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Merge pull request #27 from Changwanseo/Changwanseo-patch-3
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Update README.md
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Changwanseo authored Jan 29, 2024
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Expand Up @@ -29,31 +29,36 @@ A automatic tree-based sequence identification pipeline for fungal species
## Requirements
- Conda environment (See https://www.anaconda.com/products/individual to install)


<!--
## Installation with conda (May not work with Linux or Mac)
1. ```conda create -n FunID python=3.10```
2. ```conda activate FunID```
3. ```conda install -c cwseo FunID```
4. run ```FunID --test Penicillium ``` to check installation
If this one fails, use next one
-->

## Windows
1. Install visual c++ [here](https://visualstudio.microsoft.com/ko/visual-cpp-build-tools/)
2. ```conda create -n FunID python=3.9```
3. ```conda activate FunID```
4. ```pip install FunID```
5. run ```FunID --test Penicillium ``` to check installation

## Installation with conda (using pip - Recommended)
1. ```conda create -n FunID python=3.10```
2. ```conda activate FunID```
3. ```pip install FunID```
4. run ```FunID --test Penicillium ``` to check installation
If you are using linux system please follow "Additional information for Linux"
* For mac system, this installation probably work, but we couldn't test it because we don't have any mac device. We're looking for feedbacks in mac
* For upgrade use this command
``` pip install FunID --upgrade ```

## Additional information for Linux
* Currently, FunID is one-step installed only in Windows
* to use in linux please run this command additionally
## Linux
1. ```conda create -n FunID python=3.9```
2. ```conda activate FunID```
3. ```pip install FunID```
4. ```conda install -c bioconda raxml iqtree modeltest-ng mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree```
5. run ```FunID --test Penicillium ``` to check installation


```conda install -c bioconda raxml iqtree modeltest-ng mmseqs2 "blast>=2.12" mafft trimal gblocks fasttree```
* For intel mac system, this method probably work, but we couldn't test it because we don't have any intel mac device. We're looking for feedbacks in intel mac

## Experimental - Installation for apple silicon (M1, M2)
## Apple Silicon Mac
1. ```CONDA_SUBDIR=osx-64 conda create -n FunID python=3.10```
2. ```conda activate FunID```
3. ```conda config --env --set subdir osx-64```
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