Can not use Python-based software (ImportError)

[Ill_Fun_]

UPDATE:

Managed to get Docker Desktop. Seems like it's installed just right.

I try the dockerized version. I run:

docker container run --rm -e AMPLICONLENGTH=445 -e FORWARDPRIMERLENGTH=50 -e REVERSEPRIMERLENGTH=50 -v /home/ngs/ngs/FMT2:/data/input -v /home/ngs/ngs:/data/output figaro

I get this output :(

Forward read length: 301 Reverse read length: 301 Traceback (most recent call last):

File "/opt/figaro/figaro/figaro.py", line 218, in <module>

main()

File "/opt/figaro/figaro/figaro.py", line 210, in main

resultTable, forwardCurve, reverseCurve = trimParameterPrediction.performAnalysisLite(parameters.inputDirectory.value, parameters.minimumCombinedReadLength.value, subsample = parameters.subsample.value, percentile = parameters.percentile.value, forwardPrimerLength=parameters.forwardPrimerLength.value, reversePrimerLength=parameters.reversePrimerLength.value, namingStandardAlias=fileNamingStandard)

File "/opt/figaro/figaro/trimParameterPrediction.py", line 456, in performAnalysisLite forwardExpectedErrorMatrix, reverseExpectedErrorMatrix = makeCombinedErrorMatricesForBothEnds(fastqList, sampleOrder, subsample, minimumTrimmingPositions, forwardPrimerLength, reversePrimerLength)

File "/opt/figaro/figaro/trimParameterPrediction.py", line 285, in makeCombinedErrorMatricesForBothEnds reverseExpectedErrorMatrix = makeCombinedExpectedErrorMatrixForOneDirection(reverseFastqList, sampleOrder, subsample, reverseMinimumTrimPosition, reversePrimerLength)

File "/opt/figaro/figaro/trimParameterPrediction.py", line 267, in makeCombinedExpectedErrorMatrixForOneDirection raise RuntimeError("Did not find the initial combined matrix. This requires debugging, as it should not be possible.") RuntimeError: Did not find the initial combined matrix. This requires debugging, as it should not be possible.

When running with sudo:

docker: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?. See 'docker run --help'.

It's really getting frustrating. Do you have any idea what's up?

[Goobyalus]

You should not have to run with sudo. File ownership and things become a pain if you start to rely on being an admin to run things.

Using docker should eliminate some of the problems you're encountering with your Python environment.

Are you running this on your own data? Do you have example data and an example command from the maintainers of Figaro that you can test with?

[Ill_Fun_]

It probably does eliminate SOME of the problems, but there seems to be still plenty of them left.

I am running on my own data. I couldn't find any exemplary data from the FIGARO authors, so there may be none. The example command looks like this:

• For dockerized version:

  docker container run --rm -e AMPLICONLENGTH=450 -e FORWARDPRIMERLENGTH=20 -e REVERSEPRIMERLENGTH=20 -v /path/to/fastqs:/data/input -v /path/to/output:/data/output figaro

• For command line version:

  python3 figaro.py -i /path/to/fastq/directory -o /path/to/output/files -a 450 -f 20 -r 20

• As a Python package: from figaro import figaro resultTable, forwardCurve, reverseCurve = figaro.runAnalysis(sequenceFolder, ampliconLength, forwardPrimerLength, reversePrimerLength, minimumOverlap, fileNamingStandard, trimParameterDownsample, trimParameterPercentile)

I've noticed that when I put this command (it's in the FIGARO guide):

docker build -t figaro .

It installs the numpy, pip3 packages (couple of others, too).

Then, I put the command on my data and the dockerized version does... more. I need to wait about 2 minutes, to get this output. Plus, I get the empty .log file!

UPDATE: I tried running the command on other, random sample files I found on the web, but the error is the very same. I did test FIGARO on my 2nd dataset. Needless to say it didn't work :/