From de7492e7336c9886b7759b0187fe846192f4ba95 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <thomas.christensen@millironx.com>
Date: Thu, 1 May 2025 17:30:48 -0500
Subject: [PATCH 1/6] fix Nextflow variables

home-manager does not guarantee that
environment variables are declared in any
particular order. This meant that my
Nextflow variables that referred to
`$NXF_HOME` were declared before
`$NXF_HOME` was declared, so they were
pointing to the wrong directories. Fix
that.
---
 homes/common.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/homes/common.nix b/homes/common.nix
index 065d307..577a670 100644
--- a/homes/common.nix
+++ b/homes/common.nix
@@ -63,8 +63,8 @@ in {
       PAGER = "most";
       NXF_HOME = "${config.xdg.dataHome}/nextflow";
       NXF_CACHE = "${config.xdg.cacheHome}/nextflow";
-      NXF_CONDA_CACHEDIR = "$NXF_CACHE/conda";
-      NXF_SINGULARITY_CACHEDIR = "$NXF_CACHE/singularity";
+      NXF_CONDA_CACHEDIR = "${config.xdg.cacheHome}/nextflow/conda";
+      NXF_SINGULARITY_CACHEDIR = "${config.xdg.cacheHome}/nextflow/singularity";
       JULIA_DEPOT_PATH = "${config.xdg.dataHome}/julia:";
       JULIA_PKG_USE_CLI_GIT = "true";
     };

From c91527e4318157f930601746f1614425d5bbaea2 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <thomas.christensen@millironx.com>
Date: Thu, 1 May 2025 17:31:08 -0500
Subject: [PATCH 2/6] install Nextflow

---
 homes/common.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/homes/common.nix b/homes/common.nix
index 577a670..62de9f5 100644
--- a/homes/common.nix
+++ b/homes/common.nix
@@ -48,6 +48,7 @@ in {
       julia-bin
       lynx
       most
+      nextflow
       nil
       nixd
       nixfmt-classic

From dd68c27f8dd8205aa3f9c7de99b8f7f9e6deb54b Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <thomas.christensen@millironx.com>
Date: Thu, 1 May 2025 17:34:01 -0500
Subject: [PATCH 3/6] install btop - a cooler htop

---
 homes/common.nix | 1 +
 1 file changed, 1 insertion(+)

diff --git a/homes/common.nix b/homes/common.nix
index 62de9f5..016fc81 100644
--- a/homes/common.nix
+++ b/homes/common.nix
@@ -33,6 +33,7 @@ in {
     file = { ".p10k.zsh".source = ./../dotfiles/p10k.zsh; };
     packages = with pkgs; [
       act
+      btop
       cowsay
       earthly
       ffmpeg

From 46b255fdcf7e0f2af53a6dbcd737ebada08ffc5e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <thomas.christensen@millironx.com>
Date: Thu, 1 May 2025 17:41:54 -0500
Subject: [PATCH 4/6] add local Nextflow config

---
 homes/harmony.nix | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/homes/harmony.nix b/homes/harmony.nix
index 2943c78..ba8f207 100644
--- a/homes/harmony.nix
+++ b/homes/harmony.nix
@@ -58,4 +58,28 @@
       pinentryPackage = pkgs.pinentry-qt;
     };
   };
+  xdg = {
+    configFile = {
+      "nextflow.config".text = ''
+        params {
+            config_profile_description = 'harmony Asahi Linux local profile'
+            config_profile_contact     = 'Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>'
+            config_profile_url         = null
+
+            max_memory = 12.GB
+            max_cpus   = 12
+            max_time   = 7.d
+        }
+
+        apptainer {
+            enabled    = true
+            autoMounts = true
+        }
+
+        process {
+            executor = 'local'
+        }
+      '';
+    };
+  };
 }

From 9f0e03b29cba155d66ea93060a830d222829835e Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <thomas.christensen@millironx.com>
Date: Thu, 1 May 2025 17:45:52 -0500
Subject: [PATCH 5/6] replace conda with micromamba

---
 homes/common.nix | 21 +++------------------
 1 file changed, 3 insertions(+), 18 deletions(-)

diff --git a/homes/common.nix b/homes/common.nix
index 016fc81..7cd687b 100644
--- a/homes/common.nix
+++ b/homes/common.nix
@@ -1,24 +1,7 @@
 { config, lib, pkgs, pkgs-unstable, ... }:
 let
   conda_init = shell: ''
-    # >>> conda initialize >>>
-    # !! Contents within this block are managed by 'conda init' !!
-    __conda_setup="$(${config.xdg.dataHome}/miniconda3/bin/conda shell.${shell} 'hook' 2> /dev/null)"
-    if [ $? -eq 0 ]; then
-        eval "$__conda_setup"
-    else
-        if [ -f "${config.xdg.dataHome}/miniconda3/etc/profile.d/conda.sh" ]; then
-            . "${config.xdg.dataHome}/miniconda3/etc/profile.d/conda.sh"
-        else
-            export PATH="${config.xdg.dataHome}/miniconda3/bin:$PATH"
-        fi
-    fi
-    unset __conda_setup
-
-    if [ -f "${config.xdg.dataHome}/miniconda3/etc/profile.d/mamba.sh" ]; then
-      . "${config.xdg.dataHome}/miniconda3/etc/profile.d/mamba.sh"
-    fi
-    # <<< conda initialize <<<
+    eval "$(${pkgs.micromamba}/bin/micromamba shell hook --shell ${shell})"
 
   '';
   nd_bash_function = ''
@@ -48,6 +31,7 @@ in {
       jq
       julia-bin
       lynx
+      micromamba
       most
       nextflow
       nil
@@ -63,6 +47,7 @@ in {
     ];
     sessionVariables = {
       PAGER = "most";
+      MAMBA_ROOT_PREFIX = "${config.xdg.dataHome}/micromamba";
       NXF_HOME = "${config.xdg.dataHome}/nextflow";
       NXF_CACHE = "${config.xdg.cacheHome}/nextflow";
       NXF_CONDA_CACHEDIR = "${config.xdg.cacheHome}/nextflow/conda";

From 93f0dcc7b52b567098fb315074e435313e55b15f Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <thomas.christensen@millironx.com>
Date: Thu, 1 May 2025 17:48:37 -0500
Subject: [PATCH 6/6] Update Zed AI to Claude 3.7

---
 programs/zed.nix | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/programs/zed.nix b/programs/zed.nix
index ea6dec5..74c9cd5 100644
--- a/programs/zed.nix
+++ b/programs/zed.nix
@@ -20,7 +20,7 @@
     assistant = {
       default_model = {
         provider = "zed.dev";
-        model = "claude-3-5-sonnet-latest";
+        model = "claude-3-7-sonnet-latest";
       };
       version = "2";
     };