Merge pull request #205 from wilhelm-lab/release/0.6.2

Release/0.6.2

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: victor.giurcoiu@tum.de
 project_name: oktoberfest
 project_short_description: Public repo oktoberfest
-version: 0.6.1
+version: 0.6.2
 license: MIT

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.6.1 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.6.1 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.6.2 🌈" # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.6.2 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.1
+current_version = 0.6.2
 
 [bumpversion_files_whitelisted]
 init_file = oktoberfest/__init__.py

docs/conf.py

@@ -54,9 +54,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.6.1"
+version = "0.6.2"
 # The full version, including alpha/beta/rc tags.
-release = "0.6.1"
+release = "0.6.2"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/installation.rst

@@ -3,29 +3,26 @@
 Installation
 ============
 
-Prerequisites
-~~~~~~~~~~~~~
+Oktoberfest can be installed on all three major platforms (Linux, MacOS, Windows).
 
-Oktoberfest requires python >=3.8,<=3.11. Best practise is to use a clean conda environment (`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_).
+An installer script is provided for Linux (installers for MacOS and Windows are currently prepared), which takes care of all dependencies. For MacOS and Windows, the Docker container or manual installation can be used.
 
-If you provide RAW files, you need ThermoRawFileParser for conversion to mzML.
-Please download the latest release from the `github repository <https://github.com/compomics/ThermoRawFileParser>`_ using the provided zip file and unpack it in the desired location.
-On linux and MacOS, the default location is "/opt/compomics/". On Windows, the default location is the directory from which Oktoberfest is executed.
-You can provide the location of the executable in the config file when starting an Oktoberfest run.
+Installer script (Debian / Ubuntu only)
+---------------------------------------
 
-To make ThermoRawFileParser work on linux or MacOS, make sure mono `mono <https://www.mono-project.com/>`_ is installed.
+The installer script automatically installs dependencies and creates a new conda environment for oktoberfest. The installation takes roughly 5 minutes and follows the steps outlined in the manual installation below. Get the installer and execute the script using
 
-If you want to use percolator for rescoring, make sure you install version 3.06.1 (`percolator <https://github.com/percolator/percolator/releases/tag/rel-3-06-01>`_).
+.. code-block:: bash
 
-Using pip (recommended)
-~~~~~~~~~~~~~~~~~~~~~~~
+   wget https://raw.githubusercontent.com/wilhelm-lab/oktoberfest/main/installer.sh -O install_oktoberfest.sh
+   bash install_oktoberfest.sh
 
-.. code-block:: bash
+The installer searches for existing anaconda / miniconda installation. If none was found, it will download and install miniconda.
 
-   pip install oktoberfest
+Docker Image
+------------
 
-Docker image
-~~~~~~~~~~~~
+This is only recommended for experienced users and can take up to 30 minutes to install, depending on experience.
 
 Prerequisites:
   - `make <https://www.gnu.org/software/make/>`_
@@ -38,3 +35,55 @@ The latest stable version is always on the main branch. Then build the container
 
    make build
 
+
+Manual installation
+-------------------
+
+This is a step-by-step guide for the manual installation of all mandatory and optional dependencies which should roughly take up to 20 minutes if all dependencies are installed.
+
+Install Python
+~~~~~~~~~~~~~~
+
+Oktoberfest requires python >=3.8 and <=3.11. Best practise is to use a clean conda environment (`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_).
+Follow the installation guide for your operating system, then create a new environment using
+
+.. code-block:: bash
+
+   conda create -y -n oktoberfest python==3.10
+
+
+Optional dependencies
+~~~~~~~~~~~~~~~~~~~~~
+
+There are three dependencies that are required for specific tasks:
+
+
+`ThermoRawFileParser v1.4.3 <https://github.com/compomics/ThermoRawFileParser/releases/tag/v1.4.3>`_:
+For conversion of RAW to mzML format. Download and unpack the zip or tar.gz file. The default locations Oktoberfest expects the executable to be at "/opt/compomics/" (Linux/MacOS) or the folder from which you want to execute Oktoberfest (Windows).
+You do not need this package if you only ever provide mzML file. However, it is recommended let Oktoberfest convert RAW files for you, to ensure the mzML files are formatted in the way Oktoberfest expects it.
+For ThermoRawFileParser to work on Linux, you also need to ensure mono is installed using
+
+.. code-block:: bash
+
+   sudo apt -y update && sudo apt -y install mono-devel  # Debian / Ubuntu
+
+For MacOS, follow the instructions provided by `Mono <https://www.mono-project.com/docs/getting-started/install/mac/>`_.
+
+
+`Percolator v3.06.1 <https://github.com/percolator/percolator/releases/tag/rel-3-06-01>`_:
+This is the tool Mokapot is based on. As it has more options and is generally more stable wrt. to FDR cutoffs and deduplication, it is recommended to use this tool instead of Mokapot.
+Installable packages are provided for Linux/MacOS/Windows.
+
+
+Installing Oktoberfest
+~~~~~~~~~~~~~~~~~~~~~~
+
+Oktoberfest is listed on the Python Package Index (PyPI) and can be installed with pip. Activate your conda environment (or skip this if you use a system wide python installation) and install the package (and optionally jupyterlab) using
+
+.. code-block:: bash
+
+   conda activate oktoberfest
+   pip install oktoberfest jupyterlab
+
+
+

installer.sh

@@ -0,0 +1,107 @@
+#!/bin/bash
+
+# === install mono, ThermoRawFileParser and percolator as root === #
+
+sudo apt -y update && sudo apt -y install mono-devel unzip
+
+wget https://github.com/percolator/percolator/releases/download/rel-3-06-01/percolator-v3-06-linux-amd64.deb -O /tmp/percolator.deb
+sudo dpkg -i /tmp/percolator.deb
+rm /tmp/percolator.deb
+
+ZIP=ThermoRawFileParser1.4.2.zip
+wget https://github.com/compomics/ThermoRawFileParser/releases/download/v1.4.2/$ZIP -O /tmp/$ZIP
+sudo mkdir -p /opt/compomics
+yes | sudo unzip /tmp/$ZIP -d /opt/compomics
+rm /tmp/$ZIP
+
+# ============== user level conda setup installation ============= #
+
+INSTALLED_MINICONDA=0
+# Check if Anaconda is installed
+if command -v conda &> /dev/null; then
+    CONDA_INSTALL_DIR=$(conda info --base)
+else
+    CONDA_INSTALL_DIR="$HOME/miniconda3/"
+    echo "Miniconda not found. Installing Miniconda..."
+    wget -q https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
+    bash /tmp/miniconda.sh -b -p "$CONDA_INSTALL_DIR"
+    rm /tmp/miniconda.sh
+    conda init
+    INSTALLED_MINICONDA=1
+fi
+# Add Miniconda/Anaconda binary directory to PATH if not already present
+if [[ ":$PATH:" != *":$CONDA_INSTALL_DIR/bin:"* ]]; then
+    export PATH="$CONDA_INSTALL_DIR/bin:$PATH"
+fi
+
+# Configure conda in script
+. "$CONDA_INSTALL_DIR/etc/profile.d/conda.sh"
+# Activate base environment
+
+conda activate base
+
+# Check if the desired environment exists, create if not
+if ! conda env list | grep -q "oktoberfest"; then
+    echo "Creating conda environment..."
+    conda create -y -n oktoberfest python==3.10
+else
+    echo "Conda environment already exists. Skipping creation..."
+fi
+
+conda activate oktoberfest
+
+# Check if pip installation succeeded
+if [ $? -ne 0 ]; then
+    echo "Activating the envionment failed."
+    exit 1
+fi
+
+pip install oktoberfest jupyterlab
+
+# Check if pip installation succeeded
+if [ $? -ne 0 ]; then
+    echo "Pip installation failed."
+    exit 1
+fi
+# =========================== summary ============================ #
+
+perc_version=`percolator --help 2>&1 | head -n 1`
+if [ $? -ne 0 ]; then
+    echo "Percolator installation failed. Check logs."
+    exit 1
+fi
+
+mono_version=`mono --version | head -n 1`
+if [ $? -ne 0 ]; then
+    echo "Mono installation failed. Check logs."
+    exit 1
+fi
+
+thermo_version=`mono /opt/compomics/ThermoRawFileParser.exe --version`
+if [ $? -ne 0 ]; then
+    echo "ThermoRawFileParser installation failed. Check logs."
+    exit 1
+fi
+
+oktoberfest_version=`pip show oktoberfest | grep Version`
+if [ $? -ne 0 ]; then
+    echo "Oktoberfest installation failed. Check logs."
+    exit 1
+fi
+
+echo -e "\n"
+echo "percolator version: $perc_version"
+echo "mono version: $mono_version"
+echo "ThermoRawFileParser version: $thermo_version"
+echo "Oktoberfest version: $oktoberfest_version"
+
+echo -e "\nInstallation complete."
+if [ $INSTALLED_MINICONDA -eq 1 ]; then
+    echo "Miniconda was installed. You need to restart your shell once before you can use oktoberfest."
+fi
+echo -e "\nTo use oktoberfest, perform the following steps:"
+echo -e "\t 1. activate your environment, using \"conda activate oktoberfest\""
+echo -e "\t 2. start jupyterlab using \"jupyter lab\" or run oktoberfest directly. Type \"python -m oktoberfest\" to get info."
+
+
+exit 0

oktoberfest/__init__.py

@@ -5,7 +5,7 @@
 __author__ = """The Oktoberfest development team (Wilhelmlab at Technical University of Munich)"""
 __copyright__ = f"Copyright {datetime.now():%Y}, Wilhelmlab at Technical University of Munich"
 __license__ = "MIT"
-__version__ = "0.6.1"
+__version__ = "0.6.2"
 
 import logging.handlers
 import sys

oktoberfest/rescore/rescore.py

@@ -179,12 +179,6 @@ def rescore_with_mokapot(
 
     np.random.seed(123)
 
-    df = pd.read_csv(input_file, sep="\t", index=False)
-
-    # TODO remove this if not necessary
-    df = df.rename(columns={"Protein": "Proteins"})
-    df.to_csv(input_file, sep="\t")
-
     psms = mokapot.read_pin(input_file)
     logger.info(f"Number of PSMs used for training: {len(psms)}")