Package: alpharaw
AlphaRawAboutAn open-source Python package of the AlphaPept ecosystem from theMann
Labs at the Max Planck Institute of
Biochemistryto unify raw MS data
accession and storage. To enable all hyperlinks in this document, please
view it atGitHub.AboutLicenseInstallationPip installerDeveloper installerUsagePython and jupyter notebooksTroubleshootingCitationsHow to contributeChangelogLicenseAlphaRaw was developed by theMann Labs at the Max Planck Institute of
Biochemistryand is freely available
with anApache License. External Python packages
(available in therequirementsfolder) have their own
licenses, which can be consulted on their respective websites.InstallationPythonnet must be installed to access Thermo or Sciex raw data.For WindowsPythonnet will be automatically installed via pip.For Linux (or MacOS without M1/M2/M3/..., not tested yet)conda install mono.Install pythonnet withpip install pythonnet.Ifconda install monodoes not work, we can install Mono from mono-project websiteMono
Linux.
NOTE, the installed mono version should be at least 6.10, which
requires you to add the ppa to your trusted sources!For MacOS including M1/M2 platformInstallbrew.Install mono:brew install mono.If the pseudo mono folder/Library/Frameworks/Mono.framework/Versionsdoes not exist, create it by runningsudo mkdir -p /Library/Frameworks/Mono.framework/Versions.Link homebrew mono to pseudo mono folder:sudo ln -s /opt/homebrew/Cellar/mono/6.12.0.182 /Library/Frameworks/Mono.framework/Versions/Current. Here,6.12.0.182is the brew-installed mono version, please check your installed version. Navigate to/Library/Frameworks/Mono.framework/Versionsand runls -lto verify that the linkCurrentpoints to/opt/homebrew/Cellar/mono/6.12.0.182. IfCurrentpoints to a different installation and/or/opt/homebrew/Cellar/mono/6.12.0.182is referenced by a different link, delete the corresponding links and runsudo ln -s /opt/homebrew/Cellar/mono/6.12.0.182 Current.Install pythonnet:pip install pythonnet.AlphaRaw can be installed and used on all major operating systems
(Windows, macOS and Linux). There are three different types of
installation possible:Pip installer:Choose this installation if you want to use
AlphaRaw as a Python package in an existing Python 3.8 environment
(e.g. a Jupyter notebook).Developer installer:Choose this installation if you
are familiar with CLI tools,condaand Python. This installation allows access to all available features
of AlphaRaw and even allows to modify its source code directly.
Generally, the developer version of AlphaRaw outperforms the
precompiled versions which makes this the installation of choice for
high-throughput experiments.PipAlphaRaw can be installed in an existing Python 3.8 environment with a
singlebashcommand.Thisbashcommand can also be run directly
from within a Jupyter notebook by prepending it with a!:pipinstallalpharawInstalling AlphaRaw like this avoids conflicts when integrating it in
other tools, as this does not enforce strict versioning of dependancies.
However, if new versions of dependancies are released, they are not
guaranteed to be fully compatible with AlphaRaw. While this should only
occur in rare cases where dependencies are not backwards compatible, you
can always force AlphaRaw to use dependancy versions which are known to
be compatible with:pipinstall"alpharaw[stable]"NOTE: You might need to runpip install pip --upgradebefore installing
AlphaRaw like this. Also note the double quotes".For those who are really adventurous, it is also possible to directly
install any branch (e.g.@development) with any extras
(e.g.#egg=alpharaw[stable,development-stable]) from GitHub with e.g.pipinstall"git+https://github.com/MannLabs/alpharaw.git@development#egg=alpharaw[stable,development-stable]"DeveloperAlphaRaw can also be installed in editable (i.e. developer) mode with a
fewbashcommands. This allows to fully customize the software and
even modify the source code to your specific needs. When an editable
Python package is installed, its source code is stored in a transparent
location of your choice. While optional, it is advised to first (create
and) navigate to e.g. a general software folder:mkdir~/folder/where/to/install/softwarecd~/folder/where/to/install/softwareThe following commands assume you do not perform any additionalcdcommands anymore.Next, download the AlphaRaw repository from GitHub either directly or
with agitcommand. This creates a new AlphaRaw subfolder in your
current directory.gitclonehttps://github.com/MannLabs/alpharaw.gitFor any Python package, it is highly recommended to use a separateconda virtual environment, as
otherwisedependancy conflicts can occur with already existing
packages.condacreate--namealpharawpython=3.9-y
condaactivatealpharawFinally, AlphaRaw and all itsdependanciesneed to be
installed. To take advantage of all features and allow development (with
the-eflag), this is best done by also installing thedevelopment
dependenciesinstead of only
thecore dependencies:pipinstall-e"./alpharaw[development]"By default this installs loose dependancies (no explicit versioning),
although it is also possible to use stable dependencies
(e.g.pip install -e "./alpharaw[stable,development-stable]").By using the editable flag-e, all modifications to theAlphaRaw
source code folderare directly reflected when running
AlphaRaw. Note that the AlphaRaw folder cannot be moved and/or renamed
if an editable version is installed.UsagePythonNOTE: The first time you use a fresh installation of AlphaRaw, it is
often quite slow because some functions might still need compilation on
your local operating system and architecture. Subsequent use should be a
lot faster.Python and Jupyter notebooksAlphaRaw can be imported as a Python package into any Python script or
notebook with the commandimport alpharaw.A briefJupyter notebook tutorialon how to use
the API is also present in thenbs folder.TroubleshootingIn case of issues, check out the following:Issues: Try a few
different search terms to find out if a similar problem has been
encountered beforeDiscussions: Check
if your problem or feature requests has been discussed before.CitationsThere are currently no plans to draft a manuscript.How to contributeIf you like this software, you can give us astarto boost our
visibility! All direct contributions are also welcome. Feel free to post
a newissueor clone the
repository and create apull
requestwith a new branch.
For an even more interactive participation, check out thediscussionsand thethe Contributors License Agreement.ChangelogSee theHISTORY.mdfor a full overview of the changes made
in each version.