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luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
301 stars 37 forks source link

Installation script is not using the version of git or curl on the path #160

Closed TBradley27 closed 3 years ago

TBradley27 commented 3 years ago

Hey,

Thanks for writing what looks to be a very promising tool. I have one or two problems trying to install the latest version however:

Describe the bug The installation script attempts to use git and curl installed in /usr/bin/ rather than the version of git and curl on the path

Version: Version 0.7.2

$ octopus --version
// PASTE OUTPUT HERE

Command Command line to install octopus:

$ octopus/script/install.py --dependencies

image

TBradley27 commented 3 years ago

A quick side-note to this:

I was able to successfully (I think) compile the tool by not using the '--dependency' flag at at all when executing the installation script - and instead opting to install required dependencies via conda. This is all done within a separate conda environment I have created, dedicated to octopus installation.

The only slight problem is that even at version 7.x.x of gcc my compilation failed, but worked with version 9.3.0 of gcc

I just ran a quick job using my newly compiled instance of v0.7.2 of octopus, and everything looks good

dancooke commented 3 years ago

Hey, the automatic dependency install option is currently not working on CentOS 7 due to a problem with Homebrew. I was hoping this would be fixed by now but it's taken a while so I may look at other options soon. Your workaround using Conda should be fine - it's what I'm doing. Indeed, GCC7 doesn't work due to various compiler bugs.