{"repo":"Euro-BioImaging/BatchConvert","free":true,"listed":false,"github":"https://github.com/Euro-BioImaging/BatchConvert","clone":"git clone https://github.com/Euro-BioImaging/BatchConvert.git","description":"A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.","language":"Python","stars":31,"topics":["bioimage","conversion","file-format","image","nextflow","ome","ome-zarr","workflow","zarr","ome-zarr-converter"],"license":"MIT","category":"workflow-automation","readme_excerpt":"BatchConvert A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr. The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system Nextflow is used to perform conversion in parallel for batches of images. The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). Therefore, input and output locations can be specified as local or remote storage and file transfer will be performed automatically. The conversion can be run on HPC with Slurm. Important note: The package has been so far only tested on Ubuntu 20.04. Installation & Dependencies Installation via conda A conda package for BatchConvert exists: https://anaconda.org/Euro-BioImaging/batchconvert Conda installation of BatchConvert to a new conda environment is recommended. Simply run the following command: conda install -c euro-bioimaging -c conda-forge -c bioconda -c ome batchconvert Installation from the source BatchConvert can also be acquired by cloning this repository. In this case, Nextflow, which is the minimal dependency to run BatchConvert, should be installed and made accessible from the command line. If conda exists on your system, you can install BatchConvert together with Nextflow using the following script: If you already have Nextflow installed and accessible from the command line (or if you prefer to install it manually e.g., as shown here), ","default_branch":null,"files":null,"tree":[],"storefront":"/r/Euro-BioImaging","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Euro-BioImaging/BatchConvert/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."}