Fix installation issues and update dependencies and instructions

.gitignore

@@ -0,0 +1,5 @@
+# pixi environments
+.pixi/*
+!.pixi/config.toml
+
+target/

Cargo.toml

@@ -20,7 +20,7 @@ python = ["pyo3"]
 
 [dependencies]
 # BAM/SAM reading
-rust-htslib = "0.51"
+rust-htslib = { version = "0.44", features = ["static"] }
 
 # Parallelism
 rayon = "1.10"

README.md

@@ -16,10 +16,48 @@ Built with **Rust** for fast BAM processing and **Python/Bokeh** for interactive
 
 # Quick Start
 
-You need Rust and Python installed. Install Rust following instructions at: https://rust-lang.org/tools/install/
+You need conda installed. If you don't have it yet, you can install Miniconda following instructions at: https://docs.conda.io/en/latest/miniconda.html
 
 Then in command-line:
 
+```bash
+conda env create -f thebigbam_env.yaml
+conda activate thebigbam
+pip install git+https://github.com/bhagavadgitadu22/theBIGbam
+```
+
+Be aware that it may take quite some time to compile the Rust code during installation.
+
+To reduce the installation size, you can at the end remove the rust cache:
+
+```bash
+cargo clean
+```
+
+### Errors
+
+To avoid potential compilation errors:
+
+- On Linux: Install development headers: `sudo apt-get install libbz2-dev liblzma-dev zlib1g-dev clang libclang-dev`
+- On macOS: `brew install xz bzip2 zlib`
+- On HPC clusters: you may need to load the LLVM module first: `module load llvm`
+
+If you cannot use any of these methods and still get errors related to `libclang` during installation such as :
+
+```bash
+thread 'main' (3889591) panicked at /home/gmichoud/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/bindgen-0.69.5/lib.rs:622:31:
+        Unable to find libclang: "couldn't find any valid shared libraries matching: ['libclang.so', 'libclang-*.so', 'libclang.so.*', 'libclang-*.so.*'], set the `LIBCLANG_PATH` environment variable to a path where one of these files can be found (invalid: [])"
+
+```
+
+Please set the `LIBCLANG_PATH` environment variable to the path where your `libclang` library is located. For example:
+
+```bash
+export LIBCLANG_PATH=$(python -c "import os; print(os.environ['CONDA_PREFIX'] + '/lib')")
+```
+
+Then try installing again.
+
 ```bash
 pip install git+https://github.com/bhagavadgitadu22/theBIGbam
 ```
@@ -46,6 +84,12 @@ thebigbam calculate \
 thebigbam serve --db tests/HK97/test.db --port 5006
 ```
 
+If you're using wsl, you may need to install the package `wslu` to allow opening the browser from the wsl terminal:
+
+```bash
+sudo apt install wslu
+```
+
 Open browser to http://localhost:5006
 
 See [the installation guide](docs/INSTALL.md) for more detailed instructions.
@@ -249,4 +293,4 @@ Export any metric as a contig x sample TSV matrix:
 thebigbam export -d my_database.db --metric Coverage_mean -o coverage.tsv
 ```
 
-Run `thebigbam export -h` to see the full list of available metrics.
+Run `thebigbam export -h` to see the full list of available metrics.

docs/INSTALL.md

@@ -81,7 +81,7 @@ This installs in "editable" mode - changes to Python code take effect immediatel
 **Using conda/mamba (easiest):**
 
 ```bash
-mamba env create -f thebigbam_env.yaml
+conda env create -f thebigbam_env.yaml
 conda activate thebigbam
 pip install .  # Re-install in conda environment
 ```

pyproject.toml

@@ -9,7 +9,7 @@ description = "Compression and interactive exploration of large-scale sequencing
 readme = "README.md"
 authors = [{ name = "Martin Boutroux", email = "martinboutroux@outlook.fr" }]
 license = { text = "MIT" }
-requires-python = ">=3.9"
+requires-python = ">=3.9,<3.13"
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
@@ -18,12 +18,6 @@ classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Rust",
 ]
-
-[project.urls]
-Homepage = "https://github.com/bhagavadgitadu22/theBIGbam"
-Repository = "https://github.com/bhagavadgitadu22/theBIGbam"
-Issues = "https://github.com/bhagavadgitadu22/theBIGbam/issues"
-
 dependencies = [
     "bokeh>=3.0",
     "panel>=1.0",
@@ -33,6 +27,13 @@ dependencies = [
     "duckdb>=1.0",
 ]
 
+[project.urls]
+Homepage = "https://github.com/bhagavadgitadu22/theBIGbam"
+Repository = "https://github.com/bhagavadgitadu22/theBIGbam"
+Issues = "https://github.com/bhagavadgitadu22/theBIGbam/issues"
+
+
+
 [project.optional-dependencies]
 dev = [
     "pytest>=7.0",

thebigbam/plotting/start_bokeh_server.py

@@ -984,7 +984,7 @@ def make_data_download_callback():
     toggle_stylesheet = InlineStyleSheet(css=toggle_css_text)
 
     # Load logo as base64 to avoid static file serving issues
-    logo_path = os.path.join(static_path, "logo.png")
+    logo_path = os.path.join(static_path, "LOGO.png")
     with open(logo_path, "rb") as f:
         logo_b64 = base64.b64encode(f.read()).decode("utf-8")
 

thebigbam_env.yaml

@@ -6,3 +6,8 @@ dependencies:
   - samtools=1.23
   - bwa-mem2=2.3
   - minimap2=2.30
+  - rust>=1.72
+  - libclang
+  - python=3.12
+  - blast
+