Open vymao opened 3 years ago
Hi- Sorry about that. Can you show the commands you used to install cnv_facets?
The documentation has:
conda create -n my_project
conda activate my_project
conda install -c bioconda -c conda-forge cnv_facets
And it should work. However, I should update it and recommend to install mamba first and then use mamba install ...
instead of conda install ...
. Mamba is a lot better than conda install
so I would suggest that regardless of cnv_facets.
So install with something like:
# Install mamba in base environment
conda install mamba
# As per bioconda https://bioconda.github.io/user/install.html#set-up-channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create -n my_project
conda activate my_project
mamba install cnv_facets
Having said that, I tested it just now and it works for me. However, I'm slightly surprised that argparse
is installed at all since the recipe for cnv_facets doesn't list r-argparse
at the moment. (I'll investigate...). (Update: r-argparse
is installed by build.sh
)
See also issue https://github.com/dariober/cnv_facets/issues/35
I have tried the same command line as you suggested to download the CNV_facets and there is no activity in the system it just gets stuck at the solving environment state.
`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`
The command line used for the purpose of installing CNV_facets is the
conda create -n my_project conda activate my_project conda install -c bioconda -c conda-forge cnv_facets
Please help with this.
Nope, it doesn't work either...
Collecting package metadata (current_repodata.json): done
Solving environment: done
==> WARNING: A newer version of conda exists. <==
current version: 4.7.10
latest version: 23.5.0
Please update conda by running
$ conda update -n base -c defaults conda
## Package Plan ##
environment location: /home/jgarces/.conda/envs/cnv_facets
added / updated specs:
- mamba
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
boltons conda-forge/noarch::boltons-23.0.0-pyhd8ed1ab_0
brotli conda-forge/linux-64::brotli-1.0.9-h166bdaf_8
brotli-bin conda-forge/linux-64::brotli-bin-1.0.9-h166bdaf_8
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.19.1-hd590300_0
ca-certificates conda-forge/linux-64::ca-certificates-2023.5.7-hbcca054_0
certifi conda-forge/noarch::certifi-2023.5.7-pyhd8ed1ab_0
cffi conda-forge/linux-64::cffi-1.15.1-py310h255011f_3
charset-normalizer conda-forge/noarch::charset-normalizer-3.1.0-pyhd8ed1ab_0
colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
conda conda-forge/linux-64::conda-23.3.1-py310hff52083_0
conda-package-han~ conda-forge/noarch::conda-package-handling-2.0.2-pyh38be061_0
conda-package-str~ conda-forge/noarch::conda-package-streaming-0.8.0-pyhd8ed1ab_0
cryptography conda-forge/linux-64::cryptography-40.0.2-py310h34c0648_0
fmt conda-forge/linux-64::fmt-9.1.0-h924138e_0
icu conda-forge/linux-64::icu-72.1-hcb278e6_0
idna conda-forge/noarch::idna-3.4-pyhd8ed1ab_0
jsonpatch conda-forge/noarch::jsonpatch-1.32-pyhd8ed1ab_0
jsonpointer conda-forge/noarch::jsonpointer-2.0-py_0
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.20.1-h81ceb04_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
libarchive conda-forge/linux-64::libarchive-3.6.2-h039dbb9_1
libbrotlicommon conda-forge/linux-64::libbrotlicommon-1.0.9-h166bdaf_8
libbrotlidec conda-forge/linux-64::libbrotlidec-1.0.9-h166bdaf_8
libbrotlienc conda-forge/linux-64::libbrotlienc-1.0.9-h166bdaf_8
libcurl conda-forge/linux-64::libcurl-8.1.1-h409715c_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19
libgomp conda-forge/linux-64::libgomp-12.2.0-h65d4601_19
libiconv conda-forge/linux-64::libiconv-1.17-h166bdaf_0
libmamba conda-forge/linux-64::libmamba-1.4.2-hcea66bb_0
libmambapy conda-forge/linux-64::libmambapy-1.4.2-py310h1428755_0
libnghttp2 conda-forge/linux-64::libnghttp2-1.52.0-h61bc06f_0
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libsolv conda-forge/linux-64::libsolv-0.7.23-h3eb15da_0
libsqlite conda-forge/linux-64::libsqlite-3.42.0-h2797004_0
libssh2 conda-forge/linux-64::libssh2-1.10.0-hf14f497_3
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libxml2 conda-forge/linux-64::libxml2-2.11.4-h0d562d8_0
libzlib conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4
lz4-c conda-forge/linux-64::lz4-c-1.9.4-hcb278e6_0
lzo conda-forge/linux-64::lzo-2.10-h516909a_1000
mamba conda-forge/linux-64::mamba-1.4.2-py310h51d5547_0
ncurses conda-forge/linux-64::ncurses-6.3-h27087fc_1
openssl conda-forge/linux-64::openssl-3.1.0-hd590300_3
packaging conda-forge/noarch::packaging-23.1-pyhd8ed1ab_0
pip conda-forge/noarch::pip-23.1.2-pyhd8ed1ab_0
pluggy conda-forge/noarch::pluggy-1.0.0-pyhd8ed1ab_5
pybind11-abi conda-forge/noarch::pybind11-abi-4-hd8ed1ab_3
pycosat conda-forge/linux-64::pycosat-0.6.4-py310h5764c6d_1
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pyopenssl conda-forge/noarch::pyopenssl-23.1.1-pyhd8ed1ab_0
pysocks conda-forge/linux-64::pysocks-1.7.1-py310hff52083_5
python conda-forge/linux-64::python-3.10.11-he550d4f_0_cpython
python_abi conda-forge/linux-64::python_abi-3.10-3_cp310
readline conda-forge/linux-64::readline-8.2-h8228510_1
reproc conda-forge/linux-64::reproc-14.2.4-h0b41bf4_0
reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.4-hcb278e6_0
requests conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
ruamel.yaml conda-forge/linux-64::ruamel.yaml-0.17.27-py310h2372a71_0
ruamel.yaml.clib conda-forge/linux-64::ruamel.yaml.clib-0.2.7-py310h1fa729e_1
setuptools conda-forge/noarch::setuptools-67.7.2-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.12-h27826a3_0
toolz conda-forge/noarch::toolz-0.12.0-pyhd8ed1ab_0
tqdm conda-forge/noarch::tqdm-4.65.0-pyhd8ed1ab_1
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
urllib3 conda-forge/noarch::urllib3-2.0.2-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.40.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
yaml-cpp conda-forge/linux-64::yaml-cpp-0.7.0-h27087fc_2
zstandard conda-forge/linux-64::zstandard-0.19.0-py310hdeb6495_1
zstd conda-forge/linux-64::zstd-1.5.2-h3eb15da_6
Proceed ([y]/n)?
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(656): An error occurred while installing package 'conda-forge::pip-23.1.2-pyhd8ed1ab_0'.
Rolling back transaction: done
[Errno 2] No such file or directory: '/home/jgarces/.conda/envs/cnv_facets/lib/python3.1/site-packages/pip/_vendor/tenacity/__init__.py'
(FileNotFoundError(2, 'No such file or directory'), FileNotFoundError(2, 'No such file or directory'))
Hi,
I tried installing
cnv_facets
through conda as specified, but I am running into an issue when running the calling:I tried installing argparse through conda as well but I am getting an incompatability issue:
Is there a proper way to install this?