Question: Cannot install cutadapt or bowtie2 on windows, misunderstanding/ ignorant of something vital
0
gravatar for Merebellum
4 months ago by
Merebellum0
Merebellum0 wrote:

Hey! I'm a beginner, and trying to install cutadapt and bowtie2 for some sequencing analysis. I can't get it to work, Even though there are countless threads and webpages about this. There must be something I am misunderstanding.Can somebody please help me. this is breaking me

I work on Windows 10 2016. I can't update to windows 10 2019 due to restrictions from my university (this would have solved all my problems. Then I could install ubunut with the linux subsystem. But the IT-department said no. So that is a dead-end)

Can someone please "check my math":

Installed python38 in windows command prompt added to path. installed pip, added to path. this works error occurs when I try to install cutadapt, and bowtie2 using pip install cutadapt; pip install bowtie2 (i've attached an error message for cutadapt at the end) they suggest installing a C++ complier, visual studio but I installed it and it doesn't help me since I've no idea how to use it, and I have MinGW installed.

Installed MinGW by following the instructions on this link. Not sure if I need to "creat a path" between python and MinGW, but it didn't help. So, I also tried installing Microsoft visual studio. This was probably foolish since that's more of an editor and I don't understand it yet. I can run py scripts there so that nice.

Then I tried Miniconda3 in hopes to install bioconda. But this was impossible as well. I added the three channels "default", "conda-forge", and "bioconda". it doesn't recognize or find bwa, and it has trouble with dnaio. I've tried the follow two line, they do not work. conda install bwa conda create -n cutadaptenv cutadapt

Are there any suggestions. I need help. Really sorry for the long text!

Below is the error for when i try installing cutadapt in the command prompt for windows:

C:\Users\admin>pip install cutadapt
Collecting cutadapt
  Using cached cutadapt-2.9.tar.gz (280 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting xopen~=0.8.4
  Using cached xopen-0.8.4-py2.py3-none-any.whl (8.3 kB)
Collecting dnaio~=0.4.1
  Using cached dnaio-0.4.1.tar.gz (123 kB)
Building wheels for collected packages: cutadapt
  Building wheel for cutadapt (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: 'c:\python38\python.exe' 'c:\python38\lib\site-packages\pip\_vendor\pep517\_in_process.py' build_wheel 'C:\Users\admin\AppData\Local\Temp\tmp7wg2_4mc'
       cwd: C:\Users\admin\AppData\Local\Temp\pip-install-gw4wmje4\cutadapt
  Complete output (21 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build\lib.win32-3.8
  creating build\lib.win32-3.8\cutadapt
  copying src\cutadapt\adapters.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\align.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\filters.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\log.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\modifiers.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\parser.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\pipeline.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\report.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\utils.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\_version.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\__init__.py -> build\lib.win32-3.8\cutadapt
  copying src\cutadapt\__main__.py -> build\lib.win32-3.8\cutadapt
  running build_ext
  building 'cutadapt._align' extension
  error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/

ERROR: Failed building wheel for cutadapt
Failed to build cutadapt
ERROR: Could not build wheels for cutadapt which use PEP 517 and cannot be installed directly
cutadapt error windows bowtie2 • 446 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by Merebellum0
1

If you are in a university you should have access to a computing cluster, ask your supervisor or lab members. Working with Windows or a laptop at all is bad practice and you will soon hit a(nother) wall.

ADD REPLYlink written 4 months ago by Asaf8.3k

Thank you for your replies! I do not have access to a cluster. I checked with my supervisor and sadly it is not an option.

I noticed the error telling me about Microscoft visual C++. I tried installing it after I had installed the Visual studio but it didn't help. Is ther ea specific way it needs to be installed or linked to miniconda?

I have tried to scavenge all forums that mention cutadapt and bowtie. The problem is they say install "XX" or do this obvious thing and I don't know the obvious thing to do.

ADD REPLYlink written 4 months ago by Merebellum0
1

You do not need a cluster, just an (external) hard drive which you erase and then install Linux on. No magic here. There are plenty of tutorials online on how to make that happen. https://www.suse.com/c/how-create-external-usb-bootable-linux-hard-drive-without-dual-boot/

Still, investing some money (if this is possible) into a proper workstation would be a good idea as it makes your life so much easier. Depending on the aorkload and size of the files a laptop with e.g. only a dual-core is quickly going to reach its limits.

ADD REPLYlink modified 4 months ago • written 4 months ago by ATpoint36k
1

Another option is using a machine on the cloud. It's more expensive on the long run but easy to start with.

ADD REPLYlink written 4 months ago by Asaf8.3k

An example of something I do not understand.

when trying to install bioconda I follow the instructions on this page. follow the instructions on installing miniconda on this page (windows installer python3.7) check the path is added, check that python and pip work. type: conda update conda conda install -c anaconda mingw gcc -v (shows its present)

Go back to the bioconda page[1]. Add the three channels: conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge

conda install bwa Then I get an error saying it isn't available from the current channels? What do I do to fix this?

Error: (base) c:\Users\admin>conda install bwa Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

  • bwa

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

ADD REPLYlink written 4 months ago by Merebellum0

Especially if you are new to the field there are plenty of obstacles and challenges, make your life easier and remove the burden of running bioinformatics tools under Windows as most are tailored or even exclusive for Unix systems.

That is what I mean. Many software packages is Unix-tailored and not available on Windows. And please stop adding content to the answer field and use add comment instead to keep this thread organized.

ADD REPLYlink modified 4 months ago • written 4 months ago by ATpoint36k
0
gravatar for Mensur Dlakic
4 months ago by
Mensur Dlakic6.0k
USA
Mensur Dlakic6.0k wrote:

The error seems to be pretty obvious:

error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/

I second Asaf's suggestion: try to work in a Linux/Unix environment if possible. Most of these programs are not meant for Windows environment, and you will end up troubleshooting installations more often than you want to.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Mensur Dlakic6.0k
0
gravatar for ATpoint
4 months ago by
ATpoint36k
Germany
ATpoint36k wrote:

error: Microsoft Visual C++ 14.0 is required. Get it with "Build Tools for Visual Studio": https://visualstudio.microsoft.com/downloads/

There it is. Please also browse this forum for cutadapt-related question on Windows system. I strongly encourage (seconding Asaf's and Mensur's advice) to switch to a Unix (Mac/Linux) system. Especially if you are new to the field there are plenty of obstacles and challenges, make your life easier and remove the burden of running bioinformatics tools under Windows as most are tailored or even exclusive for Unix systems. There are of course workarounds but as said this only adds unnecessary complexity. Another advice, always read the full error messages, this most of the time tells you want is wrong.

ADD COMMENTlink modified 4 months ago • written 4 months ago by ATpoint36k
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