I have noticed this too. I am sorry for your trouble, but I don't
think you have not misconfigured anything. I think for the time being,
if you are using the local job runner samtools need to be on Galaxy's
path (you said it works when you do this right?).

Overly Technical Details: The local job runner does not merge the
command for setting the metadata on files into the main command that
gets executed - it does a second process call that doesn't utilize
your tool_dependency_dir. The cluster job runners all set metadata for
output files as part of the command itself so I believe this is not a
problem in those cases. All of that said, I do not know why the local
job runner does not set metadata externally like the cluster job
runners do.

-John

On Mon, Nov 4, 2013 at 10:39 PM, tomasz jankowski <tomasz_ja...@wp.pl> wrote:
> Hi,
> I supose it is simple misteake but i'm realy close to got mad because dealing 
> with it since friday... so I'm writing to list...
>
> I dont know why galaxy cant find samtools ininstallation dir. It seems that 
> all was done acordingly to admin manual... what I can see after sending bam 
> file is
>
> Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found
>
> I thought that galaxy doesntread env.sh file but in log file I have
>
> galaxy.tools DEBUG 2013-11-04 23:07:22,556 Building dependency shell command 
> for dependency 'samtools'
> galaxy.jobs.runners.local DEBUG 2013-11-04 23:07:22,774 (35) executing: 
> PACKAGE_BASE=/opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19; 
> export PACKAGE_BASE; . 
> /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/env.sh;
>
> all log is in attached file
>
> I have  fresh galaxy stable version of galaxy
>
> system centos 6.4 is runing on virtualmachine (vbox)
> Linux galaxy 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 
> x86_64 x86_64 x86_64 GNU/Linux
>
> main galaxy instalation dir is /opt/galaxy/galaxy-dist
>
> tools dependency directory in universe_wsgi.ini is
> tool_dependency_dir = tools_dependences
>
> [galaxy@galaxy galaxy-dist]$ ls -alh 
> /opt/galaxy/galaxy-dist/tools_dependences/samtools/
> total 16K
> drwxrwx--- 4 galaxy galaxy 4.0K Nov  4 22:31 .
> drwxrwxr-x 3 galaxy galaxy 4.0K Nov  4 22:25 ..
> drwxrwx--- 3 galaxy galaxy 4.0K Nov  4 23:04 0.1.19
> lrwxrwxrwx 1 galaxy galaxy    6 Nov  4 22:31 default -> 0.1.19
> drwxrwx--- 6 galaxy galaxy 4.0K Nov  4 22:04 samtools-0.1.19
>
>
> [galaxy@galaxy galaxy-dist]$ ls -alh 
> /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin/samtools
> -rwxrwx--- 1 galaxy galaxy 1.5M Nov  4 22:06 
> /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin/samtools
>
> [galaxy@galaxy galaxy-dist]$ cat 
> /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/env.sh
> PATH="/opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin:$PATH"
> export PATH
>
>
> When I put /opt/galaxy/galaxy-dist/tools_dependences/samtools/0.1.19/bin to 
> /home/galaxy/.bash_profile
> galaxy CAN see the samtools binaries...
>
> could you tell me what I'm doing wrong?
>
> tj
>
>
>
>
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