Issues with MOSAIC installation

[David Fuentenebro]

Dear Dr Balijepalli,

I am contacting you regarding your nice MOSAIC nanopore data analysis tool.

I saw your talk in the Nanjing Nanopore Weekly Meeting, and knew your work also previously.

You convinced me with the rigour of your event detection, and hence when I started my lab, I decided to give MOSAIC a try rather than chasing my students into my own code that comes with less nice GUI's, without a manual, etc.

Unfortunately, we're having difficulties even installing MOSAIC on a windows pc.

Below you find the detailed description of my student David, who tried the binary and source installation according to the manual, but without success.

Our key questions are:

A) Is there a way to make the binary version run on windows 10? If so, is it running locally on the pc, or computing in a cloud somewhere?

B) What are we doing wrong with  the ''workon'' command? as it is not recognised as a command.

C) Which set of dependencies do we need to install for windows 10, since 2 versions are described in the manual?

I assume for you things will sound obvious, but I have not coded in python before.

It would be great if you could advise us on how to get going with MOSAIC.

Just reaching the level of reading and processing the supplied test data as described would be perfect.

We usually use abf files which (according to the manual) are also supported.

If you have own abf test data that MOSAIC can load & process, we would love to test these, too, if possible.

Alternatively, if you think we should rather choose a different analysis routine to process conventional nanopore translocation data, please let me know.

If it would be easier/faster for you, we could also have a call – whatever works best for you.

Thank you very much, and kind regards from The Netherlands,

Sonja

_ _ _ _ _ _ _ _ _ _ _ _ _

Sonja Schmid

Assistant Professor, NanoDynamicsLab

Laboratory of Biophysics, Wageningen University
Stippeneng 4, 6708WE Wageningen

THE NETHERLANDS

Here David's detailed description:

1) First, I tried installing MOSAIC from the pre-compiled binary, as I am working from a Windows 64-bit computer, and it seemed the easiest way of getting the program.

I downloaded and extracted the file, and when I launched the MOSAIC.exe file a browser tab opened as it was supposed to. 

However, when I try to load any file using the New analysis/Load previous analysis, I am not able to successfully open any file. 

I tried this for both the MOSAIC Reference Data provided in the MOSAIC downloads page, and for some .abf files from our own set of nanopore experiments. 

The program recognises .abf and .qdf files in the specified path (please see attached image), but when I try to open such folders to select a file, .abf and .qdf files do not show up (see attached image).

2) Facing these issues, I tried installing MOSAIC from the source, to see if the problem would get solved.
But I was not able to successfully install MOSAIC following the instructions for a Windows installation. 

I installed Anaconda without further problems, but then some issues appeared. I was able to install MOSAIC dependencies from the Anaconda Prompt:
cython=0.29 pandas=0.20.3
nose=1.3.7 numpy=1.11.1 scipy=0.18.1 docutils=0.14 flask=0.12.2 matplotlib=1.5.3 pyqt=4 lmfit=0.9.3 uncertainties=2.4.8.1 PyWavelets=0.5.2 coverage=4.5.1 codecov=2.0.15

But when I tried installing MOSAIC from the downloaded source distribution (step 3, for the installation of the graphical interface), ''workon'' is not recognised as a command, and this message pops up:
workon: The term 'workon' is not recognized as the name of a cmdlet, function, script file,
or executable program. Check if you typed the name correctly or, if you included a path, Please check that this path is correct and try again. Online: 1 Character: 1 + work in C: \ Users \ David \ projects \ MOSAIC + ~~~~~~
+ CategoryInfo          : ObjectNotFound: (workon:String) [], CommandNotFoundException  
 + FullyQualifiedErrorId : CommandNotFoundException.

I tried to continue with the installation anyways and typed the following command:
(base) PS C:\Users\David\projects\MOSAIC> python setup.py mosaic_deps

But the following message appeared
Global settings not found. Using default values

Traceback (most recent call last):

  File "setup.py", line 2, in <module>

    import mosaic

  File "C:\Users\David\projects\MOSAIC\mosaic\__init__.py", line 22, in <module>

    import mosaic.partition.metaEventPartition

  File "C:\Users\David\projects\MOSAIC\mosaic\partition\metaEventPartition.py", line 42,

in <module>

    import uncertainties

ModuleNotFoundError: No module named 'uncertainties'

I think that the module 'uncertainties' is one of the dependencies I installed with Anaconda. So I am not really sure what happened there, as the module seemed properly installed. Then I realized that there was a page with an updated version of the dependencies I am supposed to install. Therefore, I started the process again,
in a new virtual environment I named mosaicENV2, and installed the updated ones:
cython==0.29.23

pandas==1.2.4

lmfit==0.9.14

uncertainties==3.1.5

PyWavelets==1.1.1

nose==1.3.7

pyinstaller==4.3

numpy==1.20.2

scipy==1.6.2

docutils==0.17.1

flask==1.1.2

coverage==5.5

codecov==2.1.11

gunicorn==20.1.0But some of them are different from the first batch of dependencies I tried to install (namely, pyqt=4 is missing and gunicorn=20.1.0
is added). Now gunicorn could not be installed. I looked it up online, and it seems that gunicorn is not compatible with Windows. Hence the questions: - Which set of dependencies am I supposed to install for windows 10? - What are we doing wrong with the ''workon'' command as it is not recognised as an command. Moreover, I tried continuing with the installation, and typed the command
export PYTHONPATH=$PYTHONPATH:~/projects/MOSAIC

But ''export'' has the same issue as ''workon'', it is not recognised as a command. So I am stuck in the source installation, and I am not sure how to solve these issues. Would be great if you can help us to use the MOSAIC software. If you have any questions, please do not hesitate to ask!

Thank you & Best regards,
David.