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
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.
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.
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.
Another option is using a machine on the cloud. It's more expensive on the long run but easy to start with.
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:
Current channels:
To search for alternate channels that may provide the conda package you're looking for, navigate to
and use the search bar at the top of the page.
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 commentinstead to keep this thread organized.