Hi Gildas, thank you for the prompt reply! I actually have tried multiple paths to the script, even just the script name as you suggested but it's always giving the same error of "no such file or directory".

On Tue, Feb 23, 2016 at 11:51 AM, Gildas Le Corguillé < lecorguille@sb-roscoff.fr> wrote:

Hi,

I think that you don’t need :

.$__tool_directory__/

<command interpreter="perl">rm_consecutive_sameScore.pl "$input1" "$output1"</command> seems enough if you join the script .pl with your wrapper .xml

Gildas

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Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 http://abims.sb-roscoff.fr

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Le 23 févr. 2016 à 17:46, Xianrong Wong wongxr@gmail.com a écrit :

<jose123.xml>

Is it this tool : https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_w...

Gildas

----------------------------------------------------------------- Gildas Le Corguillé - Bioinformatician/Bioanalyste Plateforme ABiMS (Analyses and Bioinformatics for Marine Science)

Station Biologique de Roscoff - UPMC/CNRS - FR2424 Place Georges Teissier 29680 Roscoff FRANCE tel: +33 2 98 29 23 81 http://abims.sb-roscoff.fr ------------------------------------------------------------------

Le 23 févr. 2016 à 18:35, Björn Grüning bjoern.gruening@gmail.com a écrit :

Hi,

is the script rm_consecutive_sameScore.pl part of your TS repo and next to your tool XML file or where is it stored?

Thanks, Bjoern

Am 23.02.2016 um 17:46 schrieb Xianrong Wong:

...

Hi, I'm new to publishing tools/repository on the toolshed. I have used planemo and lint and tests as well as serve all worked. I was able to use the tool. However, when I uploaded it onto the test tool shed and imported the tool on a cloud instance, I keep getting this error when running job:

Fatal error: Exit code 2 () Can't open perl script "rm_consecutive_sameScore.pl": No such file or directory

Please advise! I've been downloading and looking at what others did but I still can't figure this out.

I've attached my .xml file and here are some of the commands I used to upload the tool.

planemo shed_create --shed_target testtoolshed

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