search

interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
129 stars 44 forks source link

VIP.macOS.yml not working #98

Closed dfermin closed 10 months ago

dfermin commented 1 year ago

Hello I'm trying to install the latest version of cellxgene VIP on an M1 Mac studio machine.

I can successfully download the repo but the MacOS yaml file seems to have unresolved packages. Here is the command I'm running and the output:

mamba env create -n VIP --file VIP.macOS.yml

Looking for: ['_libgcc_mutex=0.1', 'backcall=0.2.0', 'backports=1.0', 'backports.functools_lru_cache=1.6.1', 'ca-certificates=2020.12.5', 'cairo=1.16.0', 'certifi=2020.12.5', 'decorator=4.4.2', 'fontconfig=2.13.1', 'freetype=2.10.4', 'glib=2.68.0', 'gmp=6.2.1', 'icu=64.2', 'ipykernel=5.4.3', 'ipython=7.20.0', 'ipython_genutils=0.2.0', 'jedi=0.18.0', 'jq=1.6', 'jupyter_client=6.1.11', 'jupyter_core=4.7.1', 'leidenalg=0.8.3', 'libedit=3.1.20191231', 'libffi=3.3', 'libgfortran4=7.5.0', 'libiconv=1.16', 'libpng=1.6.37', 'libsodium=1.0.18', 'libuuid=2.32.1', 'libuv=1.34.0', 'libxcb=1.13', 'libxml2=2.9.10', 'ncurses=6.2', 'nodejs=13.13.0', 'oniguruma=6.9.6', 'openssl=1.1.1h', 'pandoc=2.5', 'parso=0.8.1', 'pcre=8.44', 'pexpect=4.8.0', 'pickleshare=0.7.5', 'pip=20.3.3', 'pixman=0.38.0', 'prompt-toolkit=3.0.14', 'pthread-stubs=0.4', 'ptyprocess=0.7.0', 'pycairo=1.20.0', 'pygments=2.7.4', 'python=3.8.5', 'python-dateutil=2.8.1', 'python-igraph=0.8.2', 'python_abi=3.8', 'pyzmq=20.0.0', 'readline=8.1', 'setuptools=52.0.0', 'six=1.15.0', 'sqlite=3.33.0', 'texttable=1.6.3', 'tk=8.6.10', 'tornado=6.1', 'traitlets=5.0.5', 'wcwidth=0.2.5', 'wheel=0.36.2', 'xorg-kbproto=1.0.7', 'xorg-libice=1.0.10', 'xorg-libsm=1.2.3', 'xorg-libx11=1.6.12', 'xorg-libxau=1.0.9', 'xorg-libxdmcp=1.1.3', 'xorg-libxext=1.3.4', 'xorg-libxrender=0.9.10', 'xorg-renderproto=0.11.1', 'xorg-xextproto=7.3.0', 'xorg-xproto=7.0.31', 'xz=5.2.5', 'zeromq=4.3.3', 'zlib=1.2.11']

Could not solve for environment specs
The following packages are incompatible
├─ _libgcc_mutex 0.1**  does not exist (perhaps a typo or a missing channel);
├─ icu 64.2**  does not exist (perhaps a typo or a missing channel);
├─ leidenalg 0.8.3**  does not exist (perhaps a typo or a missing channel);
├─ libffi 3.3**  is requested and can be installed;
├─ libgfortran4 7.5.0**  does not exist (perhaps a typo or a missing channel);
├─ libuv 1.34.0**  does not exist (perhaps a typo or a missing channel);
├─ nodejs 13.13.0**  does not exist (perhaps a typo or a missing channel);
├─ pandoc 2.5**  does not exist (perhaps a typo or a missing channel);
├─ pixman 0.38.0**  does not exist (perhaps a typo or a missing channel);
├─ python-igraph 0.8.2**  does not exist (perhaps a typo or a missing channel);
├─ python 3.8.5**  is not installable because it requires
│  └─ libffi >=3.2.1,<3.3.0a0 , which conflicts with any installable versions previously reported;
└─ xorg-libx11 1.6.12**  does not exist (perhaps a typo or a missing channel).

Any suggestions for what edits to make to the VIP.macOS.yml file to fix this? Thanks

z5ouyang commented 10 months ago

Please check the 86aabcad9d69c7d536a3d97bfad31b693fac8c6c including a ONE STEP VIPlight installation for for macOS: install_VIPlight.macOS.sh (tested on M2 Ventura). Please reopen the issue, if encountering problems. Thanks for your interests!