[{"_1":2,"_315":-5,"_316":-5},"loaderData",{"_3":4,"_13":14,"_16":17,"_311":312},"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},"username","routes/_layout.r.$namespace.$reponame",{"_18":19,"_20":-5,"_21":11,"_22":11,"_23":24,"_25":26,"_27":-5,"_28":11,"_29":30,"_85":86,"_106":107,"_310":11},"canonicalUrl","https://hub.docker.com/r/dessimozlab/fastoma/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","dessimozlab","reponame","fastoma","cloudBuildSource","isAutobuildsAvailable","repo",{"_31":32,"_38":39,"_41":42,"_43":44,"_45":11,"_46":47,"_48":49,"_50":51,"_34":26,"_23":24,"_54":55,"_56":-5,"_57":58,"_59":60,"_61":62,"_63":-5,"_64":58,"_65":66,"_67":11,"_68":24,"_69":70,"_75":11,"_76":77,"_82":24,"_83":84},"categories",[33],{"_34":35,"_36":37},"name","Data science","slug","data-science","content_types",[40],"image","date_registered","2023-11-06T09:27:17.541595Z","description","Containers to run FastOMA nextflow pipeline to infer Hierarchical Orthologous Groups (HOGs)","is_private","last_updated","2025-12-29T21:05:04.120373Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[52,53],"application/vnd.oci.image.index.v1+json","application/vnd.docker.distribution.manifest.list.v2+json","pull_count",7620,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","FastOMA\n======\nFastOMA is a scalable software package to infer orthology relationship.\n\nWant to learn more about FastOMA and try it online, check out [FastOMA academy](https://omabrowser.org/oma/academy/module/fastOMA_2023) !\n\n# Input and Output:\n\n### Input:\n1. Sets of protein sequences in FASTA format (with `.fa` extension) in the folder `proteome`.\nThe name of each fasta file is the name of species. Please make sure that the name of fasta records do not contain special characters including `||`.\n\n2. Rooted Species tree in [newick format](http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-newick-trees).\nA rough species tree is enough, and it does not need to be binary (fully resolved). Besides, we do not need branch lengths. You could use the NCBI tree via ete3 package.\nNote that the name of leaves of the tree (species name) should be the same as the file name of FASTAs (without `.fa` extension) (item 1).\nAnd there shouldn't be any repeated names in leaves names and internal node names. The tree should not be with quotation.\n\n3. The omamer database which is available for download from the [OMA browser](https://omabrowser.org/oma/current/).\nThe FastOMA workflow will automatically download the omamer database for LUCA (7.7 GB) if the argument `--omamer_db` is not\nprovided on the command line. The argument can be a local file (e.g. a previously downloaded omamer database file) or\na URL to an alternative omamer database, e.g. a subset of the LUCA database which is smaller, like Primates with this [link](https://omabrowser.org/All/Primates-v2.0.0.h5) which is ~100MB. However, to have a broader reference gene families, we recommend to use the LUCA database if possible.\n\n\nYou can see an example in the [testdata](https://github.com/DessimozLab/FastOMA/tree/main/testdata/in_folder) folder.\n```\n$ ls proteome\nAQUAE.fa CHLTR.fa MYCGE.fa\n$ cat species_tree.nwk\n((AQUAE,CHLTR)inter1,MYCGE)inter2;\n```\n\nBesides, the internal node should not contain any special character (e.g. `\\` `/` or `space`).\nThe reason is that FastOMA write some files whose names contain the internal node's name.\nIf the species tree does not have label for some/all internal nodes, FastOMA labels them sequentially.\nThe updated tree will be stored in the output folder named as `species_tree_checked.nwk`.\n\n\n\n### Main output:\nOrthology information as HOG structure in [OrthoXML](https://orthoxml.org/) format\nwhich can be used with [PyHAM](https://github.com/DessimozLab/pyham).\nThe details of output are described [below](#expected-output-structure-for-test-data).\n\nAdditionally, FastOMA generates TSV files for rootlevel HOGs (deepest level) and\nmarker genes groups (one gene per species maximum) together with dumps of fasta\nfiles (one per rootlevel HOG / marker gene).\n\n\n# How to run FastOMA\n\nFastOMA is implemented as a [nextflow-workflow](https://www.nextflow.io/). As such, FastOMA can be run without\nany installation steps given the system supports running either docker containers, singularity containers or has conda\ninstalled.\n\n```bash\nnextflow run dessimozlab/FastOMA -profile docker --input_folder /path/to/in_folder --output_folder /path/to/out_folder\n```\n\nNextflow will automatically fetch the [dessimozlab/FastOMA](https://github.com/dessimozlab/FastOMA) repository and starts\nthe `FastOMA.nf` workflow. The `-profile` argument must be used to specify the profile to use. We support `docker`,\n`singularity` and `conda` which then automatically set up the necessary tools by downloading the required containers or creating\na conda environment with the necessary dependencies.\n\nSee also [How to install FastOMA](#how-to-install-FastOMA) for additional ways how to install and run FastOMA. Note also the\nsection on the different [profiles](#using-different-nextflow-profiles).\n\nFor more informaton on how Nextflow and Docker work together, see [here](https://www.nextflow.io/blog/2016/docker-and-nextflow.html).\n\n### More details on how to run\nWe provide for every commit of the repository a docker image for FastOMA on dockerhub. You can specify the container as\npart of the nextflow command with the parameter `container_version`. If you want to use the container of the current\ngit checkout version, you can specify this in the following way:\n\n```bash\nnextflow run FastOMA.nf -profile docker \\\n --container_version \"sha-$(git rev-list --max-count=1 --abbrev-commit HEAD)\" \\\n --input_folder testdata/in_folder \\\n --output_folder myresult/\n```\n\n\n# How to install FastOMA\n\nThere are four ways to run/install FastOMA detailed below:\n\n### 1. Running workflow directly\n\nThe FastOMA workflow can be run directly without any installation using nextflow's ability to fetch a workflow from github. A specific version can be selected by specifying the `-r` option to nextflow to select a specific version of FastOMA:\n\n```bash\nnextflow run desimozlab/FastOMA -r 0.2.0 -profile conda\n```\n\nThis will fetch version 0.2.0 from github and run the FastOMA workflow using the conda profile. See section [How to run fastOMA](#how-to-run-fastoma).\n\n### 2. Cloning the FastOMA repo and running from there\n\n```bash\ngit clone https://github.com/DessimozLab/FastOMA.git\ncd FastOMA\nnextflow run FastOMA.nf -profile docker --container_version \"sha-$(git rev-list --max-count=1 --abbrev-commit HEAD)\" ...\n```\n\n### 3. Manual installation (for development) in python virtual environment\n\n- install [mafft](https://mafft.cbrc.jp/alignment/software) and [FastTree](http://www.microbesonline.org/fasttree/) and ensure the software is accessible on the PATH.\n- install python >= 3.9\n- create virtual environment, activate it and install FastOMA with additional extras inside it:\n ```bash\n python3 -m venv .venv\n source .venv/bin/activate\n pip install FastOMA[report,nextflow]\n ```\n You can also install FastOMA from a clone of the repository in editable mode with `pip install -e .[report,nextflow]`.\n\n- run pipeline including with some testdata:\n ```bash\n nextflow run FastOMA.nf -profile standard --input_folder testdata/in_folder --output_folder output -with-report\n ```\n\n\n### 4. Manual installation in conda/mamba environment\nIn the FastOMA repository, we provide a conda environment file that can be used to generate a conda / mamba\nenvironment.\n\nFor Conda installation you need to first download the Miniconda installer from [this link](https://docs.anaconda.com/free/miniconda/).\n\nFor MacOS:\n```\ncurl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o Miniconda3.sh\nbash Miniconda3.sh\n```\n\nFor Linux\n```\nwget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -o Miniconda3.sh\nbashMiniconda3.sh\n```\n\nThen follow the instruction on the terminal. Finally, close and re-open the terminal and run\n```\nconda create -n fastoma python=3.9 --file environment_conda.yml\ncond activate mamba activate FastOMA\n```\nThen, clone and install fastOMA using\n```\ngit clone https://github.com/DessimozLab/FastOMA.git\n\n```\n\n\n\nAlternatively, you could use Mamba instead of Conda (which needs its own [installation](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html)).\nNote that it is not encouraged to have both Mamba and conda on one system, [more info](https://stackoverflow.com/questions/76760906/installing-mamba-on-a-machine-with-conda).\n\n```\nmamba env create -n FastOMA -f environment_conda.yml\nmamba activate FastOMA\n```\n\nAfterwards, you can run the workflow using nextflow (which is installed as part of the conda environment)\n\n```\nnextflow run FastOMA.nf -profile standard|slurm --input_folder /path/to/input_folder --output_folder /path/to/output\n```\nNote that you should use either the profile `standard` or `slurm` such the nextflow executor will use the activated environment.\n\n\n## Using different nextflow profiles\n\nNextflow provides support to run a workflow on different infrastructures. Selection of this is done using the `-profile` argument.\nFor FastOMA, we've implemented the following profiles below. Additional ones can also be created by specifying them in the `nextflow.config` file.\n\n### Docker\nWith `-profile docker` one can use docker as an execution platform. It requires docker to be installed on the system. The pipeline\nwill automatically fetch missing containers from dockerhub (e.g. dessimozlab/fastoma) if not found locally. By default, the version\n`latest` is used by the pipeline, however we provide images for any branch and release as well; even for every recent commit.\nOne can select the desired container via the `--container_version` argument\n\n```\nnextflow run FastOMA.nf -profile docker \\\n --container_version \"sha-$(git rev-list --max-count=1 --abbrev-commit HEAD)\" \\\n --input_folder testdata/in_folder \\\n --output_folder myresult/\n```\nThis will use the container that is tagged with the current commit id. Similarly, one could also use\n`--container_version \"0.2.0\"` to use the container with version `dessimozlab/fastoma:0.2.0` from dockerhub.\n\n### Singularity\nWith `-profile singularity` singularity containers will be used to run the workflow. It requires singularity to\nbe installed on your system. The containers are automatically pulled from dockerhub and converted to singularity\ncontainers. The same options as for [Docker](#docker) will be available.\n\n### Conda\nwith `-profile conda`, the FastOMA workflow will create a conda environment which contains the necessary\ndependencies and use this environment to run the workflow steps. Note that this environment does not need\nto be activated manually. If you prefer to install the dependencies inside a conda or mamba environment\nyourself, this can be achieved as described in [](#manual-installation-for-development-in-python-virtual-environment).\n\n### Slurm (with singularity/conda)\nOn a HPC system you typically run processes using a scheduler system such as slurm or LSF. We provide\nprofiles `-profile slurm`, `-profile slurm_singularity` and `-profile slurm_conda` to run FastOMA with\nthe respective engine using [slurm](https://slurm.schedmd.com/overview.html) as a scheduler system.\nIf you need a different scheduler, it is quite straight forward to\nset it up in `nextflow.config` based on the existing profiles and the documentation of\n[nextflow executors](https://www.nextflow.io/docs/latest/executor.html).\n\n\n# How to run FastOMA on the test data\nNote : If you want to use FastOMA with Docker or other profiles check on the different [here](#using-different-nextflow-profiles).\n\nFirst, cd to the `testdata` folder and download the omamer database (optional) and change its name to `omamerdb.h5`.\n```\ncd FastOMA/testdata\nwget https://omabrowser.org/All/Primates-v2.0.0.h5 # 105MB\nmv Primates-v2.0.0.h5 in_folder/omamerdb.h5\n```\n(This is for the test however, I would suggest downloading the `LUCA-v2.0.0.h5` instead of `Primates-v2.0.0.h5` for your real analysis.).\nCheck the item 2 in the [input section](https://github.com/sinamajidian/FastOMA#input) for details.\n\nNow we have such a structure in our testdata folder.\n```\n$ tree ../testdata/in_folder\n ├── omamerdb.h5\n ├── proteome\n │ ├── AQUAE.fa\n │ ├── CHLTR.fa\n │ └── MYCGE.fa\n └── species_tree.nwk\n```\n\nFinally, run the package using nextflow as below:\n```\n# cd FastOMA/testdata\nnextflow run ../FastOMA.nf \\\n --input_folder in_folder \\\n --omamer_db in_folder/omamerdb.h5 \\\n --output_folder out_folder \\\n --report \\\n -profile standard\n```\n\n\n\nNote that to have a comprehensive test, we set the default value of needed cpus as 10.\nIf you face `.command.sh: line 2: papermill: command not found`, note that the orthology inference is finished and you have them in output folder and you may want to install `pip install -e .[report]` to have `papermill` generating the report and run the last step.\n\n\n## Expected log for test data\nAfter few minutes, the run for test data finishes.\n```\n[] process > check_input () [100%] 1 of 1 ✔\n[] process > omamer_run () [100%] 3 of 3 ✔\n[] process > infer_roothogs () [100%] 1 of 1 ✔\n[] process > batch_roothogs () [100%] 1 of 1 ✔\n[] process > hog_big () [100%] 1 of 1 ✔\n[] process > hog_rest () [100%] 2 of 2 ✔\n[] process > collect_subhogs () [100%] 1 of 1 ✔\n```\n\nThe first step is to run [OMAmer](https://github.com/DessimozLab/omamer) for finding the putative gene families (putative rootHOG) based on kmer similarity.\nNext, we write them in FASTA files, which could be used to run next steps in parrallel on each FASTA gene family.\nThen, to have similar size jobs, we batch these FASTA files either as one big roothog (per job `hog_big`) or a few hundreds together as one job `hog_rest`.\nThese are decided based on the FASTA file size. Finally, once all jobs of `hog_big` and `hog_rest` are done, we `collect_subhog` and save all outputs.\n\nIf the run interrupted, by adding `-resume` to the nextflow commond line, you might be able to continue your previous nextflow job.\n\nPro-tip. Nextflow creat a folder named `work` for storing its temprorary files. The characters in the bracket of the nextflow log (not shown here) are the short form of the folder address in `work/`\nwhere the last task of such job were done.\ne.g `[3f/2efg] process > check_input (1)` you can `cd work/3f/2efg` then use tab to complete the folder name, then you can see the temporary files of `check_input` task. In such folder there are some hidden files `.command.log/sh/run`.f\n\n\n## Expected output structure for test data\n\nThe output of FastOMA includes several output files regarding orthology inference\n(`OrthologousGroups.tsv`, `RootHOGs.tsv`, `FastOMA_HOGs.orthoxml`, `orthologs.tsv.gz` and `species_tree_checked.nwk`),\na jupyter notebook based report about the dataset (`report.ipynb` and `report.html`) and four folders\n(`hogmap`, `OrthologousGroupsFasta`, `RootHOGsFasta` and `stats`).\n\nThe `hogmap` folder includes the output of [OMAmer](https://github.com/DessimozLab/omamer); each file corresponds to an input proteome.\nThe folder `OrthologousGroupsFasta` includes FASTA files, and all proteins inside each FASTA file are orthologous to each other.\nThese could be used as gene markers for species tree inference with refined resolution, [more info](https://f1000research.com/articles/9-511).\nNote that OrthologousGroups are groups of strict orthologs, with at most 1 representative per species.\nHierarchical Orthologous Groups are groups of orthologs and paralogs, defined at each taxonomic level. The file\n`FastOMA_HOGs.orthoxml` contains all the nested groups in orthoxml format. The `RootHOGs.tsv` and `RootHOGsFasta/` files contains\nthe groups at the deepest level.\n\nSo, following files and folders should appear in the folder `out_folder` which was the argument.\n```\n$tree out_folder\n├── FastOMA_HOGs.orthoxml\n├── hogmap\n│ ├── AQUAE.fa.hogmap\n│ ├── CHLTR.fa.hogmap\n│ └── MYCGE.fa.hogmap\n├── OrthologousGroupsFasta\n│ ├── OG_0000001.fa.gz\n│ ├── OG_0000002.fa.gz\n│ ├── OG_0000003.fa.gz\n│ ├ ...\n├── OrthologousGroups.tsv\n├── orthologs.tsv.gz\n├── phylostratigraphy.html\n├── report.html\n├── report.ipynb\n├── RootHOGsFasta\n│ ├── HOG:0000001.fa.gz\n│ ├── HOG:0000002.fa.gz\n│ ├── HOG:0000003.fa.gz\n│ ├ ...\n├── RootHOGs.tsv\n├── species_tree_checked.nwk\n└── stats\n ├── pipeline_dag_.html\n ├── report_.html\n ├── timeline_.html\n └── trace_.txt\n```\namong which `FastOMA_HOGs.orthoxml` is the final output in [orthoXML format](https://orthoxml.org/0.4/orthoxml_doc_v0.4.html). Its content looks like this\n\n```\n\n\n \n \n \n \n \n \n\n ...\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n```\n\nIf you are interested in specific gene in specific species, and wants to know\nproteins that are in the gene family, you can find its protein ID in the file `RootHOGs.tsv` using grep.\nThe first column of this file `RootHOGs.tsv` shows the rootHOG ID which could be searched on the [OMA browser](https://omabrowser.org/).\nNote that some of the input genes might not appear in this file.\n\nTo find list of genes that are orthologous to your gene of interest, you can search in the file `OrthologousGroups.tsv`\nwhere each line is an orthologous group. Each line corresponds to a FASTA file in the folder ` OrthologousGroupsFasta`.\n\n\nNote that some of the output files are symlink (a.k.a a symbolic link), linked to files in the folder `work` created by nextflow pipeline.\nThis means that if you remove or rename the `work` and its parents folder, you will not have access to the output files anymore.\n\nIf you are working on a large scale project, you may need to change the limitation on the number of files opened in linux using `ulimit -n 271072`.\n\nYou can learn about OMA and FastOMA on [OMA Academy](https://omabrowser.org/oma/academy/).\n\n\nRegarding temp folders:\nThe folder `temp_output` includes `gene_id_dic_xml.pickle` storing mapping between gene name and gene integer ID used for orthoxml format,\n`temp_omamer_rhogs` a folder that includes the fasta files of omamer-based gene families (described [here](https://github.com/DessimozLab/FastOMA#under-the-hood-what-are-fastoma-gene-families)).\n\nThe folder `temp_pickles` includes the pickle file of orthoxml object which are final product of FastOMA for each gene family stored in `temp_omamer_rhogs`.\nThese file can be empty when the gene family doesn't end up as a group (usually with size of 5 Byte). Gene trees and MSAs will be stored in `temp_pickles`\nif activated (in `_config.py` and fastOMA installed with `pip -e` ).\n\n\n\n### Using omamer's output\nThe first step of the FastOMA pipele is to run [OMAmer](https://github.com/DessimozLab/omamer). If you already have the hogmap files, you can put them in the `in_folder/hogmap_in`.\nThen your structure of files will be\n```\n$ tree ../testdata/\n├── in_folder\n│ ├── hogmap_in\n│ │ ├── CHLTR.fa.hogmap\n│ │ ├── MYCGE.fa.hogmap\n│ ├── omamerdb.h5\n│ ├── proteome\n│ │ ├── AQUAE.fa\n│ │ ├── CHLTR.fa\n│ │ └── MYCGE.fa\n│ └── species_tree.nwk\n└── README.md\n```\nIn this case, FastOMA uses two hogmap files and only run omamer for the `AQUAE.fa`. Then continue the rest of pipeline.\nLet's save the planet together with\n[green computational Biology](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009324).\n\n\n### Run on a cluster\nFor running on a SLURM cluster you can add `-c ../nextflow_slurm.config` to the commond line.\n\n```\n# cd FastOMA/testdata\n# rm -r out_folder work # You may remove stuff from previous run\n# ls ../FastOMA.nf\n\nnextflow ../FastOMA.nf -c ../nextflow_slurm.config --input_folder in_folder --output_folder out_folder\n```\n\nYou may need to re-run nextflow command line by adding `-resume`, if the allocated time is not enough for your dataset.\n\nYou may need to increase the number of opoened files in your system with `ulimit -n 131072` or higher as nextflow generates hundreds of files depending on the size of your input dataset.\n\n\n## Handle splice files\nYou can put the splice files in the folder `in_folder/splice`. They should be named as `species_name.splice` for each species.\nFor each row of different isforoms of a preotien, FastOMA selects the best one (based on omamer family score and isoform length).\nWe also use those proteins that are not in splice file but present in the FASTA proteome file.\n```\n$ head HUMAN.splice\nHUMAN00001;HUMAN00002;HUMAN00003;HUMAN00004;HUMAN00005;HUMAN00006\nHUMAN00007;HUMAN00008;HUMAN00009;HUMAN00010;HUMAN00011;HUMAN00012;\nHUMAN00022;HUMAN00023;HUMAN00024;\nHUMAN00027;HUMAN00028;HUMAN00029;HUMAN00030;HUMAN00031;HUMAN00032;HUMAN00033\nHUMAN00034;HUMAN00035\nHUMAN00036\nHUMAN00037\n```\n\nThe selected isforoms will be added as a new column to the input splice files stored as tsv at `out_folder/temp_output/selected_isoforms/`\n\n## Under the hood: what are fastOMA gene families?\nFirstly, those proteins that are mapped to the same OMAdb rootHOG (e.g. HOG:D0066142 for HOG:D0066142.1a.1a) by OMAmer are\ngrouped together to create query rootHOGs (no protein from OMAdb is stored), from now on called rootHOG.\nThen, as OMAmer provide us with alternative mapping, we try to merge those rootHOGs (high chance of split HOGs) that have\nmany shared mappings. The query proteins of these rootHOGs will be stored in only one rootHOG.\nThese will be saved as fasta files in `out_folder/temp_output/temp_omamer_rhogs` with file names format `HOG_LXXXXX.fa`. `L` is the release ID of OMADB.\nReplacing `_` with ':' gives the HOG ID which could be investigated in the [OMA Browser](https://omabrowser.org/oma/hog/HOG:D0114562/Sar/iham/).\n\nThere are some cases that only one protein is mapped to one rootHOG, called singleton (which is not good, we are hoping for orthologous groups/pairs).\nUsing alternative OMAmer mapping, FastOMA tries to put these to other rootHOGs. Still some will be left.\n\nFastOMA uses the [linclust](https://github.com/soedinglab/MMseqs2#cluster) software to find new gene families on set of unmapped proteins and singletons.\nThese will be saved as fasta files in `out_folder/temp_output/temp_omamer_rhogs` with file names format `HOG_clustXXXXX.fa`.\nThese are initial gene families that are used in `infer_subhogs` step, which could be split into a few smaller gene families.\n\n## Cite us\n\nMajidian, Sina, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy, Stefano Pascarelli, David Moi, Natasha Glover, Adrian M. Altenhoff, and Christophe Dessimoz. \"Orthology inference at scale with FastOMA.\" bioRxiv (2024): 2024-01. https://www.biorxiv.org/content/10.1101/2024.01.29.577392v1.full","has_starred","hub_user","immutable_tags_settings",{"_71":11,"_72":73},"enabled","rules",[74],".*","is_automated","permissions",{"_78":79,"_80":11,"_81":11},"read",true,"write","admin","user","storage_size",205151300816,"orgData",{"_87":88,"_89":90,"_91":92,"_93":24,"_94":95,"_96":95,"_97":98,"_99":95,"_100":101,"_102":95,"_103":95,"_104":95,"_105":79},"id","be8871f6b43048abac19698eea98ac26","uuid","be8871f6-b430-48ab-ac19-698eea98ac26","type","organization","orgname","full_name","","location","company","DessimozLab","profile_url","date_joined","2020-05-14T08:57:59.329937Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[108,162,171,197,222,249,274,283,292,301],{"_109":40,"_110":111,"_112":113,"_114":115,"_87":116,"_117":118,"_46":150,"_151":111,"_152":153,"_154":52,"_34":155,"_156":157,"_158":125,"_159":150,"_160":62,"_161":79},"content_type","creator",4606103,"digest","sha256:61d5fb731a5c668734cbd8150aa713ad3cc657690943dbb8cd5d78bc08295c46","full_size",390406656,1039528298,"images",[119,134,140,146],{"_120":121,"_112":122,"_123":95,"_124":125,"_126":127,"_128":129,"_130":95,"_131":-5,"_132":115,"_59":62,"_133":-5},"architecture","amd64","sha256:5adbdd1b443bd06c70fac6c8bb8406df19676116c15b09003c9da3732c648abd","features","last_pulled","2026-01-23T02:52:57.704466078Z","last_pushed","2025-12-29T21:04:58.619954844Z","os","linux","os_features","os_version","size","variant",{"_120":135,"_112":136,"_123":95,"_124":137,"_126":138,"_128":129,"_130":95,"_131":-5,"_132":139,"_59":62,"_133":-5},"arm64","sha256:b1898fa0dcff4e54397de498cd6e7aedb3ccb4b7dad5421611069f02f79111c0","2025-12-29T22:05:10.495753965Z","2025-12-29T21:04:57.899939251Z",363826471,{"_120":141,"_112":142,"_123":95,"_124":143,"_126":144,"_128":141,"_130":95,"_131":-5,"_132":145,"_59":62,"_133":-5},"unknown","sha256:f715e882e5f6e89655aa78c4c940f7bc609e8804b819b590d6b982a7f067e828","2025-12-29T22:05:11.330155805Z","2025-12-29T21:04:57.464915771Z",23686,{"_120":141,"_112":147,"_123":95,"_124":148,"_126":149,"_128":141,"_130":95,"_131":-5,"_132":145,"_59":62,"_133":-5},"sha256:8a4e593b731758070015aa5ee8c197129a5c691da3ee1bd95f300326cd4e848f","2025-12-29T22:05:10.648455071Z","2025-12-29T21:04:59.390734029Z","2025-12-29T21:05:02.821901Z","last_updater","last_updater_username","alpae","media_type","sha-3a3b950","repository",22377213,"tag_last_pulled","tag_last_pushed","tag_status","v2",{"_109":40,"_110":111,"_112":113,"_114":115,"_87":163,"_117":164,"_46":169,"_151":111,"_152":153,"_154":52,"_34":170,"_156":157,"_158":125,"_159":169,"_160":62,"_161":79},701788700,[165,166,167,168],{"_120":121,"_112":122,"_123":95,"_124":125,"_126":127,"_128":129,"_130":95,"_131":-5,"_132":115,"_59":62,"_133":-5},{"_120":135,"_112":136,"_123":95,"_124":137,"_126":138,"_128":129,"_130":95,"_131":-5,"_132":139,"_59":62,"_133":-5},{"_120":141,"_112":142,"_123":95,"_124":143,"_126":144,"_128":141,"_130":95,"_131":-5,"_132":145,"_59":62,"_133":-5},{"_120":141,"_112":147,"_123":95,"_124":148,"_126":149,"_128":141,"_130":95,"_131":-5,"_132":145,"_59":62,"_133":-5},"2025-12-29T21:05:00.15291Z","dev",{"_109":40,"_110":111,"_112":172,"_114":173,"_87":174,"_117":175,"_46":194,"_151":111,"_152":153,"_154":52,"_34":195,"_156":157,"_158":196,"_159":194,"_160":62,"_161":79},"sha256:af87766cc2635454233ffbaf1370bc8fb30cf5d9f6d1b18d65f811e56654e648",390405949,1038676172,[176,180,185,190],{"_120":121,"_112":177,"_123":95,"_124":178,"_126":179,"_128":129,"_130":95,"_131":-5,"_132":173,"_59":62,"_133":-5},"sha256:cbdafa4df4b37a554bf90878f8f54d192c2d804af3850e1ddb850a63bca3b773","2025-12-29T20:45:17.192886703Z","2025-12-27T18:23:04.76149346Z",{"_120":135,"_112":181,"_123":95,"_124":182,"_126":183,"_128":129,"_130":95,"_131":-5,"_132":184,"_59":62,"_133":-5},"sha256:5c28da89cb515ea36fb5bf84d5c29140d88ea6be22250eae1c2f34a31c4039e4","2025-12-27T20:18:57.138303663Z","2025-12-27T18:23:05.401569174Z",363826520,{"_120":141,"_112":186,"_123":95,"_124":187,"_126":188,"_128":141,"_130":95,"_131":-5,"_132":189,"_59":62,"_133":-5},"sha256:37d2d496d584d1f65de95c6b3744047fd1a7c6fe9984666958b1efb6a270d092","2025-12-27T20:18:58.327086471Z","2025-12-27T18:23:05.946038124Z",24056,{"_120":141,"_112":191,"_123":95,"_124":192,"_126":193,"_128":141,"_130":95,"_131":-5,"_132":189,"_59":62,"_133":-5},"sha256:78d119fe7eaea41213266e367f768c9559cad4fa8fae11daa7d7e978a01e9f69","2025-12-27T20:19:00.194027884Z","2025-12-27T18:23:06.433698794Z","2025-12-27T18:23:09.609137Z","sha-f0efd93","2025-12-29T21:04:59.671337167Z",{"_109":40,"_110":111,"_112":198,"_114":199,"_87":200,"_117":201,"_46":220,"_151":111,"_152":153,"_154":52,"_34":221,"_156":157,"_158":208,"_159":220,"_160":62,"_161":79},"sha256:6da9e68fd899dbc270e51edc7240b075665a0de400751860f666327578c24f94",390796171,1037119680,[202,206,211,216],{"_120":121,"_112":203,"_123":95,"_124":204,"_126":205,"_128":129,"_130":95,"_131":-5,"_132":199,"_59":62,"_133":-5},"sha256:01253c0f1b7ad72c39a8d2a9e01653714a2835cec22ff6443414dead0e322f13","2025-12-27T20:19:00.088533618Z","2025-12-23T15:50:44.480332169Z",{"_120":135,"_112":207,"_123":95,"_124":208,"_126":209,"_128":129,"_130":95,"_131":-5,"_132":210,"_59":62,"_133":-5},"sha256:5ecf85193550dcf290c7e3a4b44663060f6477ae21747d8b2f7a45dc578a7c13","2025-12-27T20:19:00.246636569Z","2025-12-23T15:50:45.635796021Z",364197898,{"_120":141,"_112":212,"_123":95,"_124":213,"_126":214,"_128":141,"_130":95,"_131":-5,"_132":215,"_59":62,"_133":-5},"sha256:2b6c13932f9a1f0d484818594dec0168aa963ebd450562a5efbb548e85546a7e","2025-12-27T20:18:58.159811716Z","2025-12-23T15:50:45.225361234Z",23933,{"_120":141,"_112":217,"_123":95,"_124":218,"_126":219,"_128":141,"_130":95,"_131":-5,"_132":215,"_59":62,"_133":-5},"sha256:8d8b1ca9db5996f2178263acc8f671e4b758693a5b86ae5a13986492887e06e2","2025-12-27T20:18:58.400957235Z","2025-12-23T15:50:46.202697404Z","2025-12-23T15:50:48.738296Z","sha-32ac18b",{"_109":40,"_110":111,"_112":223,"_114":224,"_87":225,"_117":226,"_46":246,"_151":111,"_152":153,"_154":52,"_34":247,"_156":157,"_158":248,"_159":246,"_160":231,"_161":79},"sha256:66da15c013a9d4ee1c92a76608771a3ae528ea15abb49e16a2bada75a9f0bfd8",390773745,1036292493,[227,232,237,242],{"_120":121,"_112":228,"_123":95,"_124":229,"_126":230,"_128":129,"_130":95,"_131":-5,"_132":224,"_59":231,"_133":-5},"sha256:140f5dc1f8c0bca4e9894c2e0fe50ccb8e19c5e3cb5864f5482e0e49ee3dfb14","2025-12-23T15:31:08.393736412Z","2025-12-22T21:20:18.324849795Z","inactive",{"_120":135,"_112":233,"_123":95,"_124":234,"_126":235,"_128":129,"_130":95,"_131":-5,"_132":236,"_59":231,"_133":-5},"sha256:a433f2b0ce7ff8cd1561ccb7d7e72caad1e92314b9ff7faece0b5da3b9ff42ea","2025-12-22T22:37:18.554783856Z","2025-12-22T21:20:19.543255253Z",364188334,{"_120":141,"_112":238,"_123":95,"_124":239,"_126":240,"_128":141,"_130":95,"_131":-5,"_132":241,"_59":231,"_133":-5},"sha256:85ec3b57baaed56a00ee08ce5455aa1314b68a314fd0c724210ecf08ad141c69","2025-12-22T22:37:11.899575726Z","2025-12-22T21:20:19.133626331Z",24834,{"_120":141,"_112":243,"_123":95,"_124":244,"_126":245,"_128":141,"_130":95,"_131":-5,"_132":241,"_59":231,"_133":-5},"sha256:d17bd00e8dcbb987fd25ae533ca589e772b2dca1f913b6eeb4b35eb60da7db4f","2025-12-22T22:37:09.436587248Z","2025-12-22T21:20:20.429081924Z","2025-12-22T21:20:23.663703Z","sha-2b7ae1f","2025-12-23T15:50:46.417407028Z",{"_109":40,"_110":111,"_112":250,"_114":251,"_87":252,"_117":253,"_46":272,"_151":111,"_152":153,"_154":52,"_34":273,"_156":157,"_158":256,"_159":272,"_160":62,"_161":79},"sha256:562553df58fcac352c92cdee5e84bb7b66c0416f8cd52ae4112ecd9a964d8e87",390773046,571708645,[254,258,263,268],{"_120":121,"_112":255,"_123":95,"_124":256,"_126":257,"_128":129,"_130":95,"_131":-5,"_132":251,"_59":62,"_133":-5},"sha256:f78f6e5f9dfcb8d99c5c66c237393654be1910e9734fe57040608327e0ebf9e0","2026-01-23T14:02:22.609880167Z","2025-12-22T16:36:21.102482758Z",{"_120":135,"_112":259,"_123":95,"_124":260,"_126":261,"_128":129,"_130":95,"_131":-5,"_132":262,"_59":231,"_133":-5},"sha256:d74b732ef467950c0e72979409ba67d3486c014727fe3d1afa59a9ae695c87a8","2025-12-22T22:37:05.47137807Z","2025-12-22T16:36:22.168039294Z",364186996,{"_120":141,"_112":264,"_123":95,"_124":265,"_126":266,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},"sha256:b9f41c6dd861a9a422e5e3bc5e4c6f0a91b862fb78f96a3c3cca14f5487287b9","2025-12-22T22:37:09.354834854Z","2025-12-22T16:36:20.6187113Z",25234,{"_120":141,"_112":269,"_123":95,"_124":270,"_126":271,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},"sha256:6ed820d6c2b9b1f7b55719ea49d09c904b7864eadeeec8913310c3bf659f6aab","2025-12-22T22:37:08.241907737Z","2025-12-22T16:36:22.896800388Z","2025-12-22T16:36:33.614618Z","latest",{"_109":40,"_110":111,"_112":250,"_114":251,"_87":275,"_117":276,"_46":281,"_151":111,"_152":153,"_154":52,"_34":282,"_156":157,"_158":256,"_159":281,"_160":62,"_161":79},1034913101,[277,278,279,280],{"_120":121,"_112":255,"_123":95,"_124":256,"_126":257,"_128":129,"_130":95,"_131":-5,"_132":251,"_59":62,"_133":-5},{"_120":135,"_112":259,"_123":95,"_124":260,"_126":261,"_128":129,"_130":95,"_131":-5,"_132":262,"_59":231,"_133":-5},{"_120":141,"_112":264,"_123":95,"_124":265,"_126":266,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},{"_120":141,"_112":269,"_123":95,"_124":270,"_126":271,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},"2025-12-22T16:36:31.196299Z","sha-553f860",{"_109":40,"_110":111,"_112":250,"_114":251,"_87":284,"_117":285,"_46":290,"_151":111,"_152":153,"_154":52,"_34":291,"_156":157,"_158":256,"_159":290,"_160":62,"_161":79},571708633,[286,287,288,289],{"_120":121,"_112":255,"_123":95,"_124":256,"_126":257,"_128":129,"_130":95,"_131":-5,"_132":251,"_59":62,"_133":-5},{"_120":135,"_112":259,"_123":95,"_124":260,"_126":261,"_128":129,"_130":95,"_131":-5,"_132":262,"_59":231,"_133":-5},{"_120":141,"_112":264,"_123":95,"_124":265,"_126":266,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},{"_120":141,"_112":269,"_123":95,"_124":270,"_126":271,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},"2025-12-22T16:36:28.693754Z","0",{"_109":40,"_110":111,"_112":250,"_114":251,"_87":293,"_117":294,"_46":299,"_151":111,"_152":153,"_154":52,"_34":300,"_156":157,"_158":256,"_159":299,"_160":62,"_161":79},1032121226,[295,296,297,298],{"_120":121,"_112":255,"_123":95,"_124":256,"_126":257,"_128":129,"_130":95,"_131":-5,"_132":251,"_59":62,"_133":-5},{"_120":135,"_112":259,"_123":95,"_124":260,"_126":261,"_128":129,"_130":95,"_131":-5,"_132":262,"_59":231,"_133":-5},{"_120":141,"_112":264,"_123":95,"_124":265,"_126":266,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},{"_120":141,"_112":269,"_123":95,"_124":270,"_126":271,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},"2025-12-22T16:36:26.243315Z","0.5",{"_109":40,"_110":111,"_112":250,"_114":251,"_87":302,"_117":303,"_46":308,"_151":111,"_152":153,"_154":52,"_34":309,"_156":157,"_158":256,"_159":308,"_160":62,"_161":79},1034913092,[304,305,306,307],{"_120":121,"_112":255,"_123":95,"_124":256,"_126":257,"_128":129,"_130":95,"_131":-5,"_132":251,"_59":62,"_133":-5},{"_120":135,"_112":259,"_123":95,"_124":260,"_126":261,"_128":129,"_130":95,"_131":-5,"_132":262,"_59":231,"_133":-5},{"_120":141,"_112":264,"_123":95,"_124":265,"_126":266,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},{"_120":141,"_112":269,"_123":95,"_124":270,"_126":271,"_128":141,"_130":95,"_131":-5,"_132":267,"_59":231,"_133":-5},"2025-12-22T16:36:23.788302Z","0.5.1","isPotentialSpam","routes/_layout.r.$namespace.$reponame.tags",{"_313":79,"_314":11},"isRunInDesktopEnabled","canDeleteTags","actionData","errors"]