Merge pull request #66 from NBISweden/dev-percyfal

Dev percyfal

.github/workflows/build.yml

@@ -48,6 +48,7 @@ jobs:
         run: |
           python -m ipykernel install --user --name pgip --display-name "Population Genomics in Practice (Python)"
           python -m pip install git+https://github.com/NBISweden/pgip-tools
+          python -m pip install git+https://github.com/ksamuk/pixy.git
 
       - name: Install dotenv
         run: |

Makefile

@@ -60,4 +60,7 @@ install-kernels: install-pgip ## Install python and bash kernel
 install-bcftools: ## Install bcftools manually due to issues with conda version 1.8
 	scripts/install-bcftools.sh
 
-.phony: help Makefile project production clean-site clean install-pgip install-dev install-R install-kernels bcftools
+install-pixy: ## Install pixy manually due to missing conda package
+	python -m pip install git+https://github.com/ksamuk/pixy.git
+
+.phony: help Makefile project production clean-site clean install-pgip install-dev install-R install-kernels install-bcftools install-pixy

README.md

@@ -15,13 +15,9 @@ issue](https://github.com/NBISweden/workshop-pgip/issues).
 
 ## Installation and setup, TL;DR
 
-{% note %}
-
 **Note:** this is only for developers! To view the website, navigate
 to <https://nbisweden.github.io/workshop-pgip/>.
 
-{% endnote %}
-
 Clone the repo and cd to directory
 
     git clone [email protected]:NBISweden/workshop-pgip.git
@@ -63,6 +59,7 @@ environment variable:
     make install-R
     make install-kernels
     make install-bcftools
+    make install-pixy
     make install-dev
 
 If the above commands have worked without issues you are done and you
@@ -138,6 +135,17 @@ or
 
 in the root directory.
 
+### Install pixy
+
+There currently is no pixy conda package for Python>3.9 which requires
+manuall installation with pip:
+
+    make install-pixy
+
+or
+
+    python -m pip install git+https://github.com/ksamuk/pixy.git
+
 ### Development tools
 
 There are a number of development tools in `environments-dev.yaml`