Question

我正在尝试在Ubuntu 18.04中安装一个名为WisecondorX的软件来进行基因分析。我在下面输入以下行：

conda install wisecondorx

并获得以下输出：

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: | 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
Examining backports.functools_lru_cache:  59%|▌| 104/176 [00:00<00:00, 
45709.69iExamining tk:  60%|██████████████▎         | 105/176 [00:00<00:00, 45751.29it/s]failed                                                       >                   

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

Specifications:

  - wisecondorx -> python[version='2.7.*|>=2.7,<2.8.0a0']

Your python: python=3.6

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 each other:

Package bioconductor-dnacopy conflicts for:
wisecondorx -> bioconductor-dnacopy
Package openssl conflicts for:
python=3.6 -> openssl[version='1.0.*|1.0.*,>=1.0.2l,<1.0.3a|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1c,<1.1.2a']
Package scikit-learn conflicts for:
wisecondorx -> scikit-learn
Package numpy conflicts for:
wisecondorx -> numpy
Package tk conflicts for:
python=3.6 -> tk[version='8.5.*|8.6.*|>=8.6.7,<8.7.0a0|>=8.6.8,<8.7.0a0|>=8.6.9,<8.7.0a0']
Package zlib conflicts for:
python=3.6 -> zlib[version='1.2.*|1.2.11|1.2.8|>=1.2.11,<1.3.0a0']
Package scipy conflicts for:
wisecondorx -> scipy
Package pip conflicts for:
python=3.6 -> pip
Package readline conflicts for:
python=3.6 -> readline[version='6.2.*|7.*|7.0|>=7.0,<8.0a0|>=8.0,<9.0a0']
Package r-png conflicts for:
wisecondorx -> r-png
Package libstdcxx-ng conflicts for:
python=3.6 -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
Package futures conflicts for:
wisecondorx -> futures
Package libffi conflicts for:
python=3.6 -> libffi[version='3.2.*|>=3.2.1,<3.3.0a0|>=3.2.1,<4.0a0']
Package xz conflicts for:
python=3.6 -> xz[version='5.2.*|>=5.2.3,<5.3.0a0|>=5.2.3,<6.0a0|>=5.2.4,<5.3.0a0|>=5.2.4,<6.0a0']
Package libgcc-ng conflicts for:
python=3.6 -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
Package pysam conflicts for:
wisecondorx -> pysam
Package ncurses conflicts for:
python=3.6 -> ncurses[version='5.9|5.9.*|6.0.*|>=6.0,<7.0a0|>=6.1,<6.2.0a0|>=6.1,<7.0a0']
Package bzip2 conflicts for:
python=3.6 -> bzip2[version='>=1.0.6,<2.0a0']
Package sqlite conflicts for:
python=3.6 -> sqlite[version='3.13.*|3.20.*|>=3.20.1,<4.0a0|>=3.22.0,<4.0a0|>=3.23.1,<4.0a0|>=3.24.0,<4.0a0|>=3.25.2,<4.0a0|>=3.25.3,<4.0a0|>=3.26.0,<4.0a0|>=3.28.0,<4.0a0|>=3.29.0,<4.0a0|>=3.30.1,<4.0a0']
Package r-jsonlite conflicts for:
wisecondorx -> r-jsonlite[version='>=1.5']

有关如何解决的任何线索？

Answer 1

我没有使用conda，因为我发现使用pyenv可以更轻松地管理多环境python版本。我下载了该软件包，并在虚拟化的python环境（3.8）中对其进行了编译。我再次在相同的虚拟化设置中手动编译了R包。

Answer 2

嘿，我刚遇到这个问题。我可以使用以下方法解决此问题：

# Create an env, and activate it
$ conda create --name test python=3.6  
$ conda activate test

# Clone and jump into the WisecondorX repo (assumping you already have an ssh key added to your github account)

$ git clone git@github.com:CenterForMedicalGeneticsGhent/WisecondorX.git
$ cd WisecondorX


# Use your environment's python to install the required python packages (Note you will have to install the R dependencies separately using conda).

$ which python
~/.conda/envs/test/bin/python
python setup.py install


# Check to see if WisecondorX has been installed in the test env

$ which WisecondorX
~/.conda/envs/test/bin/WisecondorX

$ WisecondorX newref --help
usage: WisecondorX newref [-h] [--nipt] [--yfrac YFRAC] [--refsize REFSIZE]
                          [--binsize BINSIZE] [--cpus CPUS]
                          infiles [infiles ...] outfile

Create a new reference using healthy reference samples

positional arguments:
  infiles            Path to all reference data files (e.g.
                     path/to/reference/*.npz)
  outfile            Path and filename for the reference output (e.g.
                     path/to/myref.npz)

optional arguments:
  -h, --help         show this help message and exit
  --nipt             Use flag for NIPT (e.g. path/to/reference/*.npz)
                     (default: False)
  --yfrac YFRAC      Use to manually set the y read fraction cutoff, which
                     defines gender (default: None)
  --refsize REFSIZE  Amount of reference locations per target (default: 300)
  --binsize BINSIZE  Scale samples to this binsize, multiples of existing
                     binsize only (default: 100000.0)
  --cpus CPUS        Use multiple cores to find reference bins (default: 1)

紧线！

使用conda安装WisecondorX时出错

2 个答案: