[{"_1":2,"_174":-5,"_175":-5},"loaderData",{"_3":4,"_13":14,"_21":22,"_153":154},"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":85,"_104":105,"_144":-5,"_145":11,"_146":17,"_147":11,"_148":-5,"_149":11,"_150":-5,"_151":152},"canonicalUrl","https://hub.docker.com/r/bromberglab/funtrp/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","bromberglab","reponame","funtrp","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","2019-01-27T01:47:36.65636Z","description","fuNTRp : function Neutral Toggle Rheostat predictor","is_private","last_updated","2019-03-02T08:11:00.596109Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52],"application/vnd.docker.container.image.v1+json","name","pull_count",428,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# fuNTRp - function Neutral/Toggle/Rheostat predictor\n\nA Random Forest-based predictor to classify protein positions by type based on the expected range of mutational impacts at that position: Neutral (most mutations have no or weak effects), Rheostat (range of effects; i.e. func-tional tuning), or Toggle (mostly strong effects).\n\n# Requirements\n- Docker (https://www.docker.com)\n- Sequence database (RostLab Big_80 database, size: 27.27 GB; http://www.rostlab.org/services/ppmi/download_file?format=gzip&file_to_download=db); A Docker image of PredictProtein (bromberglab/predictprotein) will be downloaded automatically.\n\n# Usage\n\n## 1 Get sources\nOpen a terminal and checkout the funtrp repository:\n```\ngit clone https://git@bitbucket.org/bromberglab/funtrp.git\n```\nor download the zipped version:\n```\ncurl --remote-name https://bitbucket.org/bromberglab/funtrp/get/master.zip\nunzip master.zip\n```\nThe following steps assume the current working directory as the funtrp (repository) base directory.\n\n## 2 Sequence Database\nDownload and extract the [sequence database](http://www.rostlab.org/services/ppmi/download_file?format=gzip&file_to_download=db). Move files located in *data/big/* and starting with *big_80* into the *db/* folder of the funtrp base directory; any other databases in the *data/* directory are not required and can be deleted. Open a terminal, navigate to the funtrp base directory and execute:\n```\ncd db/\nwget -O rostlab-data.txz \"http://www.rostlab.org/services/ppmi/download_file?format=gzip&file_to_download=db\"\nxz -d rostlab-data.txz\ntar xvf rostlab-data.tar\nmv data/big/big_80* .\nrm -rf data rostlab-data.tar\n```\n\n## 3 Docker image\nDocker images are available via the Docker cloud or can be build from the sources available in this repository.\n\n### 3.1 Use available docker images\nOpen a terminal and execute:\n```\ndocker pull bromberglab/predictprotein\ndocker pull bromberglab/funtrp\n```\n### 3.2 Build funtrp docker image from sources\nOpen a terminal, navigate to the funtrp base directory and execute:\n```\ndocker build -t bromberglab/funtrp .\n```\n\n## 4 Run funtrp\nfuntrp can be run using the provided binary (*funtrp.sh* in the base directory) or directly via the docker engine.\n\n### 4.1 Run funtrp using available binary\nOpen a terminal and execute:\n```\n/funtrp.sh \n```\n\n### 4.2 Run funtrp using docker engine directly\nCopy a query sequence in fasta format (.fa or .fasta)to the *mnt/* folder in the funtrp base directory (note here, that refers to the filename without any path information and refers to the query file name without extension). Then open a terminal, navigate to the funtrp base directory and execute:\n```\ndocker run --rm \\\n -v /db:/usr/share/rostlab-data/data/big \\\n -v /mnt:/mnt/local-storage \\\n bromberglab/predictprotein predictprotein \\\n --target=query.profRdb --target=query.mdisorder --target=consurf \\\n --output-dir=/mnt/local-storage/pprotein/ --work-dir=/mnt/local-storage/pprotein//tmp \\\n --seqfile=/mnt/local-storage/ \\\n --num-cpus=2 \\\n --blast-processors=10\n\ndocker run --rm \\\n -v /db:/rheostat/db \\\n -v /mnt:/mnt bromberglab/funtrp \n```\n\n## 5 Example\nOpen a terminal, navigate to the funtrp base directory and execute:\n```\n./funtrp.sh example/P37173.fasta\n```\nResults will then be available at *mnt/P37173_funtrp.csv*\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",2032426608,"orgData",{"_86":87,"_88":89,"_90":91,"_92":29,"_93":94,"_95":94,"_96":94,"_97":94,"_98":99,"_100":94,"_101":94,"_102":94,"_103":17},"id","e287667504df45c4824c324ee0631bce","uuid","e2876675-04df-45c4-824c-324ee0631bce","type","organization","orgname","full_name","","location","company","profile_url","date_joined","2017-03-14T19:02:12.185622Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[106],{"_107":40,"_108":109,"_110":111,"_86":112,"_113":114,"_46":132,"_133":134,"_135":29,"_136":52,"_53":137,"_138":139,"_140":122,"_141":132,"_142":62,"_143":17},"content_type","creator",2506149,"full_size",1054804006,48464900,"images",[115],{"_116":117,"_118":119,"_120":94,"_121":122,"_123":124,"_125":126,"_127":94,"_128":-5,"_129":130,"_59":62,"_131":-5},"architecture","amd64","digest","sha256:f9aa1870d69eaebae0d7c1dc55c6cf2ba99a2da63e87c8c02204664ce10b7d63","features","last_pulled","2026-09-21T10:51:21.31361725Z","last_pushed","2019-03-02T08:11:01Z","os","linux","os_features","os_version","size",1054803910,"variant","2019-03-02T08:11:00.270125Z","last_updater",1553753,"last_updater_username","media_type","latest","repository",6605379,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_34":155,"_162":163,"_151":172,"_173":11},{"_36":156,"_38":157,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":158,"_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":159,"_75":11,"_76":161,"_81":29,"_82":83},[],[40],[52],{"_71":11,"_72":160},[74],{"_78":17,"_79":11,"_80":11},"tags",{"_164":60,"_165":-5,"_166":-5,"_167":168},"count","next","previous","results",[169],{"_107":40,"_108":109,"_110":111,"_86":112,"_113":170,"_46":132,"_133":134,"_135":29,"_136":52,"_53":137,"_138":139,"_140":122,"_141":132,"_142":62,"_143":17},[171],{"_116":117,"_118":119,"_120":94,"_121":122,"_123":124,"_125":126,"_127":94,"_128":-5,"_129":130,"_59":62,"_131":-5},[],"canDeleteTags","actionData","errors"]

bromberglab/funtrp

Tags for bromberglab/funtrp