Reorder Sam files

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Reorder Sam files

Alexander Kurze
Hi there,
we are running a local instant of galaxy and when running Picard tools Reorder Sam files I get following error message:

"An error occurred with this dataset: ## exit code=1; stdout= Error: Unable to access jarfile /ReorderSam.jar"

Now, I thought that when installing picard-tools via the toolshed the dependency should be added automatically. I am really not sure why it looks for ReorderSam.jar in the top directory /. Any clues?

Best wishes,

Alex


--
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United Kingdom

Tel: +44 1865 613 230
Fax:+44 1865 613 341

___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: Reorder Sam files

Björn Grüning-3
Hi Alex,

can you check if all dependencies are installed. Afaik Galaxy sets an
env variable to point to the actual jar file. That env variable is
missing and the constructed path to your picard executable is looking
like $SOME_NOT_SET_ENV_VAR/ReorderSam.jar.

Hope that helps,
Bjoern

Am 17.03.2014 15:48, schrieb Alexander Kurze:

> Hi there,
> we are running a local instant of galaxy and when running Picard tools
> Reorder Sam files I get following error message:
>
> "An error occurred with this dataset: *## exit code=1; stdout= Error:
> Unable to access jarfile /ReorderSam.jar*"
>
> Now, I thought that when installing picard-tools via the toolshed the
> dependency should be added automatically. I am really not sure why it looks
> for ReorderSam.jar in the top directory /. Any clues?
>
> Best wishes,
>
> Alex
>
>
>
>
> ___________________________________________________________
> 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/
Reply | Threaded
Open this post in threaded view
|

Re: Reorder Sam files

Alexander Kurze
Hi Bjoern,

thanks for your quick answer.

My path to my picard is /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/picard/bf1c3f9f8282/picard unfortunately I cannot find a env.sh in there.
The env.sh is in the dependency folder /home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f
The env.sh points to the right folder JAVA_JAR_PATH=/home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f/jars; export JAVA_JAR_PATH

Any suggestions?

Alex


On Mon, Mar 17, 2014 at 3:31 PM, Björn Grüning <[hidden email]> wrote:
Hi Alex,

can you check if all dependencies are installed. Afaik Galaxy sets an env variable to point to the actual jar file. That env variable is missing and the constructed path to your picard executable is looking like $SOME_NOT_SET_ENV_VAR/ReorderSam.jar.

Hope that helps,
Bjoern

Am 17.03.2014 15:48, schrieb Alexander Kurze:
Hi there,
we are running a local instant of galaxy and when running Picard tools
Reorder Sam files I get following error message:

"An error occurred with this dataset: *## exit code=1; stdout= Error:
Unable to access jarfile /ReorderSam.jar*"


Now, I thought that when installing picard-tools via the toolshed the
dependency should be added automatically. I am really not sure why it looks
for ReorderSam.jar in the top directory /. Any clues?

Best wishes,

Alex




___________________________________________________________
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/




--
Alexander Kurze, DPhil
University of Oxford
Department of Biochemistry
South Parks Road
Oxford, OX1 3QU
United Kingdom

Tel: +44 1865 613 230
Fax:+44 1865 613 341

___________________________________________________________
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/
Reply | Threaded
Open this post in threaded view
|

Re: Reorder Sam files

Björn Grüning-3
Hi,

during tool execution the env variables will be set and all requirements
will be tried to resolved. Can you see at the galaxy log file during the
tool execution? You will see something like:

Building dependency shell command for dependency ...

Does that seems to be correct?
Bjoern

Am 17.03.2014 16:54, schrieb Alexander Kurze:

> Hi Bjoern,
>
> thanks for your quick answer.
>
> My path to my picard is /home/galaxy/shed_tools/
> toolshed.g2.bx.psu.edu/repos/devteam/picard/bf1c3f9f8282/picardunfortunately
> I cannot find a env.sh in there.
> The env.sh is in the dependency folder
> /home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f
> The env.sh points to the right folder
> JAVA_JAR_PATH=/home/galaxy/shed_tools/dependency/picard/1.56.0/devteam/package_picard_1_56_0/61e41d21cb6f/jars;
> export JAVA_JAR_PATH
>
> Any suggestions?
>
> Alex
>
>
> On Mon, Mar 17, 2014 at 3:31 PM, Björn Grüning <[hidden email]>wrote:
>
>> Hi Alex,
>>
>> can you check if all dependencies are installed. Afaik Galaxy sets an env
>> variable to point to the actual jar file. That env variable is missing and
>> the constructed path to your picard executable is looking like
>> $SOME_NOT_SET_ENV_VAR/ReorderSam.jar.
>>
>> Hope that helps,
>> Bjoern
>>
>> Am 17.03.2014 15:48, schrieb Alexander Kurze:
>>
>>> Hi there,
>>> we are running a local instant of galaxy and when running Picard tools
>>> Reorder Sam files I get following error message:
>>>
>>> "An error occurred with this dataset: *## exit code=1; stdout= Error:
>>> Unable to access jarfile /ReorderSam.jar*"
>>>
>>>
>>> Now, I thought that when installing picard-tools via the toolshed the
>>> dependency should be added automatically. I am really not sure why it
>>> looks
>>> for ReorderSam.jar in the top directory /. Any clues?
>>>
>>> Best wishes,
>>>
>>> Alex
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> 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/