Hi all, You will found in attachment the modification, I proposed in my first email. As I said when your script is near your xml, you just need to use the interpreter attribute in <command> Cheers 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 25 févr. 2016 à 18:36, Karen Reddy <kreddy4@jhmi.edu> a écrit :

​Dear Gildas And Bjorn,

Thanks so much for working on this! We are looking to test these tools ASAP and provide them within a workflow in an AMI (for a manuscript we are submitting to Genes and Development). Obviously, we have these scripts working from command line but we would like to also provide this to a more general audience.

We are hoping to have everything up and running by this weekend, so please let us know if you need any more information from us. As Xianrong (Jose) mentioned this all works in planemo, and the tool appears to be deposited and easily installed, but remains 'unfound'. Also, please let us know if we did something wrong!

Thanks again.

Karen

(PS you guys are awesome--Bjorn, Mo and i were just reminiscing about Galaxy 2015--are you going to Indianapolis?) From: Karen Reddy <anotherpostdoc@gmail.com <mailto:anotherpostdoc@gmail.com>> Sent: Thursday, February 25, 2016 12:26 PM To: Karen Reddy Subject: Fwd: [galaxy-dev] correctly installing to toolshed

---------- Forwarded message ---------- From: Xianrong Wong <wongxr@gmail.com <mailto:wongxr@gmail.com>> Date: Wed, Feb 24, 2016 at 2:26 PM Subject: Fwd: [galaxy-dev] correctly installing to toolshed To: Karen Reddy <anotherpostdoc@gmail.com <mailto:anotherpostdoc@gmail.com>>

I followed instructions from here for tool building.

---------- Forwarded message ---------- From: Xianrong Wong <wongxr@gmail.com <mailto:wongxr@gmail.com>> Date: Tue, Feb 23, 2016 at 1:05 PM Subject: Re: [galaxy-dev] correctly installing to toolshed To: Gildas Le Corguillé <lecorguille@sb-roscoff.fr <mailto:lecorguille@sb-roscoff.fr>> Cc: Björn Grüning <bjoern.gruening@gmail.com <mailto:bjoern.gruening@gmail.com>>, galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu>

Hi Bjoern, it's stored in the same folder as the .xml

Hi Gildas, that is the tool.

Thanks!

On Tue, Feb 23, 2016 at 12:43 PM, Gildas Le Corguillé <lecorguille@sb-roscoff.fr <mailto:lecorguille@sb-roscoff.fr>> wrote: Is it this tool : https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_w... <https://testtoolshed.g2.bx.psu.edu/view/xianrong/removing_consecutive_bins_with_same_score/c19a0a942e1b>

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 <tel:%2B33%202%2098%2029%2023%2081> http://abims.sb-roscoff.fr <http://abims.sb-roscoff.fr/> ------------------------------------------------------------------

...

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