tombo安装报错的各种解决方案

一、各种安装报错类型：

1.The following specifications were found to be incompatible with the existing python installation in your environment

UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: 

Specifications: 

- ont-tombo -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']                                                                                          

Your python: python=3.8

If python is on the left-most side of the chain, that's the version you've asked for.                                                        
When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that.
   
The following specifications were found to be incompatible with your system:
   
  - feature:/linux-64::__glibc==2.35=0                              
  - ont-tombo -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']                                                        
  - python=3.8 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.35

2. ERROR: Cannot unpack file /tmp/pip-unpack-x8u5jrfa/tombo.git (downloaded from /tmp/pip-req-build-b3_erpsj, content-type: text/html; charset=utf-8); cannot detect archive formatERROR: Cannot determine archive format of /tmp/pip-req-build-b3_erpsj

(base) test@pavilion:~$ pip install ont-tombo
Collecting ont-tombo
  Using cached https://files.pythonhosted.org/packages/34/6d/f3426707cf097d381dee752b73027920353d4a7744d8bdab696012f1bc8f/ont-tombo-1.5.1.tar.gz
ERROR: Files/directories not found in /tmp/pip-install-8rhz6gmv/ont-tombo/pip-egg-info
(base) test@pavilion:~$ pip install https://github.com/nanoporetech/tombo.git
Collecting https://github.com/nanoporetech/tombo.git
  Downloading https://github.com/nanoporetech/tombo.git
     \ 225kB 1.0MB/s
  ERROR: Cannot unpack file /tmp/pip-unpack-x8u5jrfa/tombo.git (downloaded from /tmp/pip-req-build-b3_erpsj, content-type: text/html; charset=utf-8); cannot detect archive format
ERROR: Cannot determine archive format of /tmp/pip-req-build-b3_erpsj
(base) test@pavilion:~$ git clone https://github.com/nanoporetech/tombo
Cloning into 'tombo'...
remote: Enumerating objects: 725, done.
remote: Counting objects: 100% (14/14), done.
remote: Compressing objects: 100% (11/11), done.
remote: Total 725 (delta 6), reused 7 (delta 3), pack-reused 711
Receiving objects: 100% (725/725), 38.69 MiB | 11.39 MiB/s, done.
Resolving deltas: 100% (339/339), done.
(base) test@pavilion:~$ cd tombo
(base) test@pavilion:~/tombo$ pip install -e .
Obtaining file:///home/test/tombo
ERROR: Files/directories not found in /home/test/tombo/

3. ERROR: Failed building wheel for mappy
Failed to build mappy
ERROR: Could not build wheels for mappy, which is required to install pyproject.toml-based projects

Obtaining file:///home/Caogx/software/tombo
Preparing metadata (setup.py) ... done
Collecting h5py<3 (from ont-tombo==1.5.1)
Using cached h5py-2.10.0-cp37-cp37m-manylinux1_x86_64.whl (2.9 MB)
Requirement already satisfied: numpy<1.20 in /home/Caogx/miniconda3/envs/tombo/lib/python3.7/site-packages (from ont-tombo==1.5.1) (1.19.4)
Collecting scipy (from ont-tombo==1.5.1)
Using cached scipy-1.7.3-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (38.1 MB)
Collecting cython (from ont-tombo==1.5.1)
Using cached Cython-0.29.35-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
Requirement already satisfied: setuptools>=18.0 in /home/Caogx/miniconda3/envs/tombo/lib/python3.7/site-packages (from ont-tombo==1.5.1) (68.0.0)
Collecting mappy>=2.10 (from ont-tombo==1.5.1)
Using cached mappy-2.26.tar.gz (135 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting future (from ont-tombo==1.5.1)
Using cached future-0.18.3-py3-none-any.whl
Collecting tqdm (from ont-tombo==1.5.1)
Using cached tqdm-4.65.0-py3-none-any.whl (77 kB)
Collecting six (from h5py<3->ont-tombo==1.5.1)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Building wheels for collected packages: mappy
Building wheel for mappy (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for mappy (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [12 lines of output]
running bdist_wheel
running build
running build_ext
cythoning python/mappy.pyx to python/mappy.c
building 'mappy' extension
creating build
creating build/temp.linux-x86_64-cpython-37
creating build/temp.linux-x86_64-cpython-37/python
/home/Caogx/miniconda3/envs/tombo/bin/x86_64-conda-linux-gnu-cc -Wno-unused-result -Wsign-compare -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/Caogx/miniconda3/envs/tombo/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/Caogx/miniconda3/envs/tombo/include -fPIC -I. -I/home/Caogx/miniconda3/envs/tombo/include/python3.7m -c align.c -o build/temp.linux-x86_64-cpython-37/align.o -DHAVE_KALLOC -msse4.1
/tmp/pip-build-env-94tp1s_q/overlay/lib/python3.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /tmp/pip-install-aavq5qup/mappy_3f5c07da4a554da899cd8e439bb1350d/python/mappy.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
error: command '/home/Caogx/miniconda3/envs/tombo/bin/x86_64-conda-linux-gnu-cc' failed: No such file or directory: '/home/Caogx/miniconda3/envs/tombo/bin/x86_64-conda-linux-gnu-cc'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for mappy
Failed to build mappy
ERROR: Could not build wheels for mappy, which is required to install pyproject.toml-based projects

二、各种解决方案：

1.降级python版本到3.6，并且使用mamba install命令安装：

mamba install -c bioconda ont-tombo

回答原文：

Thanks to a thread on Reddit, I learned tombo requires Python 3.6, even though the tools I'm trying to use state 3.8 in their install guides. With the downgraded Python mamba install -c bioconda ont-tombo is successfull though.
As one comment suggested, it might be reasonable to create an extra 3.6 environment just for tombo.

2.使用以下代码安装：

pip3 install -i https://pypi.tuna.tsinghua.edu.cn/simple ont-tombo

3.创建.cpp文件：

touch tombo/_c_dynamic_programming.cpp tombo/_c_helper.cpp
pip install -e .

回答原文：

Actually, creating empty .cpp files is enough to build the package.

4.创建python等于3.6 or 3.7 的虚拟环境：

conda create -n tombo python==3.6
conda activate tombo
conda install -c bioconda ont-tombo