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unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["atac-seq","bisulfite-sequencing","chip-seq","hi-c","ngs","rna-seq","snakemake","workflow"],"created_at":"2024-08-03T01:00:42.925Z","updated_at":"2026-03-17T23:17:34.722Z","avatar_url":"https://github.com/maxplanck-ie.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"===========================================================\nsnakePipes\n===========================================================\n\n.. image:: https://readthedocs.org/projects/snakepipes/badge/?version=latest\n    :target: http://snakepipes.readthedocs.io/en/latest/?badge=latest\n    :alt: Documentation Status\n\n.. image:: https://travis-ci.org/maxplanck-ie/snakepipes.svg?branch=develop\n    :target: https://travis-ci.org/maxplanck-ie/snakepipes\n    :alt: Build Staus\n\n.. image:: https://zenodo.org/badge/54579435.svg\n    :target: https://zenodo.org/badge/latestdoi/54579435\n    :alt: Citation\n\n\nsnakePipes are flexible and powerful workflows built using `Snakemake \u003chttps://snakemake.readthedocs.io\u003e`__ that simplify the analysis of NGS data.\n\n.. image:: ./docs/content/images/snakePipes_small.png\n   :scale: 20 %\n   :width: 100 px\n   :height: 100 px\n   :align: right\n\nWorkflows available\n--------------------\n\n- DNA-mapping*\n- ChIP-seq*\n- mRNA-seq*\n- noncoding-RNA-seq*\n- ATAC-seq*\n- scRNA-seq\n- Hi-C\n- Whole Genome Bisulfite Seq/WGBS\n\n**(*Also available in \"allele-specific\" mode)**\n\nInstallation\n-------------\n\nSnakepipes is a set of Snakemake workflows which use conda for installation and dependency resolution, so you will need to `install conda \u003chttps://conda.io/docs/user-guide/install/index.html\u003e`__ first.\n\nAfterward, simply run the following:\n\n``conda install mamba -c conda-forge \u0026\u0026 mamba create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes``\n\nThis will create a new conda environment called \"snakePipes\" into which snakePipes is installed. You will then need to create the conda environments needed by the various workflows. To facilitate this we provide the `snakePipes` commands:\n\n* ``conda activate snakePipes`` to activate the appropriate conda environment.\n* ``snakePipes createEnvs`` to create the various environments.\n\nIndices and annotations needed to run the workflows could be created by a simple command :\n\n``createIndices --genomeURL \u003cpath/url to your genome fasta\u003e --gtfURL \u003cpath/url to genes.gtf\u003e -o \u003coutput_dir\u003e \u003cname\u003e``\n\nwhere `name` refers to the name/id of your genome (specify as you wish).\n\nA few additional steps you can then take:\n\n1. **Modify/remove/add the organism yaml files appropriately** : these yaml files would contain location of appropriate\nGTF files and genome indexes corresponding to different organisms. The location of these files after installation can be\nfound using ``snakePipes info`` command.\n\n2. **Modify the cluster.yaml file appropriately** : This yaml file contains settings for your cluster scheduler (SGE/slurm).\nLocation revealed using ``snakePipes info`` command.\n\n\nDocumentation\n--------------\n\nFor detailed documentation on setup and usage, please visit our `read the docs page \u003chttps://snakepipes.readthedocs.io/en/latest/\u003e`__.\n\n\nCitation\n-------------\n\nIf you adopt/run snakePipes for your analysis, cite it as follows :\n\nBhardwaj, Vivek, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S. Richter, Devon P. Ryan, and Thomas Manke. 2019. “snakePipes: Facilitating Flexible, Scalable and Integrative Epigenomic Analysis.” Bioinformatics , May. `doi:10.1093/bioinformatics/btz436 \u003chttps://doi.org/10.1093/bioinformatics/btz436\u003e`__\n\n\nNote\n-------------\n\nSnakePipes are under active development. We appreciate your help in improving it further. Please use issues to the GitHub repository for feature requests or bug reports.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxplanck-ie%2Fsnakepipes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaxplanck-ie%2Fsnakepipes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxplanck-ie%2Fsnakepipes/lists"}