Question: Correctly installing to toolshed
gravatar for Xianrong Wong
2.8 years ago by
Xianrong Wong90 wrote:

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 "": 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.


The first few lines of my .xml file looks like this


<tool id="jose123" name="removes_consecutive_same_scored_bins" version="0.1.0"> <requirements> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command interpreter="perl">./ "$input1" "$output1" </command> <inputs> <param type="data" name="input1" format="bed" />


Thank you in advance!

toolshed • 807 views
ADD COMMENTlink modified 2.7 years ago by Dave B.410 • written 2.8 years ago by Xianrong Wong90

can you please link your TS repository?

ADD REPLYlink written 2.7 years ago by Martin Čech ♦♦ 4.9k
gravatar for Dave B.
2.7 years ago by
Dave B.410
United States
Dave B.410 wrote:


Is the perl interpreter installed on the cloud instance? I examined your repository on the test toolshed, and everything seems to be configured correctly.

I would however recommend changing the first line of the perl script to:

#!/usr/bin/env perl

This would handle any potential issues with perl being installed to a non-standard path.

ADD COMMENTlink written 2.7 years ago by Dave B.410
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