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arzwa / wgd

Python package and CLI for whole-genome duplication related analyses. This package is deprecated in favor of https://github.com/heche-psb/wgd.
http://wgd.readthedocs.io/en/latest/
GNU General Public License v3.0
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PAML installation in Singularity container #57

Closed Cecilia-Sensalari closed 2 years ago

Cecilia-Sensalari commented 3 years ago

Hi,

I've seen that you added a section in the readme to install PAML from source, but in the Singularity file PAML is still installed with apt-get. I suggest to add something like this to the Singularity file: apt-get install -y wget && wget http://abacus.gene.ucl.ac.uk/software/paml4.9j.tgz && tar -xzf paml4.9j.tgz && cd paml4.9j/src && make -f Makefile && mv codeml /bin && cd ../.. It's slightly different from what you wrote in your readme: I had to move codeml to /bin to make it work and replace pushd/popd with cd.

Bests, Cecilia

arzwa commented 3 years ago

Hi Cecilia, thanks for the info. Feel free to do a PR with the proposed changes (I haven't used Singularity in ages and haven't been maintaining it, so if you could update with a working Singularity file that would be great), else I'll have a look at it later.

Cecilia-Sensalari commented 3 years ago

Alright! I'm still testing the PAML installation with this new line within the ksrates container, when I have something final with it I can make the pull request with similar changes for your wgd container :)