tombo installing error by pip

[gaoxiangcao]

Hi， everyone
Due to the issue of preprocess by conda installtion, i try the pip to install tombo, however i encounter the error when i installed tombo.
how can i solve it?
(tombo) [Caogx@genosys tombo]$ pip install -e .
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

[kenneditodd]

@gaoxiangcao
I am working on modification calling and got up to preprocess to work. I'm currently resquiggling but it's taking a while to run. Here are the steps I have done so far that are working.

1. Basecall with guppy
2. Create new environment and install tombo with miniconda.
3. Use multi_to_single_fast5 (from ont_fast5_api) to convert your guppy multi-fast5 files (default output) to single-fast5.
4. Use the python code to fix your sequencing_summary.txt file

#!/usr/bin/python3

with open('sequencing_summary.txt') as file, open('sequencing_summary_fix.txt', 'w') as outfile:
    header = next(file)
    outfile.write(header)
    for line in file:
        line = line.split()
        line[0] = f"{line[1]}.fast5"
        line.append('\n')
        outfile.write("\t".join(line))

5. Run tombo preprocess
6. Run tombo resquiggle. Make sure you have the hdf5 plugin in order for this to work. Use the steps below for linux if you don't.

wget https://github.com/nanoporetech/vbz_compression/releases/download/v1.0.1/ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
tar xvzf ont-vbz-hdf-plugin-1.0.1-Linux-x86_64.tar.gz
export HDF5_PLUGIN_PATH=/your/path/to/ont-vbz-hdf-plugin-1.0.1-Linux/usr/local/hdf5/lib/plugin