SAMap
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atarashansky
conda install: can't import samap
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
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