OpenMS

Web: https://openms.de/, https://openms.readthedocs.io/en/latest/

AlphaPept and pyOpenMS

Web: AlphaPept: https://github.com/MannLabs/alphapept (latest installer), pyOpenMS: https://pyopenms.readthedocs.io/en/latest/index.html

The prerequisites involve CSD3 location, GNU C, cmake, TeX Live and Miniconda.

export root=/rds/project/rds-4o5vpvAowP0/software
source $root/py3.11/bin/activate
pip install alphapept
pip install pyopenms
pip install autowrap
pip install pytest
 

which installs alphapept 0.5.3 and pyopenms 3.3.0.

Script for testing is called alphapept_test.py ¹ which takes the following arguments,

Name	Description
`alphapept_settings.yaml`	A configuratino file containing relevant information, e.g., paths and `n_processes`.
`szwk021704i19101xms1.raw`, `szwk021704i19101xms3.raw`, `szwk021704i19101xms5.raw`	Raw spectra
`2022-07-05-reviewed-contam-UP000005640.fasta`	Database of protein sequences:

A more recent example is available from Google CoLab (AlphaPept.ipynb) as in Strauss, et al. (2024).

3.4.0

We keep the GitHub clone intact.

module load gcc/11.2.0/gcc/rjvgspag
module load texlive
git clone https://github.com/OpenMS/OpenMS
cd OpenMS/
git submodule update --init contrib
git clone https://github.com/OpenMS/THIRDPARTY/
git submodule update --init THIRDPARTY
cd $root
# build contrib
mkdir contrib-build
cd contrib-build
cmake -DBUILD_TYPE=ALL -DNUMBER_OF_JOBS=4 -Wno-dev ../OpenMS/contrib
# build OpenMS
cd $root
mkdir OpenMS-build
cd OpenMS-build
module load ceuadmin/qt/6.8.2
cmake -DCMAKE_BUILD_TYPE=Release -DOPENMS_CONTRIB_LIBS=$root/contrib-build \
      -DNUMBER_OF_JOBS=4 \
      -DBOOST_USE_STATIC=ON -DQt6_DIR=$CEUADMIN/6.8.2 -DPYOPENMS=On \
      -DSEARCH_ENGINES_DIRECTORY=$root/OpenMS/THIRDPARTY/Linux/64bit \
      -DCMAKE_INSTALL_PREFIX=$CEUADMIN/OpenMS/3.4.0 ../OpenMS
make targets
 

where the contrib-build/archives directory contains the following files (* = to obtain from -DBUILD_TYPE=).

boost_1_78_0.tar.gz
bzip2-1.0.5.tar.gz
CoinMP-1.8.3-vs22.tar.gz
eigen-3.4.0.tar.gz
glpk-4.46.tar.gz*
hdf5-1_14_3.tar.gz
kissfft-130.tar.gz*
libsvm-3.12.tar.gz
openmp-12.0.1.src.tar.xz*
Xerces-C_3_2_0.tar.gz
zlib-1.2.11.tar.gz
 

and the module ceuadmin/qt/6.8.2 is used instead for its compactness, especially CMAKE_MODULE_PATH is set. The command git clone https://github.com/OpenMS/THIRDPARTY/ downloads third-party files into the THIRDPARTY directory.

The option -DPYOPENMS=On in fact builds pyopenms as well, which can be loaded as follows,

import sys
import os

root = os.getenv('root')
sys.path.append(os.path.join(root, 'pyOpenMS'))
import pyopenms
 

More importantly, we can have the following screenshot:

$ OpenMSInfo

Full documentation: http://www.openms.de/doxygen/release/3.4.0/html/TOPP_OpenMSInfo.html
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024
   ). doi:10.1038/s41592-024-02197-7.

<< OpenMS Version >>
Version      : 3.4.0
Build time   : Mar 19 2025, 09:52:16
Git sha1     : 20ead3d
Git branch   : heads/release/3.3.0

<< Installation information >>
Data path    : /rds/project/rds-4o5vpvAowP0/software/OpenMS/share/OpenMS
Temp path    : /rds/user/jhz22/hpc-work/work
Userdata path: /home/jhz22/

<< Build information >>
Source path  : /rds/project/rds-4o5vpvAowP0/software/OpenMS/src/openms
Binary path  : /rds/project/rds-4o5vpvAowP0/software/OpenMS-build/src/openms
Binary arch  : 64 bit
Build type   : Release
LP-Solver    : COIN-OR
OpenMP       : enabled (maxThreads = 1)
SIMD extensions : SSE, SSE2, SSE3
Extra CXX flags : <none>

<< OS Information >>
Name: Linux
Version: 8.10
Architecture: 64 bit

OpenMSInfo took 0.13 s (wall), 0.00 s (CPU), 0.00 s (system), 0.00 s (user); Peak Memory Usage: 28 MB.
 

Singularity

singularity run ghcr.io/openms/openms-library-sif
singularity run ghcr.io/openms/openms-executables-sif
 

OpenMS/3.0.0-pre-develop-2022-09-28

CSD3 location

The ceuadmin/OpenMS/3.0.0-pre-develop-2022-09-28 module is at the follow location,

export Caprion=/rds/project/jmmh2/rds-jmmh2-projects/Caprion_proteomics
cd ${Caprion}
 

GNU C, cmake and Tex Live

A number of aspects are worthwhile to highlight:

OpenMS supports forc++17.
It also requires a recent version of cmake, which will recognise its associate directives ².
TeX Live is not essential for OpenMS to be functional but allows for documentation with pdfTeX – additional packages are required ³.
OpenMS requires somewhat earlier version of ghostscript which is actually available on CSD3 (GPL Ghostscript 9.25 (2018-09-13)) and we point to it via a symbolic link assuming ${HOME}/bin is on top of $PATH.

We have

module load gcc/7 cmake-3.19.7-gcc-5.4-5gbsejo texlive
ln -sf /usr/bin/ghostscript ${HOME}/bin/gs
 

In so doing gsftopk ntx-Bold-tlf-t1 600, etc. in the documentation building process will work. We obtain the much desired OpenMS_tutorial/latex_output/refman.pdf and OpenMS_tutorial.pdf.

Miniconda

This option is considerably easier and we set up the latest version.

# Step 1. Install Miniconda3
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
"$(/rds/project/jmmh2/rds-jmmh2-projects/Caprion_proteomics/miniconda3/bin/conda shell.bash hook)"
conda config --set auto_activate_base false
# Step 2. Specify module-like environment
export LD_LIBRARY_PATH=${Caprion}/miniconda3/lib:${LD_LIBRARY_PATH}
export PATH=${Caprion}/miniconda3/bin:${PATH}
export INCLUDE=${Caprion}/miniconda3/include:${INCLUDE}
export PYTHONPATH=${Caprion}/miniconda3/lib/python3.9/site-packages:${PYTHONPATH}
 

Note that Python 3.9.12 is installed, and in all cases the current environtal variables are carried over.

Only Step 2 is necessary in later calls.

OpenMS

Web: https://www.openms.de/ (Contributed software) (GitHub, https://github.com/OpenMS/OpenMS)

This procedure produces many efficient programs which are complementary to pyopenms.

cd ${Caprion}
git clone https://github.com/OpenMS/OpenMS
cd OpenMS
git submodule update --init contrib
mkdir -p contrib/archives
cd contrib/archives
wget -nd --execute="robots = off" --mirror --convert-links --no-parent --wait=5 \
     https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/source_packages/
cd -
cmake -DBUILD_TYPE=ALL contrib
cmake -DOPENMS_CONTRIB_LIBS=${Caprion}/miniconda3/lib -DCMAKE_PREFIX_PATH=contrib -DPYOPENMS=ON ../OpenMS
make targets
git clone https://github.com/OpenMS/THIRDPARTY/
 

The second wget statement is much more efficient to download all the files.

The last statement gives the most important targets for OpenMS, where TOPP refers to The OpenMS Proteomics Pipeline.

==========================================================================

The following make targets are available:
    [no target]     builds the OpenMS library, TOPP tools and UTILS tools
    OpenMS          builds the OpenMS library
    TOPP            builds the TOPP tools
    UTILS           builds the UTILS tools
    GUI             builds the GUI tools (TOPPView,...)
    test            executes OpenMS and TOPP tests
                    make sure they are built using the 'all' target
    Tutorials_build builds the code snippets of the tutorials in source/EXAMPLES
    doc             builds the doxygen and class documentation, parameters
                    documentation, and tutorial PDFs
    doc_class_only  builds only the doxygen and class documentation
                    (faster then doc and very useful when writing
                    documentation).
    doc_tutorials   builds the PDF tutorials
    help            list all available targets (very verbose)
    pyopenms           builds pyOpenMS inplace
    pyopenms_bdist_egg builds pyOpenMS bdist_egg
    pyopenms_bdist     builds pyOpenMS bdist as zip file
    pyopenms_rpm       builds pyOpenMS rpm

    (Disabled) OpenMS_coverage reporting target is not enabled (to enable use -D OPENMS_COVERAGE=ON).
               Caution: Building with debug and coverage info uses a lot of disk space (>40GB)


Single TOPP tools and UTILS have their own target, e.g. TOPPView

==========================================================================
 

Upon completion, the pyopenms package is within OpenMS/pyOpenMS. It would come handy to link bin/, lib/, etc. in the environmental variables accordingly; in particular pyOpenMS to PYTHONPATH.

Beside the codebase, various other options are possible, e.g.,

wget https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.2.0.tar.gz -O Xerces-C_3_2_0.tar.gz
cmake -DOPENMS_CONTRIB_LIBS=${Caprion}/miniconda3/lib -DCMAKE_PREFIX_PATH=contrib -DMY_CXX_FLAGS="-std=c++17" -DWITH_GUI=OFF ../OpenMS
 

For a particular version without using GitHub, it is necessary to specify explicitly, e.g.,

cd ${Caprion}
export version=3.0.0
wget -qO- https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/nightly/OpenMS-${version}-src.tar.gz | \
tar xfz -
cd ${Caprion}/OpenMS-${version}
mkdir -p contrib/archives
wget -nd --execute="robots = off" --mirror --convert-links --no-parent --wait=5 \
     https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/source_packages/
cd -
cmake -DBUILD_TYPE=ALL contrib
cmake -DGIT_TRACKING=OFF -DENABLE_UPDATE_CHECK=OFF -DOPENMS_CONTRIB_LIBS=contrib \
      -DPYOPENMS=OFF -DOPENMS_COVERAGE=OFF ../OpenMS-${version}
 

Sigularity

singularity pull docker://ghcr.io/openms/openms-library:3.0.0
singularity pull docker://ghcr.io/openms/openms-executables::3.0.0
 

Legacy

As with instances elsewhere, this section is kept not only for historical reasons but also for some useful information.

Python itself is lightweight but more involved.

Python

The installations involve environements for several versions of Python, e.g., Python 3.7/3.8.

module load python/3.7
virtualenv py37
source py37/bin/activate
 

module load python/3.8
virtualenv py38
source py38/bin/activate
 

Note the virtualenv py3[7|8] lines are unnecessary after the installations.

AlphaPept

This requires Python >= 3.8.

cd ${Caprion}
module load python/3.8
source py38/bin/activate
pip install pyyaml --prefix=${Caprion}/py38
pip install numba --prefix=${Caprion}/py38
pip install tqdm --prefix=${Caprion}/py38
pip install h5py --prefix=${Caprion}/py38
pip install fastcore --prefix=${Caprion}/py38
pip install psutil --prefix=${Caprion}/py38
pip install click --prefix=${Caprion}/py38
pip install Bio --prefix=${Caprion}/py38
pip install networkx --prefix=${Caprion}/py38
pip install sqlalchemy --prefix=${Caprion}/py38
pip install matplotlib --prefix=${Caprion}/py38
pip install sklearn --prefix=${Caprion}/py38
python -m pip install --upgrade numpy --user
wget -qO- https://github.com/MannLabs/alphapept/archive/refs/tags/v0.4.8.tar.gz | \
tar xvfz -
cd alphapept-0.4.8
python setup.py install --prefix=${Caprion}/py38
 

Be careful with conflicts of packages.

The newest features are through the nightly build/wheel (needs to be version 3.0+).

wget -qO- https://nightly.link/OpenMS/OpenMS/workflows/pyopenms-wheels/nightly/Linux-wheels.zip\?status\=completed
unzip Linux-wheels.zip\?status\=completed
 

We have

Archive:  Linux-wheels.zip?status=completed
 Length   Method    Size  Cmpr    Date    Time   CRC-32   Name
--------  ------  ------- ---- ---------- ----- --------  ----
96180971  Defl:N 95271735   1% 09-25-2022 00:41 37b53f6d  pyopenms_nightly-3.0.0.dev20220924-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
76497352  Defl:N 75780910   1% 09-25-2022 00:41 63b654a1  pyopenms_nightly-3.0.0.dev20220924-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
56599302  Defl:N 56080139   1% 09-25-2022 00:41 86fa8bd7  pyopenms_nightly-3.0.0.dev20220924-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
--------          -------  ---                            -------
229277625         227132784   1%                            3 files
 

It turned out only the first file is approppriate on CSD3, so we proceeded with

module load python/3.7
source py37/bin/activate
pip install pyopenms_nightly-3.0.0.dev20220924-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl --no-cache-dir  --prefix=${Caprion}/py37
 

However, a call to python pyopenms_test.py gave the following error messages,

3.0.0.dev20220924
Traceback (most recent call last):
  File "pyopenms_test.py", line 36, in <module>
    df = pd.read_pickle(pkl_input_filename)
  File "/rds/project/jmmh2/rds-jmmh2-projects/Caprion_proteomics/py37/lib/python3.7/site-packages/pandas/io/pickle.py", line 217, in read_pickle
    return pickle.load(handles.handle)  # type: ignore[arg-type]
ValueError: unsupported pickle protocol: 5
 

pyOpenMS

As will become obvious, the addresses were random with a hybrid of integrated and manual compiling.

git clone https://github.com/OpenMS/OpenMS
cd OpenMS
git submodule update --init contrib
cmake -DBUILD_TYPE=list ../OpenMS/contrib
cmake -DBUILD_TYPE=ALL -DNUMBER_OF_JOBS=4 ../OpenMS/contrib
# https://sourceforge.net/projects/open-ms/files/contrib/
cd archives
wget https://src.fedoraproject.org/lookaside/pkgs/libsvm/libsvm-3.12.tar.gz/a1b1083fe69a4ac695da753f4c83ed42/libsvm-3.12.tar.gz
cmake -DBUILD_TYPE=LIBSVM
wget https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.2.0.tar.gz -O Xerces-C_3_2_0.tar.gz
# manual build is necessary!
wget http://www.coin-or.org/download/source/CoinMP/CoinMP-1.8.3.tgz -O CoinMP-1.8.3-vs22.tar.gz
cmake -DBUILD_TYPE=COINOR
wget https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.tar.gz
cmake -DBUILD_TYPE=BOOST
wget https://sources.libreelec.tv/mirror/sqlite/sqlite-autoconf-3150000.tar.gz
cmake -DBUILD_TYPE=SQLITE
wget https://sourceforge.net/projects/open-ms/files/contrib/WildMagic5.tar.gz
cmake -DBUILD_TYPE=WILDMAGIC
wget https://sourceforge.net/projects/kissfft/files/kissfft/v1_3_0/kiss_fft130.tar.gz -O kissfft-130.tar.gz
wget https://sourceforge.net/projects/open-ms/files/contrib/glpk-4.46.tar.gz
cmake -DBUILD_TYPE=GLPK
# https://www.hdfgroup.org/packages/hdf5-1105-source/#
cmake -DBUILD_TYPE=HDF5
wget https://zlib.net/fossils/zlib-1.2.11.tar.gz
cmake -DBUILD_TYPE=ZLIB
wget https://src.fedoraproject.org/repo/pkgs/bzip2/bzip2-1.0.5.tar.gz/3c15a0c8d1d3ee1c46a1634d00617b1a/bzip2-1.0.5.tar.gz
cmake -DBUILD_TYPE=BZIP2
wget https://gitlab.com/libeigen/eigen/-/archive/3.3.4/eigen-3.3.4.tar.gz
tar xvfz eigen-3.3.4.tar.gz
cd eigen-3.3.4
mkdir build
cd build
cmake .. -DCMAKE_INSTALL_PREFIX=${Caprion}/OpenMS/contrib
make install
cd ${Caprion}/OpenMS
cmake -DOPENMS_CONTRIB_LIBS=contrib -DCMAKE_PREFIX_PATH=contrib -DCMAKE_INSTALL_PREFIX=${Caprion} ../OpenMS
 

Now pyOpenMS is compiled with the following scripts

cd ${Caprion}/OpenMS
module load python/3.8
source ${Caprion}/bin/activate
pip install setuptools  --prefix=${Caprion}/py38
pip install pip  --prefix=${Caprion}/py38
pip install autowrap  --prefix=${Caprion}/py38
pip install nose  --prefix=${Caprion}/py38
pip install numpy  --prefix=${Caprion}/py38
pip install wheel  --prefix=${Caprion}/py38
cmake -DPYOPENMS=ON
make pyopenms
 

Further information is available from cmake website ².

References

Strauss MT, et al., AlphaPept: a modern and open framework for MS-based proteomics. Nat Commun 15, 2168 (2024). https://doi.org/10.1038/s41467-024-46485-4.

Rost HL, et al., OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13, 9: 741-748 (2016). doi:10.1038/nmeth.3959.

Pfeuffer J, et al. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods 21, 365–367 (2024). https://doi.org/10.1038/s41592-024-02197-7

A summary of commands

Table: Summary from Pfeuffer et al. (2024)

Graphical Tools	TOPPView	A viewer for mass spectrometry data.
	TOPPAS	An assistant for GUI-driven TOPP workflow design.
	INIFileEditor	An editor for OpenMS configuration files.
	SwathWizard	A user-friendly step-by-step wizard for SWATH data analysis.
File Converter	FileConverter	Converts between different MS file formats.
	GNPSExport	Export MS/MS data in .MGF format for GNPS.
	IDFileConverter	Converts between different identification file formats.
	MSstatsConverter	Convert to MSstats input file format.
	MzTabExporter	Exports various XML formats to an mzTab file.
	TargetedFileConverter	Converts targeted files (such as tsv or TraML files).
	TextExporter	Exports various XML formats to a text file.
	TriqlerConverter	Convert to Triqler input file format.
File Filtering / Extraction / Merging	DatabaseFilter	Filter protein databases.
	DecoyDatabase	Creates decoy peptide databases from normal ones.
	DTAExtractor	Extracts spectra of an MS run file to several files in DTA format.
	FileFilter	Extracts or manipulates portions of data from peak, feature or consensus feature files.
	FileInfo	Shows basic information about the file, such as data ranges and file type.
	FileMerger	Merges several MS files into one file.
	IDFilter	Filters results from protein or peptide identification engines based on different criteria.
	IDMerger	Merges several protein/peptide identification files into one file.
	IDRipper	Splits protein/peptide identifications according their file-origin.
	IDSplitter	Splits protein/peptide identifications off of annotated data files.
	MapStatistics	Extract extended statistics on the features of a map for quality control.
	MzMLSplitter	Splits an mzML file into multiple parts.
Spectrum processing: Centroiding	PeakPickerHiRes	Peak detection in high-resolution profile mass spectra.
	PeakPickerIterative	Peak detection in high-resolution profile TOF data (based on PeakPickerHiRes with some postprocessing)
	PeakPickerWavelet	Peak detection in low-resolution (ion trap) profile mass spectra.
Spectrum processing:	BaselineFilter	Removes the baseline from profile spectra using a top-hat filter.
peak smoothing & normalization	NoiseFilterGaussian	Removes noise from profile spectra using a Gaussian smoothing.
	NoiseFilterSGolay	Removes noise from profile spectra using Savitzky-Golay smoothing.
	MapNormalizer	Normalizes peak intensities in an MS run.
	SpectraFilterBernNorm	Scales and filters spectra according to the Bern norm.
	SpectraFilterNLargest	Keeps only the n largest peaks per spectrum.
	SpectraFilterNormalizer	Scale intensities per spectrum to either sum to 1 or have a maximum of 1.
	SpectraFilterParentPeakMower	Removes high peaks that could stem from unfragmented precursor ions.
	SpectraFilterScaler	Assigns new intensity per spectrum according to intensity rank.
	SpectraFilterSqrtMower	Scales the intensity of peaks to their sqrt.
	SpectraFilterThresholdMower	Removes all peaks below an intensity threshold.
	SpectraFilterWindowMower	Retains the highest peaks in a sliding or jumping window.
Spectrum processing: Misc	MaRaClusterAdapter	Run the spectral clustering implemented in MaRaCluster.
	Resampler	Transforms an LC-MS map into an equally-spaced (in RT and m/z) map.
	SpectraMerger	Merges spectra from an LC-MS map, either by precursor or by RT blocks.
Mass Correction and Calibration	InternalCalibration	Applies an internal mass calibration (using PSMs or fixed masses).
	ExternalCalibration	Applies an external mass calibration.
	HighResPrecursorMassCorrector	Correct the precursor entries of tandem MS scans for high resolution data.
	IDRTCalibration	Can be used to calibrate RTs of peptide hits linearly to standards.
	PrecursorMassCorrector	Correct the precursor m/z entries of tandem MS scans (low-res only).
	TOFCalibration	Applies time of flight mass calibration.
Quantitation	ConsensusMapNormalizer	Normalizes maps of one consensusXML file (after linking).
	Decharger	Decharges and merges different feature charge variants of the same chemical entity.
	EICExtractor	Quantifies signals at given positions in (raw or picked) LC-MS maps.
	ERPairFinder	Evaluates pair ratios on enhanced resolution (ER = zoom) scans.
	FeatureFinderCentroided	Detects two-dimensional features in centroided LC-MS data.
	FeatureFinderIdentification	Detects two-dimensional features in MS1 data based on peptide identifications.
	FeatureFinderIsotopeWavelet	Detects two-dimensional features in uncentroided (=raw) LC-MS (low-res)
	FeatureFinderMetabo	Detects two-dimensional features in centroided LC-MS data of metabolites.
	FeatureFinderMetaboIdent	Detects features in MS1 data corresponding to small molecule identifications.
	FeatureFinderMRM	Quantifies features LC-MS/MS MRM data.
	FeatureFinderMultiplex	Identifies peptide multiplets (pairs, triplets etc., e.g. for SILAC or Dimethyl labeling) and determines their relative abundance.
	IsobaricAnalyzer	Extracts and normalizes TMT and iTRAQ information from an MS experiment.
	MassTraceExtractor	Annotates mass traces in centroided LC-MS maps.
	MetaboliteAdductDecharger	Decharges and merges different feature charge variants of the same small molecule.
	MetaProSIP	Detect labeled peptides from protein-SIP experiments.
	MultiplexResolver	Resolves conflicts between identifications and quantifications in multiplex data.
	ProteinQuantifier	Computes protein abundances from annotated feature/consensus maps.
	ProteinResolver	A peptide-centric algorithm for protein inference.
	ProteomicsLFQ	Perform label-free quantification in a single tool.
	SeedListGenerator	Generates seed lists for feature detection.
Identification of	CometAdapter	Identifies MS/MS spectra using Comet (external).
Proteins/Peptides	LuciphorAdapter	Scores potential phosphorylation sites in order to localize the most probable sites.
(SearchEngines)	MascotAdapter	Identifies MS/MS spectra using Mascot (external).
	MascotAdapterOnline	Identifies MS/MS spectra using Mascot (external).
	MSFraggerAdapter	Peptide Identification with MSFragger.
	MSGFPlusAdapter	Identifies MS/MS spectra using MSGFPlus (external).
	NovorAdapter	De novo sequencing from tandem mass spectrometry data.
	SageAdapter	Identifies MS/MS spectra using Sage (external).
	SimpleSearchEngine	A simple database search engine for annotating MS/MS spectra.
	SpecLibSearcher	Identifies peptide MS/MS spectra by spectral matching with a searchable spectral library.
	SpectraSTSearchAdapter	An interface to the ‘SEARCH' mode of the SpectraST program (external, beta).
	XTandemAdapter	Identifies MS/MS spectra using XTandem (external).
Identification Processing	ConsensusID	Computes a consensus identification from peptide identifications of several identification engines.
	Digestor	Digests a protein database in-silico.
	DigestorMotif	Digests a protein database in-silico (optionally allowing only peptides with a specific motif) and produces statistical data for all peptides.
	Epifany	Bayesian protein inference based on PSM probabilities.
	FalseDiscoveryRate	Estimates the false discovery rate on peptide and protein level using decoy searches.
	IDConflictResolver	Resolves ambiguous annotations of features with peptide identifications.
	IDExtractor	Extracts n peptides randomly or best n from idXML files.
	IDMapper	Assigns protein/peptide identifications to feature or consensus features.
	IDMassAccuracy	Calculates a distribution of the mass error from given mass spectra and IDs.
	IDPosteriorErrorProbability	Estimates posterior error probabilities using a mixture model.
	IDScoreSwitcher	Switches between different scores of peptide or protein hits in identification data.
	PeptideIndexer	Refreshes the protein references for all peptide hits.
	PercolatorAdapter	Applies the percolator algorithm to protein/peptide identifications.
	PhosphoScoring	Scores potential phosphorylation sites in order to localize the most probable sites.
	ProteinInference	Infer proteins from a list of (high-confidence) peptides.
	PSMFeatureExtractor	Creates search engine specific features for PercolatorAdapter input.
	SequenceCoverageCalculator	Prints information about idXML files.
	SpecLibCreator	Creates an MSP-formatted spectral library.
	StaticModification	Allows to attach a set of fixed modifications to an idXML file (MS/MS search results), e.g. to add 15N (N15) labeling post-hoc.
Map Alignment	MapAlignerIdentification	Corrects RT distortions between maps based on common peptide identifications using one map as reference.
	MapAlignerPoseClustering	Corrects RT distortions between maps using a pose clustering approach (not using pep-ids and alinear model)
	MapAlignerSpectrum	Corrects RT distortions between maps by spectrum alignment.
	MapAlignerTreeGuided	Corrects RT distortions between maps based on common peptide identifications guided by a similarity tree.
	MapRTTransformer	Applies RT transformations to maps.
Feature linking	FeatureLinkerLabeled	Groups corresponding isotope-labeled features in a feature map.
	FeatureLinkerUnlabeled	Groups corresponding features from multiple maps.
	FeatureLinkerUnlabeledQT	Groups corresponding features from multiple maps using a QT clustering approach.
	FeatureLinkerUnlabeledKD	Groups corresponding features from multiple maps using a KD tree.
Targeted Experiments	AssayGeneratorMetabo	Generates an assay library using DDA data (Metabolomics).
and OpenSWATH	ClusterMassTracesByPrecursor	Identifies precursor mass traces and tries to correlate them with fragment ion mass traces in SWATH maps.
	MRMMapper	MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).
	MRMPairFinder	Evaluates labeled pair ratios on MRM features.
	MRMTransitionGroupPicker	Picks peaks in MRM chromatograms.
	OpenSwathAnalyzer	Picks peaks and finds features in an SRM experiment.
	OpenSwathAssayGenerator	Generates filtered and optimized assays using TraML files.
	OpenSwathChromatogramExtractor	Extract chromatograms (XIC) from a MS2 map file.
	OpenSwathConfidenceScoring	Computes confidence scores for OpenSwath results.
	OpenSwathDecoyGenerator	Generates decoys according to different models for a specific TraML.
	OpenSwathDIAPreScoring	SWATH (data-idependent acquisition) pre-scoring
	OpenSwathFeatureXMLToTSV	Converts a featureXML to a tsv.
	OpenSwathFileSplitter	Splitting a single SWATH / DIA file into a set of files, each containing one SWATH window.
	OpenSwathMzMLFileCacher	Caching of large mzML files.
	OpenSwathRewriteToFeatureXML	Rewrites results from mProphet back into featureXML.
	OpenSwathRTNormalizer	Align an SRM / SWATH run to a normalized retention time space.
	OpenSwathWorkflow	Complete workflow to run OpenSWATH.
Cross-linking	OpenPepXL	Search for peptide pairs linked with a labeled cross-linker
	OpenPepXLLF	Search for cross-linked peptide paris in tandem MS spectra.
	RNPxlSearch	Annotates RNA-peptide cross-links in MS/MS spectra.
	RNPxlXICFilter	Removes MS2 spectra from treatment based on the fold change between control and treatment for RNA-to-peptide cross-linking experiments.
	XFDR	Calculates false discovery rate estimates on cross-link identifications.
Top down	FLASHDeconv	Computes a feature deconvolution from Top down MS data.
Quality Control	QualityControl	A one-in-all QC tool to generate an augmented mzTab.
	DatabaseSuitability	Calculates the suitability of a database for peptide identification search using a de novo approach.
	QCCalculator	Calculates basic quality parameters from MS experiments and compiles data for subsequent QC into a qcML file.
	QCEmbedder	Embeds tables or plots generated externally as attachments to existing quality parameters in qcML files.
	QCExporter	Extracts several quality parameter from several runs/sets from a qcML file into a tabular (text) format - counterpart to QCImporter.
	QCExtractor	Extracts a table attachment of a given quality parameter from a qcML file as tabular (text) format.
	QCImporter	Imports several quality parameters from a tabular (text) format into a qcML file - counterpart to QCExporter.
	QCMerger	Merges two qcML files together.
	QCShrinker	Removes extra verbose table attachments from a qcML file that are not needed anymore, e.g. for a final report.
Metabolite Identification	AccurateMassSearch	Finds potential HMDB IDs within the given mass error window.
	MetaboliteSpectralMatcher	Identifies small molecules from tandem MS spectra.
	SiriusAdapter	De novo metabolite identification.
RNA	NucleicAcidSearchEngine	Search MzML files for oligonucleotides and their modifications.
	RNADigestor	Digests an RNA sequence database in-silico.
	RNAMassCalculator	Calculates masses and mass-to-charge ratios of RNA sequences.
Misc / Helpers	ClusterMassTraces	Cluster mass traces occurring in the same map together.
	DeMeanderize	Orders the spectra of MALDI spotting plates correctly.
	ExecutePipeline	Executes workflows created by TOPPAS.
	GenericWrapper	Allows the generic wrapping of external tools.
	ImageCreator	Creates images from MS1 data (with MS2 data points indicated as dots).
	INIUpdater	Updates INI and TOPPAS files from previous versions of OpenMS as parameters and storage method might have change
	MassCalculator	Calculates masses and mass-to-charge ratios of peptide sequences.
	MetaProSIP	Performs proteinSIP on peptide features for elemental flux analysis.
	OpenMSInfo	Print system information.
	TICCalculator	Calculates the TIC of a raw mass spectrometric file.
[for developers]	CVInspector	Visualization and validation of PSI mapping and CV files.
	FuzzyDiff	Compares two files, tolerating numeric differences.
	JSONExporter	Exports .oms (SQLite) files in JSON format
	OpenMSDatabasesInfo	prints the content of OpenMS' enzyme and modification databases to a TSV file.
	SemanticValidator	SemanticValidator for analysisXML and mzML files.
	XMLValidator	Validates XML files against an XSD schema.

Other URLs

OpenMS, SourceForge; GITTER, wikiwand, OpenSWATH.
tlmgr, tlmgr.pdf, Installing_Extra_Packages, pkginstall, Rstudio query.

Benchmark

Download file from Dropbox.
```
ln -s alphapept-0.4.8 alphapept
unzip hpc_setup.zip
```
which gives alphapept_test.py and pyopenms_test.py above along with data files. ↩

The website https://cmake.org/cmake/help/latest/module/FindPython.html explains several options which appear unnecessary for cmake 3.19.

export Python_LIBRARY_DIRS=${Caprion}/miniconda3/lib
export Python_INCLUDE_DIR=${Caprion}/miniconda3/include
export Python_EXECUTABLE=${Caprion}/miniconda3/bin/python
 

↩ ↩²

tlmgr – the TEX Live Manager

The required newtx, fontaxes and xtab package can be installed as follows,

tlmgr init-usertree
tlmgr option repository ftp://tug.org/historic/systems/texlive/2015/tlnet-final --user-mode
tlmgr install --user-mode newtx
tlmgr install --user-mode fontaxes
tlmgr install --user-mode xtab
 

For instance tlmgr info newtx command gives the following information,

package:     newtx
category:    Package
shortdesc:   Alternative uses of the TX fonts, with improved metrics
longdesc:    The bundle splits txfonts.sty (from the TX fonts distribution) into two independent packages, newtxtext.sty and newtxmath.sty, each with fixes and enhancements. newtxmath's metrics have been re-evaluated to provide a less tight appearance, and to provide a libertine option that substitutes Libertine italic and Greek letter for the existing math italic and Greek glyphs, making a mathematics package that matches Libertine text quite well. newtxmath can also use the maths italic font provided with the garamondx package, thus offering a garamond-alike text-with- maths combination.
installed:   Yes
revision:    39072
sizes:       doc: 865k, run: 7429k
relocatable: Yes
cat-version: 1.463
cat-date:    2015-12-11 20:31:08 +0100
cat-license: lppl1.3
cat-topics:  font font-maths font-type1
cat-related: minion2newtx
collection:  collection-fontsextra
 

See also https://ctan.org/pkg/newtx. Also related is # Karl's Path SEarch Library WHICH (kpsewhich), e.g., kpsewich tikz. ↩