From ff353fe0386856a230d69d7ec100a4d217ff7616 Mon Sep 17 00:00:00 2001
From: Johannes Alneberg <alneberg@kth.se>
Date: Tue, 16 Jan 2024 10:49:33 +0100
Subject: [PATCH 1/3] Working dockerfile for arm64

---
 Dockerfile       | 41 +++++++++++++++++++++++++++++++++++++----
 environment.yml  |  9 ++++-----
 requirements.txt |  4 ++++
 setup.py         |  8 ++------
 4 files changed, 47 insertions(+), 15 deletions(-)
 create mode 100644 requirements.txt

diff --git a/Dockerfile b/Dockerfile
index c79f571..a8b2449 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -5,12 +5,45 @@ LABEL author="Remi-Andre Olsen" \
       maintainer="remi-andre.olsen@scilifelab.se"
 
 USER root
+
+# Check for arm64 architecture to install minimap2
+ARG TARGETARCH
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      # Install compliation tools for minimap2
+      apt-get update;\
+      apt-get install -y curl build-essential libz-dev;\
+    fi
+
+ENV MINIMAP_VERSION=2.26
+
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      # Download minimap2
+      curl -L https://github.com/lh3/minimap2/archive/refs/tags/v${MINIMAP_VERSION}.tar.gz | tar -zxvf - ;\
+    fi
+
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      # Compile minimap2
+      cd minimap2-${MINIMAP_VERSION};\
+      make arm_neon=1 aarch64=1; \
+      # Add to path
+      mv minimap2 /usr/local/bin/;\
+    fi
+
 COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /
-RUN micromamba env create -n anglerfish && micromamba install -y -n anglerfish -f /environment.yml && micromamba clean --all --yes 
-ENV PATH /opt/conda/envs/anglerfish/bin:$PATH
+COPY --chown=$MAMBA_USER:$MAMBA_USER requirements.txt /
+
+RUN if [ "$TARGETARCH" = "arm64" ]; then \
+      grep -v 'minimap2' /environment.yml > /environment.tmp.yml ;\
+    else \
+      cp /environment.yml /environment.tmp.yml ;\
+    fi ;\
+    chown $MAMBA_USER:$MAMBA_USER /environment.tmp.yml
 
 # Add source files to the container
 ADD . /usr/src/anglerfish
 WORKDIR /usr/src/anglerfish
-RUN eval "$(micromamba shell hook --shell bash)" && micromamba activate anglerfish && python -m pip install .
-USER $MAMBA_USER
+
+RUN micromamba install -y -n base -f /environment.tmp.yml && micromamba clean --all --yes
+
+RUN eval "$(micromamba shell hook --shell bash)" && micromamba activate base && python -m pip install . 
+USER $MAMBA_USER
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
index f695b3d..b36521a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -3,8 +3,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - conda-forge::biopython=1.79
-  - conda-forge::python-levenshtein=0.23.0
-  - conda-forge::numpy=1.22.0
-  - bioconda::minimap2=2.20
-  - conda-forge::pyyaml=6.0
+  - bioconda::minimap2=2.26
+  - pip
+  - pip:
+    - -r requirements.txt
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..9fd76d3
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,4 @@
+numpy==1.26.3
+biopython==1.83
+levenshtein==0.23.0
+pyyaml==6.0.1
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 72b5591..e1bbfad 100644
--- a/setup.py
+++ b/setup.py
@@ -30,12 +30,8 @@
     python_requires=">=3.7",
     packages = find_packages(),
     package_data = {"":["config/adaptors.yaml"]},
-    install_requires=[
-        'python-levenshtein==0.23.0',
-        'biopython==1.79',
-        'numpy==1.22.0',
-        'pyyaml==6.0'
-    ],
+    # Read requirements.txt
+    install_requires=[x.strip() for x in open("requirements.txt").readlines()],
     entry_points={
         "console_scripts": [
             "anglerfish=anglerfish.anglerfish:anglerfish",

From f306ecdc0dcc554c2068bd8789b14ca236ec427d Mon Sep 17 00:00:00 2001
From: Johannes Alneberg <alneberg@kth.se>
Date: Tue, 16 Jan 2024 11:59:15 +0100
Subject: [PATCH 2/3] Add back pre-commit and prettier to conda env

---
 environment.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/environment.yml b/environment.yml
index 3a1e3ed..dfdf6bd 100644
--- a/environment.yml
+++ b/environment.yml
@@ -8,3 +8,5 @@ dependencies:
   - pip
   - pip:
     - -r requirements.txt
+  - conda-forge::pre-commit
+  - conda-forge::prettier
\ No newline at end of file

From 5609e0db09350bc0e40b694930a173cc966d2517 Mon Sep 17 00:00:00 2001
From: Johannes Alneberg <alneberg@kth.se>
Date: Tue, 16 Jan 2024 12:02:23 +0100
Subject: [PATCH 3/3] Ruff formatting of environment.yml

---
 environment.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/environment.yml b/environment.yml
index dfdf6bd..ec2d96d 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,6 +7,6 @@ dependencies:
   - bioconda::minimap2=2.26
   - pip
   - pip:
-    - -r requirements.txt
+      - -r requirements.txt
   - conda-forge::pre-commit
-  - conda-forge::prettier
\ No newline at end of file
+  - conda-forge::prettier