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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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installation through bioconda not working #779

Closed NuriaDiaz closed 2 years ago

NuriaDiaz commented 2 years ago

Hi, I'm trying to install hicexplorer with bioconda "conda install -c bioconda hicexplorer" and it isn't working. I get the following issue:

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.

Other conda packages can be installed without problem.

Thanks :)

joachimwolff commented 2 years ago

Please try mamba instead of conda: conda install mamba -c conda-forge mamba install hicexplorer -c condo-forge -c bioconda

NuriaDiaz commented 2 years ago

Also not working:

`(hic) diaz@uwe:/media/data/nuria/hic/bams$ conda install mamba -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/diaz/anaconda3/envs/hic

added / updated specs:

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
charset-normalizer-2.0.12  |     pyhd8ed1ab_0          35 KB  conda-forge
conda-4.11.0               |  py310hff52083_0        16.9 MB  conda-forge
conda-package-handling-1.7.3|  py310h6acc77f_1         1.0 MB  conda-forge
icu-69.1                   |       h9c3ff4c_0        13.2 MB  conda-forge
libarchive-3.5.2           |       hccf745f_1         1.6 MB  conda-forge
libmamba-0.21.2            |       h3985d26_0         1.5 MB  conda-forge
libmambapy-0.21.2          |  py310h69d3e99_0         320 KB  conda-forge
libsolv-0.7.19             |       h780b84a_5         445 KB  conda-forge
libxml2-2.9.12             |       h885dcf4_1         760 KB  conda-forge
mamba-0.21.2               |  py310hf87f941_0          42 KB  conda-forge
pybind11-abi-4             |       hd8ed1ab_3          10 KB  conda-forge
pycosat-0.6.3              |py310h6acc77f_1009         236 KB  conda-forge
pyopenssl-22.0.0           |     pyhd8ed1ab_0          49 KB  conda-forge
reproc-14.2.3              |       h7f98852_0          28 KB  conda-forge
reproc-cpp-14.2.3          |       h9c3ff4c_0          20 KB  conda-forge
ruamel_yaml-0.15.80        |py310h6acc77f_1006         724 KB  conda-forge
setuptools-60.9.2          |  py310hff52083_0         1.2 MB  conda-forge
tqdm-4.62.3                |     pyhd8ed1ab_0          80 KB  conda-forge
yaml-cpp-0.6.3             |       he1b5a44_4         208 KB  conda-forge
------------------------------------------------------------
                                       Total:        38.3 MB

The following NEW packages will be INSTALLED:

brotlipy conda-forge/linux-64::brotlipy-0.7.0-py310h6acc77f_1003 certifi conda-forge/linux-64::certifi-2021.10.8-py310hff52083_1 cffi conda-forge/linux-64::cffi-1.15.0-py310h0fdd8cc_0 charset-normalizer conda-forge/noarch::charset-normalizer-2.0.12-pyhd8ed1ab_0 colorama conda-forge/noarch::colorama-0.4.4-pyh9f0ad1d_0 conda conda-forge/linux-64::conda-4.11.0-py310hff52083_0 conda-package-han~ conda-forge/linux-64::conda-package-handling-1.7.3-py310h6acc77f_1 cryptography conda-forge/linux-64::cryptography-36.0.1-py310h685ca39_0 icu conda-forge/linux-64::icu-69.1-h9c3ff4c_0 idna conda-forge/noarch::idna-3.3-pyhd8ed1ab_0 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2 libarchive conda-forge/linux-64::libarchive-3.5.2-hccf745f_1 libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5 libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0 libmamba conda-forge/linux-64::libmamba-0.21.2-h3985d26_0 libmambapy conda-forge/linux-64::libmambapy-0.21.2-py310h69d3e99_0 libsolv conda-forge/linux-64::libsolv-0.7.19-h780b84a_5 libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000 libxml2 conda-forge/linux-64::libxml2-2.9.12-h885dcf4_1 lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1 lzo conda-forge/linux-64::lzo-2.10-h516909a_1000 mamba conda-forge/linux-64::mamba-0.21.2-py310hf87f941_0 pip conda-forge/noarch::pip-22.0.3-pyhd8ed1ab_0 pybind11-abi conda-forge/noarch::pybind11-abi-4-hd8ed1ab_3 pycosat conda-forge/linux-64::pycosat-0.6.3-py310h6acc77f_1009 pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0 pyopenssl conda-forge/noarch::pyopenssl-22.0.0-pyhd8ed1ab_0 pysocks conda-forge/linux-64::pysocks-1.7.1-py310hff52083_4 python conda-forge/linux-64::python-3.10.2-h62f1059_0_cpython python_abi conda-forge/linux-64::python_abi-3.10-2_cp310 readline conda-forge/linux-64::readline-8.1-h46c0cb4_0 reproc conda-forge/linux-64::reproc-14.2.3-h7f98852_0 reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.3-h9c3ff4c_0 requests conda-forge/noarch::requests-2.27.1-pyhd8ed1ab_0 ruamel_yaml conda-forge/linux-64::ruamel_yaml-0.15.80-py310h6acc77f_1006 setuptools conda-forge/linux-64::setuptools-60.9.2-py310hff52083_0 six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0 sqlite conda-forge/linux-64::sqlite-3.37.0-h9cd32fc_0 tqdm conda-forge/noarch::tqdm-4.62.3-pyhd8ed1ab_0 tzdata conda-forge/noarch::tzdata-2021e-he74cb21_0 urllib3 conda-forge/noarch::urllib3-1.26.8-pyhd8ed1ab_1 wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0 yaml conda-forge/linux-64::yaml-0.2.5-h7f98852_2 yaml-cpp conda-forge/linux-64::yaml-cpp-0.6.3-he1b5a44_4 zstd conda-forge/linux-64::zstd-1.5.2-ha95c52a_0

Proceed ([y]/n)? y

Downloading and Extracting Packages libxml2-2.9.12 | 760 KB | ################################################################################################################## | 100% pybind11-abi-4 | 10 KB | ################################################################################################################## | 100% pycosat-0.6.3 | 236 KB | ################################################################################################################## | 100% setuptools-60.9.2 | 1.2 MB | ################################################################################################################## | 100% conda-4.11.0 | 16.9 MB | ################################################################################################################## | 100% yaml-cpp-0.6.3 | 208 KB | ################################################################################################################## | 100% conda-package-handli | 1.0 MB | ################################################################################################################## | 100% pyopenssl-22.0.0 | 49 KB | ################################################################################################################## | 100% charset-normalizer-2 | 35 KB | ################################################################################################################## | 100% libsolv-0.7.19 | 445 KB | ################################################################################################################## | 100% libmamba-0.21.2 | 1.5 MB | ################################################################################################################## | 100% tqdm-4.62.3 | 80 KB | ################################################################################################################## | 100% libmambapy-0.21.2 | 320 KB | ################################################################################################################## | 100% libarchive-3.5.2 | 1.6 MB | ################################################################################################################## | 100% ruamel_yaml-0.15.80 | 724 KB | ################################################################################################################## | 100% mamba-0.21.2 | 42 KB | ################################################################################################################## | 100% reproc-14.2.3 | 28 KB | ################################################################################################################## | 100% reproc-cpp-14.2.3 | 20 KB | ################################################################################################################## | 100% icu-69.1 | 13.2 MB | ################################################################################################################## | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done (hic) diaz@uwe:/media/data/nuria/hic/bams$ mamba install hicexplorer -c condo-forge -c bioconda

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███████████████/ /██/ /██/ /██/ /████████████████████████ / / \ / \ / \ / \ _ / / _/ _/ _/ \ o _, / _/ ___/ ` |/ ███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗ ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗ ██╔████╔██║███████║██╔████╔██║██████╔╝███████║ ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║ ██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║ ╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝

    mamba (0.21.2) supported by @QuantStack

    GitHub:  https://github.com/mamba-org/mamba
    Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['hicexplorer']

condo-forge/linux-64 12.6kB @ 25.3kB/s 404 failed 0.5s r/linux-64 595.8kB @ 861.3kB/s 0.2s [+] 1.1s condo-forge/noarch ━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0.0 B / ??.?MB @ ??.?MB/s 1.1s bioconda/linux-64 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━ 427.8kB / ??.?MB @ 401.7kB/s 1.1s bioconda/noarch ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1MB / ??.?MB @ 1.9MB/s 1.1s conda-forge/linux-64 ━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3MB / ??.?MB @ 3.1MB/s 1.1s pkgs/main/linux-64 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.3MB / ??.?MB @ 1.3MB/s 0.4s

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/conda/exceptions.py", line 1080, in __call__
    return func(*args, **kwargs)
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/mamba/mamba.py", line 940, in exception_converter
    raise e
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/mamba/mamba.py", line 934, in exception_converter
    exit_code = _wrapped_main(*args, **kwargs)
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/mamba/mamba.py", line 890, in _wrapped_main
    result = do_call(args, p)
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/mamba/mamba.py", line 752, in do_call
    exit_code = install(args, parser, "install")
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/mamba/mamba.py", line 496, in install
    index = load_channels(pool, channels, repos)
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/mamba/utils.py", line 122, in load_channels
    index = get_index(
  File "/home/diaz/anaconda3/envs/hic/lib/python3.10/site-packages/mamba/utils.py", line 103, in get_index
    is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Multi-download failed.

$ /home/diaz/anaconda3/envs/hic/bin/mamba install hicexplorer -c condo-forge -c bioconda

environment variables: CIO_TEST= CONDA_DEFAULT_ENV=hic CONDA_EXE=/home/diaz/anaconda3/bin/conda CONDA_PREFIX=/home/diaz/anaconda3/envs/hic CONDA_PREFIX_1=/home/diaz/anaconda3 CONDA_PROMPT_MODIFIER=(hic) CONDA_PYTHON_EXE=/home/diaz/anaconda3/bin/python CONDA_ROOT=/home/diaz/anaconda3/envs/hic CONDA_SHLVL=2 CURL_CA_BUNDLE= PATH=/home/diaz/bin:/home/diaz/anaconda3/envs/hic/bin:/home/diaz/anaconda3/ condabin:/home/diaz/bin:/home/diaz:/home/diaz/cellranger- arc/cellranger-arc-2.0.0:/media/data/nuria/single_cell/cellranger- 4.0.0:/media/data/nuria/nanopore/ont-guppy-cpu/bin:/usr/local/sbin:/us r/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games: /snap/bin:/home/diaz/anaconda3/envs/homer/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE= UBUNTU_MENUPROXY=

 active environment : base
active env location : /home/diaz/anaconda3/envs/hic
        shell level : 2
   user config file : /home/diaz/.condarc

populated config files : /home/diaz/.condarc conda version : 4.11.0 conda-build version : not installed python version : 3.10.2.final.0 virtual packages : linux=5.13.0=0 glibc=2.34=0 unix=0=0 archspec=1=x86_64 base environment : /home/diaz/anaconda3/envs/hic (writable) conda av data dir : /home/diaz/anaconda3/envs/hic/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/condo-forge/linux-64 https://conda.anaconda.org/condo-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://conda.anaconda.org/r/linux-64 https://conda.anaconda.org/r/noarch package cache : /home/diaz/anaconda3/envs/hic/pkgs /home/diaz/.conda/pkgs envs directories : /home/diaz/anaconda3/envs/hic/envs /home/diaz/.conda/envs platform : linux-64 user-agent : conda/4.11.0 requests/2.27.1 CPython/3.10.2 Linux/5.13.0-23-generic ubuntu/21.10 glibc/2.34 UID:GID : 1003:1003 netrc file : None condo-forge/noarch 12.6kB @ 11.3kB/s 404 failed 1.1s (hic) diaz@uwe:/media/data/nuria/hic/bams$ `

ebioman commented 1 year ago

Hi little note here, you used

Please try mamba instead of conda: conda install mamba -c conda-forge mamba install hicexplorer -c condo-forge -c bioconda

Hi little note, it should be:

mamba install hicexplorer -c conda-forge -c bioconda not condo. Mamba is not catching that...

NuriaDiaz commented 1 year ago

Thanks for the note!

ratheraarif commented 3 months ago

I got the following error while installing


bioconda/osx-arm64 (check zst)                      Checked  0.5s
bioconda/noarch (check zst)                         Checked  0.1s
pkgs/main/osx-arm64 (check zst)                    Checked  0.1s
pkgs/main/noarch (check zst)                       Checked  0.0s
pkgs/r/osx-arm64 (check zst)                        Checked  0.0s
pkgs/r/noarch (check zst)                          Checked  0.0s
bioconda/osx-arm64                                 354.0 B @   2.1kB/s  0.2s
pkgs/main/noarch                                   714.2kB @ 461.6kB/s  1.4s
conda-forge/osx-arm64                               10.2MB @   3.3MB/s  3.1s
pkgs/r/osx-arm64                                   108.0 B @  33.0 B/s  0.1s
pkgs/r/noarch                                        2.1MB @ 518.0kB/s  2.4s
pkgs/main/osx-arm64                                  2.5MB @ 596.0kB/s  4.1s
bioconda/noarch                                      5.3MB @   1.0MB/s  5.1s
conda-forge/noarch                                  15.0MB @   2.1MB/s  7.1s

Pinned packages:
  - python 3.11.*

Could not solve for environment specs
The following packages are incompatible
└─ hicexplorer is not installable because there are no viable options
   ├─ hicexplorer [2.2|2.2.1|2.2.2|2.2.3] would require
   │  └─ pybigwig, which does not exist (perhaps a missing channel);
   ├─ hicexplorer 3.0.1 would require
   │  └─ krbalancing >=0.0.4 , which does not exist (perhaps a missing channel);
   ├─ hicexplorer 3.0.2 would require
   │  └─ krbalancing 0.0.4 , which does not exist (perhaps a missing channel);
   ├─ hicexplorer [3.1|3.2|...|3.7.4] would require
   │  └─ krbalancing >=0.0.5 , which does not exist (perhaps a missing channel);
   └─ hicexplorer [3.5.2|3.5.3|...|3.7.2] would require
      └─ biopython <1.77 , which does not exist (perhaps a missing channel).
joachimwolff commented 3 months ago

Please do not post in long closed issues.

The issue you have is macOS specific, we do not support arm-64 platform so far. Therefore you have to install hicexplorer to a x86 environment and run it via Apple Rosetta 2. To do so, you have to define the x86 folder to enforce the architecture change:

CONDA_SUBDIR=osx-64 conda create -n hicexplorer_x86_environment python=3.10 hicexplorer=3.7.3