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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
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Unable to install using Conda #62

Closed InfiniteLaugh closed 2 years ago

InfiniteLaugh commented 2 years ago

Hello!

I just ran Conda to install ViewBS and apparently, there's some conflicts in the environment, listed below. My perl version is v5.26.2 and python version 2.7.5 (python 3 also not working). I try to install the correct version of environments but it seemed not to work well. I was working on the research in DNA methylation and this software seems to meet my target. I will be delighted if you are willing to offer me some help! Best wishes & Happy Chinese new year !!!

` 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. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with a past explicit spec that is not an explicit spec in this operation (perl):

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package _libgcc_mutex conflicts for: _libgcc_mutex perl=5.26.2 -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='|0.1',build='main|conda_forge|main'] viewbs -> libgcc-ng[version='>=9.4.0'] -> _libgcc_mutex[version='|0.1',build='main|conda_forge|main'] perl-app-cpanminus -> libgcc -> _libgcc_mutex=[build=free] libgomp -> _libgcc_mutex==0.1[build='main|conda_forge'] _openmp_mutex -> _libgcc_mutex==0.1[build='main|conda_forge']

Package libgomp conflicts for: libgomp _openmp_mutex -> libgomp[version='>=7.5.0']

Package libgcc-ng conflicts for: viewbs -> libgcc-ng[version='>=9.3.0|>=9.4.0'] perl-app-cpanminus -> perl[version='>=5.26.2,<5.27.0a0'] -> libgcc-ng[version='>=7.2.0|>=7.5.0'] perl=5.26.2 -> libgcc-ng[version='>=7.2.0|>=7.5.0'] libgcc-ng viewbs -> perl[version='>=5.26.2,<5.26.3.0a0'] -> libgcc-ng[version='>=7.2.0|>=7.5.0|>=7.3.0']

Package _openmp_mutex conflicts for: perl=5.26.2 -> libgcc-ng[version='>=7.5.0'] -> _openmp_mutex[version='>=4.5'] viewbs -> libgcc-ng[version='>=9.4.0'] -> _openmp_mutex[version='>=4.5'] _openmp_mutex

Package libstdcxx-ng conflicts for: viewbs -> r-reshape2 -> libstdcxx-ng[version='7.2.0.*|>=7.2.0|>=7.3.0'] perl-app-cpanminus -> libgcc -> libstdcxx-ng[version='>=7.2.0']

Package perl conflicts for: perl-app-cpanminus -> perl[version='5.22.0.*|>=5.26.2,<5.27.0a0'] perl-app-cpanminus -> perl-threaded -> perl perl=5.26.2The following specifications were found to be incompatible with your system:

Your installed version is: 2.17

`

xie186 commented 2 years ago

Could you please let me know your conda version and the command lines you ran starting from how you built the environment? Thanks.

InfiniteLaugh commented 2 years ago

Could you please let me know your conda version and the command lines you ran starting from how you built the environment? Thanks.

Glad to receive your reply!

  1. My conda version is 4.11.0
  2. To verify the problem specifically, I, therefore, delete the previous environment that I modified many times and create a new one. The code is as follow:

conda create -n viewbs conda activate viewbs conda install -c bioconda viewbs

Then I received a shorter error:

` 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. Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with your system:

Your installed version is: 2.17

`

Under this environment, the perl version is 5.16.3, python version is 2.7.5 & 3.9.5.

Thanks again!

xie186 commented 2 years ago

Sorry for the late response. Not sure why this happens. Here is an alternative way to use ViewBS:

  1. install singularity on your server.
  2. Run the command line below: 
    singularity -d build viewbs0.1.11.img docker://xie186/viewbs:0.1.11

    You will get a file named viewbs0.1.11.img.

  3. Then you can use ViewBS:
singularity exec viewbs0.1.11.img ViewBS --help

Hope this helps. I'll try my best to fix the conda issue. Thanks again.

InfiniteLaugh commented 2 years ago

Sorry for the late response. Not sure why this happens. Here is an alternative way to use ViewBS:

  1. install singularity on your server.
  2. Run the command line below:
singularity -d build viewbs0.1.11.img docker://xie186/viewbs:0.1.11

You will get a file named viewbs0.1.11.img. 3. Then you can use ViewBS:

singularity exec viewbs0.1.11.img ViewBS --help

Hope this helps. I'll try my best to fix the conda issue. Thanks again.

Thanks for your answer!

I installed singularity and proceed the first command, and successfully got a file viewbs0.1.11.img: singularity -d build viewbs0.1.11.img docker://xie186/viewbs:0.1.11

However, the second command faced with FATAL error: singularity exec viewbs0.1.11.img ViewBS --help

The error information was as below:

INFO: Converting SIF file to temporary sandbox... FATAL: while extracting viewbs0.1.11.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create user namespace: user namespace disabled : exit status 1

I use root to run this command but get this instead: perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). /bin/bash: /usr/bin/lesspipe.sh: No such file or directory

Wish to receive your reply!

xie186 commented 2 years ago

Did you install singularity yourself? Or you just used the one already installed by the admins? Try to install it yourself using conda: https://anaconda.org/conda-forge/singularity

What's the version of singularity? Thanks.

InfiniteLaugh commented 2 years ago

Did you install singularity yourself? Or you just used the one already installed by the admins? Try to install it yourself using conda: https://anaconda.org/conda-forge/singularity

What's the version of singularity? Thanks.

I installed singularity using conda, and its version is 3.8.6 Then I run the command chown softwares:softwares /opt/local/cluster-utils/conda/envs/singularity371 followed by the instructing in this site: https://zhuanlan.zhihu.com/p/392073989

xie186 commented 2 years ago

This is becuase of the configuration of singularity. Please see the info here: https://sylabs.io/guides/3.5/admin-guide/user_namespace.html

I noticed there were some updates of conda. Please try the command line again:

conda create -n viewbs -c bioconda viewbs
InfiniteLaugh commented 2 years ago

This is becuase of the configuration of singularity. Please see the info here: https://sylabs.io/guides/3.5/admin-guide/user_namespace.html

I noticed there were some updates of conda. Please try the command line again:

conda create -n viewbs -c bioconda viewbs

Hello, Thanks for your answer. I tried conda to install viewbs again, but unfortunately, still not working. Therefore, I installed a virtual machine with centos on my PC and successfully installed the program with root. LOL Thanks again for your patient answers!