Hello Dave, I got interrupted before I could reply to the second suggestion from Jorrit:
> Not sure about specifying the absolute path for the tool dependency dir, >but I always use it. using the absolute path of the tool dependency dir had no effect. > Also, my env.sh neither has a #!/bin/bash shebang line, nor quote marks >around the tool path. Removed shebang, quote marks (these are in the wiki example): no effect. > If you are in the hhsuite/default/ dir and source env.sh, can you then >run hhblits yourself (as galaxy user, or whoever owns the tools)? This helped: it looks like I had to specify an additional env variable HHDIR to make it work. So definitely making progress. However, the error was not that the executable was not found, but that HHDIR was missing. I now know I have to use the env.sh BUT: galaxy is not sourcing env.sh. That is my problem. I am confused by your question: if I go with the env.sh solution, I am assuming I do not need to create a 'default' directory and do not need the <requirement> tag. Is this correct? Isabelle On 6/2/14 10:34 AM, "Dave Bouvier" <d...@bx.psu.edu> wrote: >Isabelle, > >In order to help track down the cause of this issue, could you provide >the output of the following two commands? > >ls -lh tool_dependencies/hhsuite/ >ls -lh tool_dependencies/hhsuite/default/ > > --Dave B. > >On Mon 02 Jun 2014 01:29:44 PM EDT, Isabelle Phan wrote: >> I tried >> <requirements> >> <requirement type="package">hhsuite</requirement> >> </requirements> >> >> >> and that had no effect. >> >> >> I. >> >> ------------------------------ >> >> Message: 3 >> Date: Sat, 31 May 2014 03:51:55 +0200 >> From: Bj?rn Gr?ning <bjoern.gruen...@gmail.com> >> To: galaxy-dev@lists.bx.psu.edu >> Subject: Re: [galaxy-dev] tool dependencies fail >> Message-ID: <538935bb.7020...@gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi, >> >> can you try: >> >> <requirements> >> <requirement type="package">hhsuite</requirement> >> </requirements> >> >> Hope that helps, sorry for the short answer I'm too tired :) >> Bjoern >> >> >> >> >> >> >> >> ___________________________________________________________ >> 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/ >> >> 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
