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

----------------------------------------------------------------- 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 17:46, Xianrong Wong wongxr@gmail.com a écrit :

<jose123.xml>

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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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> wrote:

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

---

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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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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: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/