无法在命令提示符或 anaconda 提示符下安装 Snakemake

Question

I'm trying to install Snakemake.

When I try to use pip, I receive the following error message:

ERROR: Complete output from command 'C:\Python\Python37\python.exe' -u -c 'import setuptools, tokenize;__file__='"'"'C:\\Users\\ANGELA~1\\AppData\\Local\\Temp\\pip-install-1kbp7voq\\datrie\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\ANGELA~1\AppData\Local\Temp\pip-record-_eliva3i\install-record.txt' --single-version-externally-managed --compile:
ERROR: running install
running build
running build_clib
building 'libdatrie' library
creating build
creating build\temp.win-amd64-3.7
creating build\temp.win-amd64-3.7\libdatrie
creating build\temp.win-amd64-3.7\libdatrie\datrie
C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.21.27702\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ilibdatrie "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.21.27702\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.21.27702\include" /Tclibdatrie\datrie\alpha-map.c /Fobuild\temp.win-amd64-3.7\libdatrie\datrie\alpha-map.obj
alpha-map.c
libdatrie\datrie\alpha-map.c(27): fatal error C1083: Cannot open include file: 'ctype.h': No such file or directory
error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2019\\Community\\VC\\Tools\\MSVC\\14.21.27702\\bin\\HostX86\\x64\\cl.exe' failed with exit status 2
----------------------------------------
ERROR: Command "'C:\Python\Python37\python.exe' -u -c 'import setuptools, tokenize;__file__='"'"'C:\\Users\\ANGELA~1\\AppData\\Local\\Temp\\pip-install-1kbp7voq\\datrie\\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record 'C:\Users\ANGELA~1\AppData\Local\Temp\pip-record-_eliva3i\install-record.txt' --single-version-externally-managed --compile" failed with error code 1 in C:\Users\ANGELA~1\AppData\Local\Temp\pip-install-1kbp7voq\datrie\

I've downloaded C++ and python build tools for MS Visual studio 2019. I've also upgraded setup tools.

When I try to install using the anaconda prompt, I get this:

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

 > - snakemake -> pygraphviz

conda install pygraphviz also yields the same message, and I've appended conda-forge to the channels.

Answer 1

conda install -c bioconda snakemake

The package is in the bioconda channel. It's good practice to hit up https://anaconda.org/ and search for any new packages you want to install since the website will actually tell you in which channel the package is.

Answer 2

PyPI

The pip error has some related questions (eg, Cannot open include file: 'ctype.h': No such file or directory ), but I didn't see any VS2019-specific solutions. And the older solutions seem to have various causes, which sounds like a mess to me.

Conda

I'd still try the Conda route. The issue here is that the default Snakemake build requires pygraphviz and that's not available for win-64 platform through any of your channels.

No Graphviz

The easiest alternative is to opt for the snakemake-minimal package instead, which doesn't have the pygraphviz dependency. The only thing Snakemake uses Graphviz for is to generate DAG plots, which in my experience is practically useless for anything but rather trivial pipelines anyway. The minimal version also leaves out remote file support (eg, DropBox interfacing) and fancy report generation. So, if you just need core functionality, then run

conda install snakemake-minimal

(I'm assuming you already have Bioconda + Conda Forge channels.)

Graphviz

If you really want the Graphviz plot or other extras, you could try something like

conda activate
conda install graphviz pip
pip install pygraphviz
conda install snakemake

That is, make sure to use the pip in your Conda env , and only use it to install pygraphviz . However, using both PyPI and Conda can lead to an unstable env .

There are some user channels on Anaconda Cloud that have win-64 builds of pygraphviz , but I do not recommend sourcing from random user channels unless you trust them.

Answer 3

According to this issue , snakemake cannot currently be installed right away using pip under python3.7. It's dependency datrie cannot be installed automatically.

On the issue discussion, there is a suggested workaround: first installing datrie from git, then snakemake :

pip3 install git+https://github.com/pytries/datrie.git
pip3 install snakemake

Answer 4

See https://github.com/snakemake/snakemake/issues/246

This is not a bug with snakemake , but a known issue with datrie . There is a PR currently open which solves this problem, but until it is merged, the following solutions should work.

A previous issue on bitbucket has dealt with this for python3.7.

Workaround

Python3.7

pip3 install git+https://github.com/pytries/datrie.git
pip3 install snakemake

Python3.8

pip3 install "git+https://github.com/ashwinvis/datrie.git@python3.8"
pip3 install snakemake

Answer 5

The error shows that the package you are trying to install uses Microsoft VCC compiler

 No such file or directory error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.21.27702\bin\HostX86\x64\cl.exe' failed with exit status 2 

Install Microsoft Visual Studio 2019 to solve this issue