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phylo42 / PEWO

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
MIT License
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INSTALL.sh cannot find conda installation #9

Open balabanmetin opened 3 years ago

balabanmetin commented 3 years ago

I have miniconda 4.6.10 installed in my machine. In this version, "conda" command does not execute a binary file directly, it is a function added to .bashrc during installation. INSTALL.sh checks whether conda is installed using the "command -v" command. this command cannot locate functions defined in bashrc. As a result, PEWO installation fails with the error message : PEWO installer: Command 'conda' not found. PEWO installer: This is a requirement to PEWO installation. See documentation.

blinard-BIOINFO commented 3 years ago

Hi, command is a bash built-in and PEWO installation script calls #!/bin/bash. And as you mentionned, conda installation adds an init block at the end of the bashrc file. Not this is default behaviour, but alternatives initialisation methods exists.

I agree this make one assumption : bash is installed and used to install PEWO. Now, considering that the vast majority of Unix systems comes with bash built-in, this should be fine.

In your case, you need to understand if your bashrc is not read correctly at session initialisation or if the conda init block is somehow not functionnal. If it was, the conda command would be available in your bash session, this is the default behaviour in a bash+conda installation.

Maybe you run a session in a cluster (via slumr/qsub?) which do not use bash ? another user which has another bashrc not containing the conda init block ?

Also, if you have suggestion for an alternative test, I'm happy to consider them.