Re: [galaxy-dev] wrapper for tool with multiple outputs

[Devon Ryan]

Hi Jochen,

Don't have it use /tmp, but rather the current working directory and
then everything will work. Galaxy jobs are run in individual working
directories, so you can exploit that to ensure that files aren't
overwritten.

Devon
--
Devon Ryan, Ph.D.
Email: dpr...@dpryan.com
Data Manager/Bioinformatician
Max Planck Institute of Immunobiology and Epigenetics
Stübeweg 51
79108 Freiburg
Germany


On Wed, Jan 4, 2017 at 12:32 PM, Jochen Bick  wrote:
> Hi,
>
> I have a tool that produces multiple output files a log file, two bam files.
> (https://github.com/nugentechnologies/nudup)
>
> The tool it self provides an option called --out to specify a path to a
> directory with a prefix that will be added to the output files:
>
> --out /tmp/out
>
> this will produce 3 files:
>
> /tmp/out_dup_log.txt
> /tmp/out.sorted.dedup.bam
> /tmp/out.sorted.markdup.bam
>
> so my question is if this out prefix will give me problems overwriting next
> output files coming from this tool?
>
>
> Cheers Jochen
>
>
>
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[galaxy-dev] wrapper for tool with multiple outputs

[Jochen Bick]

Hi,

I have a tool that produces multiple output files a log file, two bam 
files. (https://github.com/nugentechnologies/nudup)


The tool it self provides an option called --out to specify a path to a 
directory with a prefix that will be added to the output files:


--out /tmp/out

this will produce 3 files:

/tmp/out_dup_log.txt
/tmp/out.sorted.dedup.bam
/tmp/out.sorted.markdup.bam

so my question is if this out prefix will give me problems overwriting 
next output files coming from this tool?



Cheers Jochen



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[galaxy-dev] installation error on venv dependencies.xml

[Bakker, Linda]

Hi All,

I posted my question before the holidays but i got not reply. Can someone 
please point me in the right direction?
I am having some problems with my tool dependencies to setup a python venv.

Dependencies.xml looks like this:
[X]
[X][cid:7b48a44d-07dd-4838-8f90-5024d9d22593]

When i install my tool from the toolshed, it fails to install the venv 
dependency with this error message:

[X][cid:0f2c174a-5011-423f-9eaf-ef2ed88c353d]

I am not sure what the problem exactly seems to be. os.py should be a default 
python package right or do i need to specify it in the dependencies file?
Together with our system administrator, we have been trying to solve the issue, 
but no luck so far.
Is my dependencies.xml file ok?

Thanks & a happy new year!

with regards ,
 Linda Bakker



--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bak...@wur.nl



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