Cannot install latest DeepVariant via Conda

[lok27395]

Describe the issue: Cannot install latest DeepVariant via Conda in my new environment

Error prompts, similar to that of #736

If having everything in default, I can have python=2.7 and deepvariant=0.7.0; but cannot update to 1.15 or latest

Setup

• Operating system: CentOS Linux release 7.4.1708 (ssh to university, docker unavailable)
• DeepVariant version: 0.7.0 installable, but cannot get 1.15 or latest
• Installation method (Docker, built from source, etc.): conda
• Type of data: N/A

Steps to reproduce:

• Command: $ create -n deepvariant python=3.8 (current version 3.8.19) $ conda install deepvariant

• Error trace: (if applicable)

#warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY - many times warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE warning libmamba Problem type not implemented SOLVER_RULE_STRICT_REPO_PRIORITY - many times failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• package deepvariant-0.4.1-np113py27_0 requires python 2.7*, but none of the providers can be installed

Could not solve for environment specs The following packages are incompatible ├─ deepvariant is installable with the potential options │ ├─ deepvariant [0.10.0|0.7.2|0.8.0|0.9.0] would require │ │ └─ tensorflow 1.12.* , which conflicts with any installable versions previously reported; │ ├─ deepvariant [0.10.0|1.0.0] would require │ │ └─ tensorflow 2.0.* , which conflicts with any installable versions previously reported; │ ├─ deepvariant [0.4.1|0.6.0|0.6.1|0.7.0] would require │ │ └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed; │ ├─ deepvariant [0.7.1|0.7.2] would require │ │ └─ tensorflow 1.11.* , which conflicts with any installable versions previously reported; │ └─ deepvariant [1.0.0|1.1.0|...|1.5.0] would require │ └─ tensorflow-estimator 2.0.* , which conflicts with any installable versions previously reported; └─ pin-1 is not installable because it requires └─ python 3.8.* , which conflicts with any installable versions previously reported.

Thanks guys.

[lok27395]

have also tried instruction by

pichuan

but still the same

[lucasbrambrink]

Hi,

Just to make sure I understand the issue: you are able to successfully install DeepVariant 0.7.0 with Python 2.7, but you are unable to install 1.15 or later; the goal is for you to install the latest version of DeepVariant, 1.6.0.

The relevant error that I see is:

deepvariant [1.0.0|1.1.0|...|1.5.0] would require
│ └─ tensorflow-estimator 2.0.* , which conflicts with any installable versions previously reported;

Is it possible to resolve this conflict? I will try myself to see if I can get it to work on GCP, and report back.

[lok27395]

Hi Lucas,

yes, the only version I can install is DeepVariant 0.7.0.

I tried to install tensorflow-estimator first (v2.13.1) but still have same error as mentioned.

Thanks!

[pichuan]

Hi @lok27395 , unfortunately, our team doesn't officially support the Conda version. I'll close this issue now.