Question: Planemo tutorial test - "Failed to resolve dependency" "Error loading a set of Dynamic Display Application links"
0
gravatar for esch0041
18 months ago by
esch004160
esch004160 wrote:

I have been trying to follow the tutorial "The Basics" under "Building Galaxy Tools ... using Planemo and I have been getting. When I run

planemo test --install_galaxy --test_output test-output/test_output.dat --test_data test-data/ seqtk_seq.xml

my test fails, and I see several WARNINGs and ERRORs (date-times removed for brevity):

galaxy.visualization.genomes ERROR ... Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmp61S67V/galaxy-dev/tool-data/twobit.loc' galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". galaxy.tools.deps WARNING ... Failed to resolve dependency on 'samtools', ignoring galaxy.tools.deps WARNING ... Failed to resolve dependency on 'samtools', ignoring galaxy.tools.deps WARNING ... Failed to resolve dependency on 'seqtk', ignoring galaxy.tools.deps WARNING ... Failed to resolve dependency on 'samtools', ignoring galaxy.visualization.genomes ERROR ... Error reading twobit.loc: [Errno 2] No such file or directory: '/tmp/tmp61S67V/galaxy-dev/tool-data/twobit.loc' galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "bam_iobio". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "vcf_iobio". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "igv_broad_genomes". galaxy.datatypes.display_applications.application ERROR ... Error loading a set of Dynamic Display Application links: Unable to find data table named "biom_simple_display". galaxy.tools.deps WARNING ... Failed to resolve dependency on 'samtools', ignoring galaxy.tools.deps WARNING ... Failed to resolve dependency on 'samtools', ignoring galaxy.tools.deps WARNING ... Failed to resolve dependency on 'seqtk', ignoring galaxy.tools.deps WARNING ... Failed to resolve dependency on 'samtools', ignoring galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring galaxy.tools.deps: WARNING: Failed to resolve dependency on 'seqtk', ignoring galaxy.tools.deps: WARNING: Failed to resolve dependency on 'samtools', ignoring

I speculate that I am not providing the correct dependency resolution, database, and tool directory options.

What do I need to do differently to get the test in the tutorial to pass?

Thank you.

ADD COMMENTlink modified 17 months ago by Martin Čech ♦♦ 4.2k • written 18 months ago by esch004160
0
gravatar for Martin Čech
17 months ago by
Martin Čech ♦♦ 4.2k
United States
Martin Čech ♦♦ 4.2k wrote:

Hello, there is no --test-output option for planemo test command. (see http://planemo.readthedocs.io/en/latest/commands.html#test-command) and you do not need to specify the --test-data folder if it is the default test-data/.

I just tried the command planemo test --install_galaxy on the seqtk example from the tutorial and it worked fine (I used the virtual appliance). Did you check why your test fail? See the /opt/galaxy/tools/seqtk/tool_test_output.html file for results.

ADD COMMENTlink written 17 months ago by Martin Čech ♦♦ 4.2k
1

Martin,

Thank you very much for your response.

What a difference a few days make!

Now, when I run with the same command as before, I still see most or all of the warnings and errors, but my test passes. Granted, I did this with a new virtualenv. I did it outside the VM; previously, my test failed both outside and inside the VM.

As I recall, the test previously was failing because a file was not found, but I guess that point is moot now. I can't say that I feel comfortable about all the warnings and errors, but clearly they do not represent an issue that thwarts the test.

Regarding --test-output, both the link that you cited, and the output of

planemo test --help

say

--test_output PATH Output test report (HTML - for humans) defaults to tool_test_output.html.

and I just confirmed that indeed the test result was written to the file that I specified, test-output/test_output.dat

ADD REPLYlink written 17 months ago by esch004160

The warning and errors come from within Galaxy - it is quite a complex framework with many dependencies and the version you obtain with --install_galaxy is very barebone, disposable, and one-purpose - so that is why you are seeing those.

And sorry about that --test_output confusion, you were right it exists, I was loking at a wrong command. :D

Glad it works for you. Thanks for using Galaxy and Planemo.

ADD REPLYlink written 17 months ago by Martin Čech ♦♦ 4.2k
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