{"repo":"zmahnoor14/MAW","free":true,"listed":false,"github":"https://github.com/zmahnoor14/MAW","clone":"git clone https://github.com/zmahnoor14/MAW.git","description":"Metabolome Annotation Workflow","language":"Jupyter Notebook","stars":26,"topics":["workflow","metabolomics-pipeline","mass-spectrometry"],"license":null,"category":"workflow-automation","readme_excerpt":"This repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. It performs spectral database dereplication using R Package Spectra and compound database dereplication using SIRIUS OR MetFrag . Final candidate selection is done in Python using RDKit and PubChemPy.The classification of the tentative candidates from the input data are classified using CANOPUS and ClassyFire, which will be updated to accomodate NPClassifier soon. Installation MAW is available as docker containers and as CWL workflow description. It can be used via both channels, however at the moment, SIRIUS is only accomodated with the docker containers, (the workflow will be completely operable in CWL in the future). At the moment, the CWL version can be used with MetFrag. Given below are the instructions on installation either via CWL (option to use MetFrag with all the additional features of the workflow) or via Docker (options to run either SIRIUS or MetFrag in addition to all other features of the workflow). With CWL, multiple files can be be executed with MAW in parallel. it is recommended to use HPC for bigger files via a batch system such as SLURM ( = 10 precursor masses). Common Workflow Language (CWL) Users can run MAW with CWL with just one command without pulling individual docker images. 1. install cwltool 2. Download cwl/Workflow R Script all.r and cwl/Workflow Python Script all.py. These will be the scripts used by MAW CWL. 3. Download ","default_branch":null,"files":null,"tree":[],"storefront":"/r/zmahnoor14","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/zmahnoor14/MAW/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}