Yesterday we discovered what Björn has communicated and added it to the Trello card for this issue:
It also seems that your tool is attempting to use samtools. Tgis is in your config:
<requirements> <requirement type="binary">samtools</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements>
and this is in your script:
#Run samtools idxstats: cmd = "samtools idxstats %s > %s" % (bam_file, tabular_filename) return_code = os.system(cmd)
I belive a fix for this would be to change the name of your repository_dependencies.xml fie to be tool_dependencies.xml, and change the current contents of the file to define a complext repository dependencies for samtools. So the current contents of your repository_dependencies.xml file:
<?xml version="1.0"?> <repositories description="This requires the samtools 0.1.19 binaries"> <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </repositories>
becomes the following in your renamed tool_dependencies.xml file:
<tool_dependency> <package name="samtools" version="0.1.9"> <repository name="package_samtools_0_1_19" owner="iic" /> </package> </tool_dependency>
This is all discussed in the following section of the Tool Shed wiki:
Let me know if this doesn't correct this problem.
Greg Von Kuster
On Nov 13, 2013, at 6:47 AM, Peter Cock firstname.lastname@example.org wrote:
On Wed, Nov 13, 2013 at 10:43 AM, Björn Grüning email@example.com wrote:
sorry for coming late to this thread.
I may be wrong, but you are only specifying a repository_dependecies.xml file. You probably only need to rename it to tool_dependencies.xml file, otherwise the tool can not import it. I guess the env.sh file is not created if no tool_dependencies.xml file is present.
Yes, I think you are right about repository_dependecies.xml versus tool_dependencies.xml but that would happen later - at this point my tool hasn't actually tried to use samtools itself.
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