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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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