Canu v1.7 failing due to GNUplot dependency

[rorycraig337]

Hi,

I had the same issue at install as #49, and got around this by using canu v1.7.1. However, this is crashing at the assemble stage as my environment lacks the gnuplot dependency (as far as I know, this is bypassed automatically if absent in later versions of canu). I can get around this by adding "gnuplotTested=true" as a parameter when running canu - could you possibly point me in the direction of which files/lines I need to change to run with this parameter?

Cheers, Rory

[paudano]

I pushed a change to include this in the Canu command. Thanks! You should be able to git pull and run it.

If you pull the change, you don't need to modify anything, but the code is in rules/assemble_group.snakefile starting at line 334.

shell(
    """set +e; """
    """timeout {params.max_runtime} canu """
        """-pacbio-raw """
        """{input.fasta} """
        """genomeSize={genome_size} """
        """-d {canu_dir} """
        """-p asm """
        """useGrid=false """
        """gnuplotTested=true """
        """corMhapSensitivity=high """
        """corMinCoverage=2 """
        """correctedErrorRate=0.045 """  # Was errorRate=0.035
        """-pacbio-raw """
        """>{log} 2>&1; """
    """RET_CODE=$?; """
    """if [ ${{RET_CODE}} -ne 0 ]; then """
        """if [ ${{RET_CODE}} -eq 124 ]; then """
            """echo "Assembly timeout ({params.max_runtime})"; """
        """else """
            """echo "Assembly error: Return code = ${{RET_CODE}}"; """
        """fi; """
    """fi; """
)

Closing for now, but feel free to re-open if there is still a problem.

[paudano]

I removed "gnuplotTested=true", it was taken out in Canu 1.8. Sorry about that. See the previous post about how to fix it in your install.

[rorycraig337]

Perfect, thank you - everything now working well!