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EmmaLRussell wants to merge 10 commits into main from piranha-installer

.github/workflows/piranha-installer-ubuntu.yml

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+    name: Piranha Installer for Ubuntu
+    on:
+      push:
+        branches: [ main ]
+        paths:
+          - 'piranha-installer/**'
+          - './github/workflows/**'
+      pull_request:
+        branches: [ main ]
+    defaults:
+      run:
+        working-directory: ./piranha-installer
+    jobs:
+      build-piranha-exe:
+        runs-on: ubuntu-latest
+        steps:
+          - name: Check out source
+            uses: actions/checkout@v4
+          - name: Install micromamba
+            uses: mamba-org/setup-micromamba@v2
+            with:
+              environment-file: ./piranha-installer/environment.yml
+          - name: Build Piranha exe
+            shell: bash -el {0}
+            run: ./scripts/build-installer
+          - name: Upload exe as artifact
+            uses: actions/upload-artifact@v4
+            with:
+              name: piranha-exe-ubuntu
+              path: ./piranha-installer/dist/piranha
+              retention-days: 1
+      test-piranha-exe:
+        needs: build-piranha-exe
+        runs-on: ubuntu-latest
+        steps:
+          - name: Check out source # Get source just to have access to test data and run script
+            uses: actions/checkout@v4
+          - name: Make empty dist folder # So we can run the same script as in local dev, manually create dist folder...
+            run: mkdir dist
+          - name: Download Piranha exe # ...and download the exe to it
+            uses: actions/download-artifact@v4
+            with:
+              name: piranha-exe-ubuntu
+              path:
+                ./piranha-installer/dist
+          - name: Add executable permission
+            run: chmod u+x dist/piranha
+          #- name: TMATE
+          #  uses: mxschmitt/action-tmate@v3
+          - name: Test Piranha exe
+            run: ./scripts/test-run-exe

.gitignore

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		.idea

README.md

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     # piranhaNET
-    Typescript user interface for piranha on desktop and web
+    Typescript user interface for [piranha](https://github.com/polio-nanopore/piranha) on desktop and web.
+    ### :wrench: This is a work in progress. :wrench:
+    We will provide a Typescript front end for piranha, which can be built and distributed as an Electron application,
+    or deployed as a web application.
+    This repo contains the following components in its directories. See the READMEs in each directory for more details:
+    * `piranha-installer` - a [pyinstaller](https://pyinstaller.org) project for piranha allowing it to be bundled with the
+    Electron app installer.

piranha-installer/.gitignore

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+    build
+    dist
+    test_results

piranha-installer/README.md

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+    # piranhaNET: piranha-installer
+    [Pyinstaller](https://pyinstaller.org) project for piranha.
+    `piranha.spec` defines the installer configuration.
+    ### Pre-requisites
+    * [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)
+    ### Development
+    Run all commands from this folder.
+    Create a local conda environment (you only need to do this once): `micromamba env create --file environment.yml`
+    Activate the conda environment: `micromamba activate piranha-installer`
+    Build piranha to an executable with pyinstaller: `./scripts/build-installer`
+    Run the executable on test data: `./scripts/test-run-exe`
+    To add a new dependency, update environment.yml then run: `micromamba env update --file environment.yml`

piranha-installer/entrypoint.py

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+    import subprocess
+    import sys
+    from piranha import command
+    name, *args = sys.argv
+    # Decide from args whether this is the top level entrypoint to a
+    # piranha run, or an invocation of snakemake.
+    # (This is needed because snakemake uses sys.executable to launch
+    # new workflows, expecting the exe to be python or python3, but that
+    # is not the case when running from this executable!)
+    if (args[0] == "-m" and args[1] == "snakemake"):
+        # Run snakemake
+        subprocess.run(
+          ["python3", *args],
+          stdout=sys.stdout,
+          stderr=sys.stdout,
+          check=True,
+       )
+    else:
+        # Run piranha
+        command.main(args)

piranha-installer/environment.yml

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+    name: piranha-installer
+    channels:
+      - conda-forge
+      - bioconda
+      - defaults
+    dependencies:
+      - conda
+      - medaka=1.11.3
+      - piranha-polio
+      - python
+      - snakemake
+      - pyinstaller
+      - tzdata=2025a # 2025c and latest 2025b breaks pyinstaller!

piranha-installer/piranha.spec

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+    # -*- mode: python ; coding: utf-8 -*-
+    from conda.core.envs_manager import list_all_known_prefixes
+    # Get the root of the installed piranha package in order to copy data files etc into the installer
+    env_root = list(filter(lambda prefix: prefix.endswith("piranha-installer"), list_all_known_prefixes()))[-1]
+    python_version = "3.9"
+    piranha_package_root = "{env_root}/lib/python{python_version}/site-packages/piranha/".format(env_root = env_root, python_version = python_version)
+    a = Analysis(
+        ['entrypoint.py'],
+        pathex=[],
+        binaries=[],
+        datas=[
+         (piranha_package_root + 'scripts', './piranha/scripts'),
+         (piranha_package_root + 'analysis', './piranha/analysis'),
+         (piranha_package_root + 'data', './piranha/data')
+        ],
+        hiddenimports=[
+        ],
+        hookspath=[],
+        hooksconfig={},
+        runtime_hooks=[],
+        excludes=[],
+        noarchive=False,
+        optimize=0,
+    )
+    pyz = PYZ(a.pure)
+    exe = EXE(
+        pyz,
+        a.scripts,
+        a.binaries,
+        a.datas,
+        [],
+        name='piranha',
+        debug=False,
+        bootloader_ignore_signals=False,
+        strip=False,
+        upx=True,
+        console=True,
+        disable_windowed_traceback=False,
+        argv_emulation=False,
+        target_arch=None,
+        codesign_identity=None,
+        entitlements_file=None,
+    )

piranha-installer/scripts/build-installer

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+    #!/usr/bin/env bash
+    set -ex
+    pyinstaller piranha.spec --noconfirm

piranha-installer/scripts/test-run-exe

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+    #!/usr/bin/env bash
+    set -ex
+    out_dir=test_results
+    rm -rf $out_dir
+    ./dist/piranha -i test_data/demultiplexed -b test_data/barcodes.csv -pc Pos1,P2 -nc "my negative control" -o $out_dir --verbose

piranha-installer/test_data/barcodes.csv

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+    barcode,sample,date,well
+    barcode01,MixedTest,2022-01-01,A01
+    barcode02,PureTest,2022-01-02,B01
+    barcode03,WTTest,2022-01-07,C01
+    barcode04,VDPVTest,2022-01-05,D05
+    barcode05,negative,,D06
+    barcode06,positively,,D07
+    barcode07,somemixed,2022-03-01,H12

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