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atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
MIT License
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conda install: can't import samap #137

Open jowodo opened 7 months ago

jowodo commented 7 months ago

This is how I installed samap: 

conda create -y -n samap-1.0.15 -c bioconda samap=1.0.15

Then, I wanted to test it: 

conda activate samap-1.0.15
python3 -c 'import samap'

This was the output:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/samap/__init__.py", line 6, in <module>
    import scanpy as sc
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/scanpy/__init__.py", line 18, in <module>
    from . import datasets, logging, queries, external, get
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/scanpy/external/__init__.py", line 3, in <module>
    from . import pp
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/scanpy/external/pp/__init__.py", line 5, in <module>
    from ._magic import magic
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/scanpy/external/pp/_magic.py", line 7, in <module>
    from legacy_api_wrap import legacy_api
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/legacy_api_wrap.py", line 21, in <module>
    __version__ = get_version(__file__)
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/get_version/__init__.py", line 273, in get_version
    version = method(parent)
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/get_version/__init__.py", line 118, in get_version_from_vcs
    vcs_root = find_vcs_root(parent, vcs=vcs)
  File "/home/apps/conda/miniconda3/envs/samap-1.0.15/lib/python3.7/site-packages/get_version/__init__.py", line 151, in find_vcs_root
    vcs_e = _detect_vcs()
TypeError: _detect_vcs() missing 2 required positional arguments: 'expected_vcs' and 'path'

Related: #16

jowodo commented 7 months ago

The manual conda install worked nearly as specified in the README. I only had to add anndata to the conda packages. 

VERSION=1.0.15
URL='https://github.com/atarashansky/SAMap'
DESCRIPTION="SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms."
ENVNAME="samap"
LATESTVERSIONCMD='wget -q -O - https://raw.githubusercontent.com/atarashansky/SAMap/main/README.md | head -n1 | cut -d" " -f5'
conda create -y -n $ENVNAME-$VERSION -c conda-forge python=3.9 numpy=1.23.5 pip pybind11 h5py=3.8.0 leidenalg python-igraph texttable anndata # anndata was added here!
conda activate $ENVNAME-$VERSION
mkdir -p $CONDA_PREFIX/share
pushd $CONDA_PREFIX/share
git clone https://github.com/atarashansky/SAMap.git samap.git
pushd samap.git
python3 -m pip install .
popd
popd
`conda list # manual installation` ``` $ conda list WARNING conda.gateways.disk.delete:unlink_or_rename_to_trash(188): Could not remove or rename /home/apps/conda/miniconda3/envs/samap-1.0.15/conda-meta/python-igraph-0.11.3-py39h007bc96_1.json. Please remove this file manually (you may need to reboot to free file handles) # packages in environment at /home/apps/conda/miniconda3/envs/samap-1.0.15: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge anndata 0.10.3 pyhd8ed1ab_0 conda-forge arpack 3.8.0 nompi_h0baa96a_101 conda-forge array-api-compat 1.4 pyhd8ed1ab_0 conda-forge bleach 6.1.0 pypi_0 pypi bokeh 3.2.2 pypi_0 pypi bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.24.0 hd590300_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2023.11.17 pypi_0 pypi charset-normalizer 3.3.2 pypi_0 pypi colorcet 3.0.1 pypi_0 pypi contourpy 1.2.0 pypi_0 pypi cycler 0.12.1 pypi_0 pypi dill 0.3.7 pypi_0 pypi exceptiongroup 1.2.0 pyhd8ed1ab_0 conda-forge fast-histogram 0.12 pypi_0 pypi fonttools 4.47.0 pypi_0 pypi glpk 5.0 h445213a_0 conda-forge gmp 6.3.0 h59595ed_0 conda-forge h5py 3.8.0 nompi_py39h89bf01e_101 conda-forge harmonypy 0.0.9 pypi_0 pypi hdf5 1.14.0 nompi_hb72d44e_103 conda-forge hnswlib 0.7.0 pypi_0 pypi holoviews-samap 1.0.1 pypi_0 pypi icu 73.2 h59595ed_0 conda-forge idna 3.6 pypi_0 pypi igraph 0.10.8 pypi_0 pypi importlib-metadata 7.0.0 pypi_0 pypi importlib-resources 6.1.1 pypi_0 pypi jinja2 3.1.2 pypi_0 pypi joblib 1.3.2 pypi_0 pypi keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 pypi_0 pypi krb5 1.21.2 h659d440_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge leidenalg 0.10.1 py39h3d6467e_1 conda-forge libaec 1.1.2 h59595ed_1 conda-forge libblas 3.9.0 20_linux64_openblas conda-forge libcblas 3.9.0 20_linux64_openblas conda-forge libcurl 8.5.0 hca28451_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libiconv 1.17 hd590300_2 conda-forge liblapack 3.9.0 20_linux64_openblas conda-forge libleidenalg 0.11.1 h00ab1b0_0 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxml2 2.12.3 h232c23b_0 conda-forge libzlib 1.2.13 hd590300_5 conda-forge linkify-it-py 2.0.2 pypi_0 pypi llvmlite 0.39.1 pypi_0 pypi markdown 3.5.1 pypi_0 pypi markdown-it-py 3.0.0 pypi_0 pypi markupsafe 2.1.3 pypi_0 pypi matplotlib 3.8.2 pypi_0 pypi mdit-py-plugins 0.4.0 pypi_0 pypi mdurl 0.1.2 pypi_0 pypi natsort 8.4.0 pyhd8ed1ab_0 conda-forge ncurses 6.4 h59595ed_2 conda-forge networkx 3.2.1 pypi_0 pypi numba 0.56.3 pypi_0 pypi numpy 1.23.5 py39h3d75532_0 conda-forge openssl 3.2.0 hd590300_1 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge pandas 2.1.4 py39hddac248_0 conda-forge panel 1.2.3 pypi_0 pypi param 1.13.0 pypi_0 pypi patsy 0.5.4 pypi_0 pypi pillow 10.1.0 pypi_0 pypi pip 23.3.2 pyhd8ed1ab_0 conda-forge pybind11 2.11.1 py39h7633fee_2 conda-forge pybind11-global 2.11.1 py39h7633fee_2 conda-forge pyct 0.5.0 pypi_0 pypi pynndescent 0.5.11 pypi_0 pypi pyparsing 3.1.1 pypi_0 pypi python 3.9.18 h0755675_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.9 4_cp39 conda-forge pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge pyviz-comms 3.0.0 pypi_0 pypi pyyaml 6.0.1 pypi_0 pypi readline 8.2 h8228510_1 conda-forge requests 2.31.0 pypi_0 pypi sam-algorithm 1.0.2 pypi_0 pypi samap 1.0.15 pypi_0 pypi scanpy 1.9.3 pypi_0 pypi scikit-learn 1.3.2 pypi_0 pypi scipy 1.11.4 py39h474f0d3_0 conda-forge seaborn 0.13.0 pypi_0 pypi session-info 1.0.0 pypi_0 pypi setuptools 68.2.2 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge statsmodels 0.14.1 pypi_0 pypi stdlib-list 0.10.0 pypi_0 pypi texttable 1.7.0 pyhd8ed1ab_0 conda-forge threadpoolctl 3.2.0 pypi_0 pypi tk 8.6.13 noxft_h4845f30_101 conda-forge tornado 6.4 pypi_0 pypi tqdm 4.66.1 pypi_0 pypi typing-extensions 4.9.0 pypi_0 pypi tzdata 2023c h71feb2d_0 conda-forge uc-micro-py 1.0.2 pypi_0 pypi umap-learn 0.5.5 pypi_0 pypi urllib3 2.1.0 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi wheel 0.42.0 pyhd8ed1ab_0 conda-forge xyzservices 2023.10.1 pypi_0 pypi xz 5.2.6 h166bdaf_0 conda-forge zipp 3.17.0 pypi_0 pypi zstd 1.5.5 hfc55251_0 conda-forge ```