f community_webapp.log" (without the quotes) from your > Galaxy install directory. Can you respond back with the content? > > Thanks, > > Greg Von Kuster > > On Apr 8, 2012, at 1:58 PM, Amanda Zuzolo wrote: > >> Hello all, >> >> I've recently been trying to implement a local instance of the tool >> shed, and have followed the tutorials on the wiki, but when I run sh >> run_community.sh, it doesn't do anything. I have mercurial installed, >> so that shouldn't be a problem, and I've used the example >> community_wsgi.ini and run_community.sh. I can pastebin what I have if >> it would help. Thank you in advance. >> >> >> -- >> Amanda Zuzolo >> Bioengineering Major, George Mason University >> Metabiome Informatics Group, Environmental Biocomplexity >> ___ >> 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: >> >> http://lists.bx.psu.edu/ > -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity Peer Advisor, Volgenau School of Engineering ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Issues with local instance of toolshed?
Hi Amanda, I'll need to see your paster log to be able to help on this one. You can view it using "tail -f community_webapp.log" (without the quotes) from your Galaxy install directory. Can you respond back with the content? Thanks, Greg Von Kuster On Apr 8, 2012, at 1:58 PM, Amanda Zuzolo wrote: > Hello all, > > I've recently been trying to implement a local instance of the tool > shed, and have followed the tutorials on the wiki, but when I run sh > run_community.sh, it doesn't do anything. I have mercurial installed, > so that shouldn't be a problem, and I've used the example > community_wsgi.ini and run_community.sh. I can pastebin what I have if > it would help. Thank you in advance. > > > -- > Amanda Zuzolo > Bioengineering Major, George Mason University > Metabiome Informatics Group, Environmental Biocomplexity > ___ > 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: > > http://lists.bx.psu.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: http://lists.bx.psu.edu/
[galaxy-dev] Issues with local instance of toolshed?
Hello all, I've recently been trying to implement a local instance of the tool shed, and have followed the tutorials on the wiki, but when I run sh run_community.sh, it doesn't do anything. I have mercurial installed, so that shouldn't be a problem, and I've used the example community_wsgi.ini and run_community.sh. I can pastebin what I have if it would help. Thank you in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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: http://lists.bx.psu.edu/
