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EichlerLab / smrtsv2

Structural variant caller
MIT License
53 stars 6 forks source link

Python problem #47

Closed woodoo46 closed 4 years ago

woodoo46 commented 4 years ago

Hi,

When I tried to install smrtsv2, I had the following problem

**UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment:

Specifications:

Your python: python=3.6.2**

What should I do to solve it? Thanks!

paudano commented 4 years ago

Are you installing this on Linux?

I tried building the dependencies on the latest commit (2.0.1) in case something change, but I am unable to replicate this error. Given the versions, I thought Conda would provide a consistent environment for each install, but it's not as simple as I hoped.

You can edit the canu version in "dep/conda/install_tools.sh". I would try Canu 1.7.1("canu=1.7.1") and see if that solves the problem. Since the tool versions will change from the SMRT-SV version, be sure to keep track of these changes in case you need them to report methods.

Let me know if this help.

zihhuafang commented 4 years ago

Hi,

I am also trying to install smrtsv2 on cluster (Linux). I also ran into the same issue and changing the version of Canu did not solve the problem ( I have tried version 1.7 and 1.9).

I did have canu 1.8 installed on the cluster. I am wondering if I can also export it to the $PATH to solve this issue.

paudano commented 4 years ago

In dep/conda/Makefile, line 28 is bin/conda create --yes --name tools python=3.6.2. Try changing that version to 3.5.3 from 3.6.2.

To use your Canu install, comment out canu in the install process (see above) and link the canu executable into dep/bin.

I'll see if I can do anything to make the Conda builds more robust in future releases. I'm still not sure why I was able to deploy the dependencies with the same build script if the Python version was not supported by Canu.

Let me know if any of this works for you.

zihhuafang commented 4 years ago

I managed to make it work by changing the path of canu in dep/Makefile. It did not work for me when I changed the version of python in the dep/conda/Makefile.

There are still some issues with other conda packages for tools, but I just manually installed it when activate dep/conda/build/envs/tools.

paudano commented 4 years ago

Are you able to share the changes you made to get it working? It might be helpful to document it for others who might have similar issues.

zihhuafang commented 4 years ago

Sorry for the late reply. I have been busy with other analyses.

In dep/Makefile, I provided my own canu path (I have canu 1.8 installed locally) to generate symlink as followed:
ln -sf /your/path/to/canu bin/canu

For packages that are installed via conda, I have problem to install gxx_linux-64=7.3.0. I deleted gxx_linux-64=7.3.0 in the /dep/conda/install_tools.shand installed it manually when activate dep/conda/build/envs/tools environment (using conda activate dep/conda/build/envs/tools). I also checked all the symlinks in /dep/bin are correct. If not, I just manually installed the packages that was missing.

Hope this help for ppl having issues installing the tools.