How can I update OrthoFinder

Question

[mirza]

Hi,

I have OrthoFinder 1.0.7 installed in my workstation (OS- Ubuntu16.04). It is installed in bin dir in HOME. But, it is not working properly, It has been updated thrice since this release and the latest version is v1.1.4.

1. How can I update my version? $ sudo apt-get update did not work.

and if not possible

1. How can I uninstall it so that I can install the latest version? I tried

$ sudo apt-get --purge remove OrthoFinder

and

$ sudo apt-get --purge remove OrthoFinder-1.0.7

but both returned,

E: Unable to locate package OrthoFinder.

p.s. I did rename my dir from OrthoFinder-1.0.7 to OrthoFinder :(

[GenoMax]

Then rename the directory back to original name and see if uninstall works.

[Michael]

This is likely not a ubuntu package, and not managed by apt. How did you install it the first time, it is mot likely updated in the same way as initially installed.

[mirza]

According to the manual, we just need to download and untar the file and it should run. Test we need to run

OrthoFinder: OrthoFinder-1.0.6/orthofinder -h. OrthoFinder

and it printed its ‘help’ text. I realized what you are saying so I tried to remove it using the --purge command but was unsuccessful. Since, it did not involve any configuring or installation, will simple "remove" work??

[Michael]

You can simply delete the folder and content using rm, apt or apt -get only work with repository packages. OrthoFinder is a python script, so you need python installed, and it lists some dependencies in its manual: https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf

[mirza]

ok. I hv installed all the dependencies mentioned and checked them. But somehow it's always returns that blast+ is not installed although it is and works separately and prints all help text (I posted this issue but couldn't get any help) So, I am guessing may be there's some problem with this version and want to try with the latest version.

Answer 1

[mirza]

The latest version OrthoFinder1.1.4 is running successfully.

Answer 2

[david_emms]

Hi

Just to say, you can download the latest version of OrthoFinder, untar it anywhere on your computer and just run it from there. You don't need put it in your bin directory, you can just run it by typing the path to the version you want to call.

All the best David

[margaretlazzeroni]

Hi @David_emms. I'm planning to use Orthofinder to scan for orthologous groups across a set of genes in snakes. I'm working with whole genome data. I realize Orthofinder requires proteomic data as input. Before I attempt to transform my genomic data into proteomic data, I wanted to check if there is a way to by-pass this? Have any recent updates enabled Orthofinder to accept whole genome data as input?

Thank you for your help!

Maggie