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Tian-Dechao / diffDomain

DiffDomain is a statistically sound method for detecting differential TADs between conditions
MIT License
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diffDomain installation #17

Open architghosh opened 4 months ago

architghosh commented 4 months ago

Hi,

We're facing a few failed attempts when trying to install diffdomain on our HPC cluster (from the container itself)... For approach one, a conda environment, we tried our personal account on a standalone server with internet access, because it appears to access a mirror site is not in our firewall list. the error message with the command line conda env create --name diffdomain -f environment_linux.yml

... CondaEnvException: Pip failed Pip subprocess error: ERROR: Ignored the following versions that require a different python version: 0.12.0 Requires-Python >=3.8; 0.12.0rc1 Requires-Python >=3.8; 0.12.1 Requires-Python >=3.8 ERROR: Could not find a version that satisfies the requirement diffdomain-py3==0.2.0 (from versions: 0.1.0, 0.1.1, 0.1.2, 0.1.3, 0.1.4, 0.1.6, 0.1.7, 0.1.8, 0.1.9, 0.2.1, 0.2.2) ERROR: No matching distribution found for diffdomain-py3==0.2.0

For a container approach, I am able to pull a apptainer image on a login node on seadragon2 using the command: apptainer pull docker://guming5/diffdomain-centos7:v1 But the instruction of using the container, " "In this image, there is a contact conda environment named diffdomain (/home/work/.conda/envs/diffdomain) meeting all requests, in which you can use the diffDomain Python3 version directly." I failed to change to user 'work', it asks a password.

I was wondering if you could provide any suggestions to resolve the above errors.

Thank you!

Archit

varunkas commented 4 days ago

I have the same problem. In my local machine, running docker, I am able to switch user to "work". But when running using singularity, su work asks for a password. Can you please help? Thanks

varunkas commented 3 days ago

After reading a bit, I realise that su work inside an singularity container is only possible when it is launched with singularity shell --fakeroot option. However, our HPC does not allow this... I am wondering if there is any other way? Is it possible to get a version of the docker image, where the conda environments are installed outside of the home environment? Thank you very much!

Tian-Dechao commented 3 days ago

Please first try install DiffDomain with other options.

Thank you for your suggestion. While we plan to incorporate this feature into the updated Docker version of DiffDomain, it won't be implemented in the coming weeks.

varunkas commented 3 days ago

Dear @Tian-Dechao , thank you very much for getting back to me. Yes, I did try installation with Conda earlier, but I got an error when running the python script. Turns out that the error was not related to the installation, but rather to the header in the TAD.bedpe file generated by arrowhead. Once I removed these headers, everything ran through. And the results look great! Thank you very much for the nice tool.