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carolzhou / multiPhATE2

multiPhATE with comparative genomics
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conda environment notes #15

Closed xvazquezc closed 3 years ago

xvazquezc commented 3 years ago

Hi, I've been testing the program using a full conda installation and I ran into a few installation issues related to some of the dependencies and I thought it would be a good idea to report them.

BLAST+: by default the environment installed blast=2.6.0 but the makeblastdb fails due to a libssl.so.1.0.0, which might be a package-specific. Solved by forcing the installation of a newer version conda install "blast>2.6"

BioPython: not sure if it's specific to my system but the Annotation script was given an error with from Bio import SeqIO. I tested other biopython packages with the same issue. Solved by installing it via pip in the same conda env.

libiconv: transeq failed when called by phate_genomeSequence.py due to missing library libiconv.so.2. Installed as conda install libiconv solved it.

Cheers, Xabi

carolzhou commented 3 years ago

Thank you, Xabi. Yes, these are system-specific issues, and it is very helpful of you to point them out. My testing is limited to the very few platforms I have access to, so having knowledgeable users find these types of issues is enormously helpful. I will add text to the readme for the benefit of other users. Again, thank you for your contribution, and thank you for using multiPhATE2. -Carol

On Tue, Jan 12, 2021 at 8:05 PM xvazquezc notifications@github.com wrote:

Hi, I've been testing the program using a full conda installation and I ran into a few installation issues related to some of the dependencies and I thought it would be a good idea to report them.

BLAST+: by default the environment installed blast=2.6.0 but the makeblastdb fails due to a libssl.so.1.0.0, which might be a package-specific. Solved by forcing the installation of a newer version conda install "blast>2.6"

BioPython: not sure if it's specific to my system but the Annotation script was given an error with from Bio import SeqIO. I tested other biopython packages with the same issue. Solved by installing it via pip in the same conda env.

libiconv: transeq failed when called by phate_genomeSequence.py due to missing library libiconv.so.2. Installed as conda install libiconv solved it.

Cheers, Xabi

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carolzhou commented 3 years ago

May I ask what machine and operating system you are running multiPhATE2 on?

xvazquezc commented 3 years ago

Sure. It is a HPC server running CentOS 7. But I'm installing it on my own account for individual use/testing and with no modules loaded (to avoid any potential conflict with the conda-installed packages).

carolzhou commented 3 years ago

Thank you!