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