[{"_1":2,"_152":-5,"_153":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_131":132},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11,"_20":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_23":24,"_25":-5,"_26":11,"_27":11,"_28":29,"_30":31,"_32":-5,"_33":11,"_34":35,"_84":-5,"_85":86,"_124":-5,"_125":11,"_126":17,"_127":11,"_128":-5,"_129":130},"canonicalUrl","https://hub.docker.com/r/brsynth/retropath2-wrapper/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","brsynth","reponame","retropath2-wrapper","cloudBuildSource","isAutobuildsAvailable","repo",{"_36":37,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":70,"_75":11,"_76":77,"_81":29,"_82":83},"categories",[],"content_types",[40],"image","date_registered","2020-05-08T15:56:30.28715Z","description","","is_private","last_updated","2020-06-11T08:25:20.501112Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",346,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# Retropath2.0 wrapper\n\n\nImplementation of the KNIME retropath2.0 workflow. Takes for input the minimal (dmin) and maximal (dmax) diameter for the reaction rules and the maximal path length (maxSteps). The tool expects the following files: `rules.csv`, `sink.csv` and `source.csv` and produces results in an output folder.\n\n## Standalone\n\n### Prerequisites\n\n* Python 3\n\n### Quick start\nThe main code is `src/RetroPath2.py` and can be run as the following:\n```\npython src/RetroPath2.py \\\n -sinkfile \\\n -sourcefile \\\n -max_steps 3 \\\n -rulesfile \\\n -topx 100 \\\n -dmin 0 \\\n -dmax 1000 \\\n -mwmax_source 1000 \\\n -mwmax_cof 1000 \\\n -timeout 30 \\\n -outdir \\\n -is_forward False\n```\n\n\n## Docker\n\nRetroPath2 can be run into a docker container.\n\n### Prerequisites\n\n* Docker - [Install](https://docs.docker.com/install/)\n\n### Installation\nBefore running the container, the image has to be built with:\n```\ncd docker\ndocker-compose build\n```\n\n### Run\nThen, the tool is runnable by:\n```\ncd docker\n./RetroPath2.sh\n -sinkfile \\\n -sourcefile \\\n -max_steps 3 \\\n -rulesfile \\\n -topx 100 \\\n -dmin 0 \\\n -dmax 1000 \\\n -mwmax_source 1000 \\\n -mwmax_cof 1000 \\\n -timeout 30 \\\n -outdir \\\n -is_forward False\n```\n\nTo call the tool with fresh code:\n```\ndocker-compose run --rm -v :/home/src retropath2\n```\n\nTo call the tool from any location:\n```\ncd docker\ndocker-compose run --rm \\\n -v :/home/source.csv:ro \\\n -v :/home/sink.csv:ro \\\n -v :/home/rules.csv:ro \\\n -v :/home/outdir \\\n -w /home \\\n retropath2 python src/RetroPath2.py \\\n -sinkfile \\\n -sourcefile \\\n -max_steps 3 \\\n -rulesfile \\\n -topx 100 \\\n -dmin 0 \\\n -dmax 1000 \\\n -mwmax_source 1000 \\\n -mwmax_cof 1000 \\\n -timeout 30 \\\n -outdir \\\n -is_forward False\n```\n\n## Test\nAll modes can be tested with:\n```\ncd test\n./run[-in-docker].sh\n```\n\n\n\n\n### How to cite RetroPath2.0?\nPlease cite:\n\nDelépine B, Duigou T, Carbonell P, Faulon JL. RetroPath2.0: A retrosynthesis workflow for metabolic engineers. Metabolic Engineering, 45: 158-170, 2018. DOI: https://doi.org/10.1016/j.ymben.2017.12.002\n","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":17,"_79":11,"_80":11},"read","write","admin","user","storage_size",1242801629,"orgData","recentTags",[87],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":96,"_46":113,"_114":90,"_115":29,"_116":52,"_53":117,"_118":119,"_120":104,"_121":113,"_122":62,"_123":17},"content_type","creator",7497403,"full_size",1242651933,"id",99530887,"images",[97],{"_98":99,"_100":101,"_102":44,"_103":104,"_105":106,"_107":108,"_109":44,"_110":-5,"_111":92,"_59":62,"_112":-5},"architecture","amd64","digest","sha256:83366960c95253ef52056e352d6705381065b2dcd894eda6c583593ef8dc4b8c","features","last_pulled","2026-09-15T20:31:47.813196692Z","last_pushed","2020-06-11T00:00:35Z","os","linux","os_features","os_version","size","variant","2020-06-11T08:25:20.203043Z","last_updater","last_updater_username","media_type","latest","repository",8999487,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":133,"_140":141,"_129":150,"_151":11},{"_36":134,"_38":135,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":136,"_53":31,"_28":29,"_54":55,"_56":40,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":29,"_69":137,"_75":11,"_76":139,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":138},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_142":60,"_143":-5,"_144":-5,"_145":146},"count","next","previous","results",[147],{"_88":40,"_89":90,"_91":92,"_93":94,"_95":148,"_46":113,"_114":90,"_115":29,"_116":52,"_53":117,"_118":119,"_120":104,"_121":113,"_122":62,"_123":17},[149],{"_98":99,"_100":101,"_102":44,"_103":104,"_105":106,"_107":108,"_109":44,"_110":-5,"_111":92,"_59":62,"_112":-5},[],"canDeleteTags","actionData","errors"]

brsynth/retropath2-wrapper

Tags for brsynth/retropath2-wrapper