- Bjoern's suggestion of adding the requirements parent tags around
your requirement tag is absolutely needed.
- Be sure to restart Galaxy every time you change the tool file (or
reload the tool using the admin menu).
- Can you share your full tool XML file?
- What job runner are you using? If you haven't really played around
with job_conf.xml or universe_wsgi.ini it should be just be the local
job runner.
- Can you verify you do not have a file called
dependency_resolvers_conf.xml in your Galaxy root directory - you can
break this process if you have mis-defined dependency resolvers.
- Finally - can you share Galaxy's log around the time it is trying to
run this tool -

If Galaxy can find your dependency it should have a line like (except
not with samtools):

galaxy.tools.deps DEBUG 2014-06-05 08:11:30,739 Building dependency
shell command for dependency 'samtools'

If Galaxy cannot find your dependency it should have a line like

galaxy.tools.deps DEBUG 2014-06-05 08:13:12,777 Building dependency
shell command for dependency 'samtools'
galaxy.tools.deps WARNING 2014-06-05 08:13:12,777 Failed to resolve
dependency on 'samtools', ignoring

If neither kind of line can be found - Galaxy is having problems
parsing this data from your tool file. If one exists - then Galaxy
understands that it should try to find the dependency but cannot -
this could mean tool_dependency_dir is wrong, a mis-spelling exists,
the symbolic link is wrong, etc.... If you have the top-line but the
app is still not on your path (shouldn't be the case since sourcing
the file before running Galaxy works) - then there is a problem inside
of env.sh.

-John


On Mon, Jun 2, 2014 at 1:07 PM, Isabelle Phan
<isabelle.p...@seattlebiomed.org> wrote:
> Galaxy is not sourcing env.sh
>
> I tried sourcing it before restarting galaxy and it worked. So that's the
> issue.
>
> How do I get galaxy to source env.sh?
>
> $ ls -lh tool_dependencies/hhsuite/
> total 8
> drwxr-xr-x@ 11 iphan  SBRI\Domain Users   374B Jun  2 10:54 2.0.16/
> lrwxr-xr-x   1 iphan  SBRI\Domain Users     7B Jun  2 10:54 default@ ->
> 2.0.16/
> $
> $ ls -lh tool_dependencies/hhsuite/default/
> total 784
> -rw-r--r--@  1 iphan  SBRI\Domain Users    20K Mar 19  2013 CHANGES
> -rw-r--r--@  1 iphan  SBRI\Domain Users    36K Mar 19  2013 LICENSE
> -rw-r--r--@  1 iphan  SBRI\Domain Users   6.0K Mar 19  2013 README
> drwxr-xr-x@ 10 iphan  SBRI\Domain Users   340B May 30 13:18 bin/
> -rwxrwxrwx+  1 iphan  SBRI\Domain Users   186B Jun  2 10:54 env.sh*
> -rw-r--r--@  1 iphan  SBRI\Domain Users   319K Mar 19  2013
> hhsuite-userguide.pdf
> drwxr-xr-x@  3 iphan  SBRI\Domain Users   102B May 30 13:18 include/
> drwxr-xr-x@  6 iphan  SBRI\Domain Users   204B May 30 13:20 lib/
>
>
>
>
> thanks,
>
> Isabelle
>
>
>
> On 6/2/14 10:50 AM, "Isabelle Phan" <isabelle.p...@seattlebiomed.org>
> wrote:
>
>>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"
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>>>>
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>>>>    http://galaxyproject.org/search/mailinglists/
>>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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