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\n Also check our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\nInstall the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](clades.nextstrain.org).\n\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\n\ngit clone https://github.com/neherlab/webclades\ncd webclades/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `webclades/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd webclades/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `webclades/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `webclades/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n\n```\n\nand run:\n\n```bash\ncd webclades/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n\n```\n\nIn order to publish a beta version, name the version in `webclades/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/neherlab/webclades\ncd webclades/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `webclades/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.4.0-beta.6","_nodeVersion":"14.9.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-JksBp0T8UGCnOATHFwDTYIJPy1jMurFMOy1mKkGXsZcgjxsV3/KXnEpnXeJiR8g/+6Pi6cLaOD1AK4SUREyadg==","shasum":"d7b94db3a07033d9215ac15b3d4819e1df7c3344","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.4.0-beta.6.tgz","fileCount":4,"unpackedSize":2283226,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.4\r\nComment: 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\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0-alpha.0","_nodeVersion":"14.13.1","_npmVersion":"6.14.8","dist":{"integrity":"sha512-BJGDqEz1aehCpSGuSiDpvj4OivGX57uC47DbLndBeCDRq7lTQKmYlAXyJKPTN7IYazG+GQhFDOv/Vl89uqTG4w==","shasum":"ee9b0d8a4246afad9e3bd8c6296f6b7be4247c27","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0-alpha.0.tgz","fileCount":15,"unpackedSize":4003859,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n\r\nwsFcBAEBCAAQBQJfhF2mCRA9TVsSAnZWagAAoBUQAI5+TS8saGeiWKqoyXEg\n7ftr8dg9HDOu0hPN5M7Ao8F2tLzdVR5y5q2N+j6hkMzDrKLnCNblmFau8UuS\ni4ZbQEC9m8arI+gudjp/1b3kEmL5rl0qrrezxGYRIZ6S8Ne8A+WOCF+Kz+on\n0nWV4NgklSh2l8lAHzfFb6qfUSuHQ3VFZUZYchQcEr9C2HIGBcch9s1u1Ov3\neW3gxfIWVq4SX9JQWQQaDn9NTnkUtyh2ti0NgFT+C/mh3IygrPpeaHqzPzCW\nGYZ55zcHxXEabP+bMwobnDi5QZbb5pyXmbRrgwwPkZfQYFAY988OtCKvKmED\nJL4N+QBQuCKwldbTwEshZT+tmhw/oish3V4eD0kc9uxNd8CMNY5GGhDPiUKM\nIIYQ9yGj6WQ6eKKLHxJABj9/JQqi9vi9vGAX1Qqz7Vt8+isWLVl3h74WTGaQ\nsfSI9PGagPkV5DMWD2DrJy2YeIl/7hWrtREXu+XmLwRRVsfCbWK9vv+vZfti\n6938WTfdFqS/jhwqzg+C+T60VZ0Cu4ctUURIX+n4v2FEddCtFaen9SvjIo9o\n32eW/uhPOf5vWrYaajlQD0yqJ8PEkEYm6fnr0h9PLqdm/O2xHadp6zqxVyTe\n1A9l8tBBQAG5HKBGPmnsnqbM0XjjwwR45IJ2SGbX2ljYdO6sb+2/syx737Pq\njjQz\r\n=jtvo\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCID9PMXVrXvqqBvzDerGFoQFwDHgRA1IkG9tYLE7I5Fo/AiEAvD+aIi79uvzB1x9VQNEY7rMaBLXI0FC6ceDN9/uEvpw="}]},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0-alpha.0_1602510246137_0.17976446302275595"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information and installation instructions are available: in Nextclade Web application: https://clades.nextstrain.org/, in official documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/, on GitHub: https://github.com/nextstrain/nextclade"},"0.8.0-alpha.1":{"name":"@neherlab/nextclade","version":"0.8.0-alpha.1","description":"Clade assignment, mutation calling, and sequence quality checks","homepage":"https://clades.nextstrain.org","repository":{"type":"git","url":"git+https://github.com/nextstrain/nextclade.git"},"keywords":["nextstrain","nextclade","phylogenetics","clade","mutations","qc"],"bugs":{"url":"https://github.com/nextstrain/nextclade/issues"},"bin":{"nextclade":"dist/nextclade.js","nextclade.js":"dist/nextclade.js"},"engines":{"node":">=10"},"main":"dist/nextclade.js","license":"MIT","publishConfig":{"access":"public"},"readme":"# Nextclade\n\nClade assignment, mutation calling, and sequence quality checks\n\n---\n\n

\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0-alpha.1","_nodeVersion":"14.13.1","_npmVersion":"6.14.8","dist":{"integrity":"sha512-yRsz4eLS60xINYhV639QmK18+1qyhN1jA7Her0aYz8Tsx364grhxCus8FkBhsq/mashm2zdoUR6xQPN4Of2Mwg==","shasum":"5df06f0d0caa164535244869820ceb03e9c7a33a","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0-alpha.1.tgz","fileCount":15,"unpackedSize":4005007,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n\r\nwsFcBAEBCAAQBQJfhU5gCRA9TVsSAnZWagAAmMgP+wZhqQaaB3GVqXluanMi\nLqfLDiDSnd3dvLyEcL6K8BKaaHQDlyTgo8lOenPmcAVxmY/aN+NE58RpyqP2\ndObhFHrLgmsHsWO53JCpL7lDJ1Yp3FLBMDCe9rWQbFXlvEOR/8A6AZkuwwAp\nbwksNM5aziKIyyRIrOA9gWHcHefxTEPOTZnwQWANS9YLfSDrqBoUxVqEEqOT\nGRxbq0fbwwuP+fTzOJ/JvXRzkSh7jq4jpvMSKFUJ41Z+0koggIKaJ7t8Ftwf\nKSmFbF66bbQvYLbNfJot8h+MJkUiXS0uvQ7ZTCipsBOPdjztjHGarhvNiRrh\nQPgr09RFrwAoOhIqaq1OASdWMZTDHcSAB6z6QVSKvh4DZyo+2QJyz3vAb5Q4\n7CPzthtaDbbZawqY9FOC+mcjt703i+QDlFQXRL/FESB3kbJ2aNuqIqlseiW0\njSP8cFJiD7lwI1/wC7LdqvCksRHhdExj7jGI/2bqfcuqHh72KF0YqDIupDd7\nznZXVNElK8UkqE9Od1q7vbDGNRbztEtBqt6fx4UUdgRzcoAR2sYcN+ismk7o\nlC11gCvJSiT7OEh3ITS+ak3VMaCTqn9oS1nIjYCSc0TwVF7Coov6ux8bQuCZ\nnJlh64J8vcnJvL5G50GbMFIkM0q0lXLHc5hdgVhFxDJNx12cPw4qI0Uwlsu3\nNLwb\r\n=Ur6j\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEQCIBcNJYu1QIwKs5KeEqqITubiwPGJWJmjjSaaYjN8g3wqAiAGnzCNyzzn+fIUcTbXbMrFrkyJP8hDLySqglOgOyoS4A=="}]},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0-alpha.1_1602571871351_0.6094726677656153"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information and installation instructions are available: in Nextclade Web application: https://clades.nextstrain.org/, in official documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/, on GitHub: https://github.com/nextstrain/nextclade"},"0.8.0-alpha.2":{"name":"@neherlab/nextclade","version":"0.8.0-alpha.2","description":"Clade assignment, mutation calling, and sequence quality checks","homepage":"https://clades.nextstrain.org","repository":{"type":"git","url":"git+https://github.com/nextstrain/nextclade.git"},"keywords":["nextstrain","nextclade","phylogenetics","clade","mutations","qc"],"bugs":{"url":"https://github.com/nextstrain/nextclade/issues"},"bin":{"nextclade":"dist/nextclade.js","nextclade.js":"dist/nextclade.js"},"engines":{"node":">=10"},"main":"dist/nextclade.js","license":"MIT","publishConfig":{"access":"public"},"readme":"# Nextclade\n\nClade assignment, mutation calling, and sequence quality checks\n\n---\n\n

\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0-alpha.2","_nodeVersion":"14.13.1","_npmVersion":"6.14.8","dist":{"integrity":"sha512-qEtlw5lW+FxL2bLstlWiPwTJFVGnp9AS/PVl+SlmPQ1L8ToQjQ/N41BmXSAtTosE3dS2QOE14sTOsTDixlEePQ==","shasum":"2465b852d619a297dbfd8832391a0821bc7a43ec","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0-alpha.2.tgz","fileCount":15,"unpackedSize":4005052,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\nTuA7\r\n=Z12c\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEQCIGayX9/H1Wmk1F+ea1GbBx9wWi7fmB3MqF7LGES2DkvKAiA79A4I9zJ0hfbOHoCdChz/RqGVKy/IKPR51J0M3AF24g=="}]},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0-alpha.2_1602580562975_0.4730168703055555"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information and installation instructions are available: in Nextclade Web application: https://clades.nextstrain.org/, in official documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/, on GitHub: https://github.com/nextstrain/nextclade"},"0.8.0-alpha.4":{"name":"@neherlab/nextclade","version":"0.8.0-alpha.4","description":"Clade assignment, mutation calling, and sequence quality checks","homepage":"https://clades.nextstrain.org","repository":{"type":"git","url":"git+https://github.com/nextstrain/nextclade.git"},"keywords":["nextstrain","nextclade","phylogenetics","clade","mutations","qc"],"bugs":{"url":"https://github.com/nextstrain/nextclade/issues"},"bin":{"nextclade":"dist/nextclade.js","nextclade.js":"dist/nextclade.js"},"engines":{"node":">=10"},"main":"dist/nextclade.js","license":"MIT","publishConfig":{"access":"public"},"readme":"# Nextclade\n\nClade assignment, mutation calling, and sequence quality checks\n\n---\n\n

\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0-alpha.4","_nodeVersion":"14.15.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-rD+mkM+UkVy150SeQ4ubU3bZYZDdANT3NJAnffapoSqg1Q3Hn6vGT/ngN7vGwUyn71FlXYvEifKqht+cSRwrJQ==","shasum":"acbdd12b7cf6314ce74a43207fa3458ef7c25852","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0-alpha.4.tgz","fileCount":15,"unpackedSize":5766153,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\nW9eE\r\n=iXqy\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEYCIQCRrYkYRcnjkg2UtIgl7ABUCn4crazSqCi5pyCkFJ1BSQIhALuPyW6v+et+k6pp8JiG4A/Ipudq8vdoG0L4+2bz48n4"}]},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0-alpha.4_1604101765531_0.42560743392750267"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information and installation instructions are available: in Nextclade Web application: https://clades.nextstrain.org/, in official documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/, on GitHub: https://github.com/nextstrain/nextclade"},"0.8.0-alpha.5":{"name":"@neherlab/nextclade","version":"0.8.0-alpha.5","description":"Clade assignment, mutation calling, and sequence quality checks","homepage":"https://clades.nextstrain.org","repository":{"type":"git","url":"git+https://github.com/nextstrain/nextclade.git"},"keywords":["nextstrain","nextclade","phylogenetics","clade","mutations","qc"],"bugs":{"url":"https://github.com/nextstrain/nextclade/issues"},"bin":{"nextclade":"dist/nextclade.js","nextclade.js":"dist/nextclade.js"},"engines":{"node":">=10"},"main":"dist/nextclade.js","license":"MIT","publishConfig":{"access":"public"},"readme":"# Nextclade\n\nClade assignment, mutation calling, and sequence quality checks\n\n---\n\n

\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0-alpha.5","_nodeVersion":"14.15.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-RtvFGwVqNKe7zKrzhNJkEWT8tZYqVapaqDt9R6vIUpMVXzjhvJOaVVlj2zq+xaJ8HPQ+c4tJLKa6q3SihQ6iBA==","shasum":"6076a5a0ffa3c44b4a2444511259cee292dee809","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0-alpha.5.tgz","fileCount":15,"unpackedSize":5766246,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\nH+jj\r\n=lozd\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCICRJ5QHNnEBpmnP7gRM0LcwInkqmxu+OIQAWxwSn0L1YAiEAs2DLPkMJUmAhSDQDM8E9F9Vrt/88w1F1YTKuJEonJXI="}]},"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0-alpha.5_1604484562666_0.9201029072194524"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information and installation instructions are available: in Nextclade Web application: https://clades.nextstrain.org/, in official documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/, on GitHub: https://github.com/nextstrain/nextclade"},"0.8.0-alpha.6":{"name":"@neherlab/nextclade","version":"0.8.0-alpha.6","description":"Clade assignment, mutation calling, and sequence quality checks","homepage":"https://clades.nextstrain.org","repository":{"type":"git","url":"git+https://github.com/nextstrain/nextclade.git"},"keywords":["nextstrain","nextclade","phylogenetics","clade","mutations","qc"],"bugs":{"url":"https://github.com/nextstrain/nextclade/issues"},"bin":{"nextclade":"dist/nextclade.js","nextclade.js":"dist/nextclade.js"},"engines":{"node":">=10"},"main":"dist/nextclade.js","license":"MIT","publishConfig":{"access":"public"},"readme":"# Nextclade\n\nClade assignment, mutation calling, and sequence quality checks\n\n---\n\n

\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0-alpha.6","_nodeVersion":"14.15.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-+6tdeAZ/Bt+z+JJFhn8Zu8OstQXYz2ZGWl5yEM+qlvySnUhIR0dPDzNTZxOTuJ7cN2S9XXCT2l2KOkyw/hvTaQ==","shasum":"d32e68f3bee12b762921b61715ae7cf84045d908","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0-alpha.6.tgz","fileCount":15,"unpackedSize":5775944,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\nYAC2\r\n=dnCi\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCIB0luD0l0NlSSv+T+gfxWeaH/tR9UfypXe/iPWjDcK1DAiEApVWhT/52iaXeBfqZhdXwaDhWz/hIZSDY1K5/hq52XxE="}]},"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0-alpha.6_1604594891971_0.3263518129314751"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information and installation instructions are available: in Nextclade Web application: https://clades.nextstrain.org/, in official documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/, on GitHub: https://github.com/nextstrain/nextclade"},"0.8.0-alpha.7":{"name":"@neherlab/nextclade","version":"0.8.0-alpha.7","description":"Clade assignment, mutation calling, and sequence quality checks","homepage":"https://clades.nextstrain.org","repository":{"type":"git","url":"git+https://github.com/nextstrain/nextclade.git"},"keywords":["nextstrain","nextclade","phylogenetics","clade","mutations","qc"],"bugs":{"url":"https://github.com/nextstrain/nextclade/issues"},"bin":{"nextclade":"dist/nextclade.js","nextclade.js":"dist/nextclade.js"},"engines":{"node":">=10"},"main":"dist/nextclade.js","license":"MIT","publishConfig":{"access":"public"},"readme":"# Nextclade\n\nClade assignment, mutation calling, and sequence quality checks\n\n---\n\n

\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge alpha version:\n\n```bash\nnpm install --global @neherlab/nextclade@alpha\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0-alpha.7","_nodeVersion":"14.15.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-9xbV+IsB6zRmYZCCMq4Cv5C5JX/rtjBkPN1za1YK3xCmswNTBi2tiB4qmU3dc1/swYr678aruRKbLJtTQPGopA==","shasum":"fcc216807d1a649f47cfaac4e9e68b5387ab5640","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0-alpha.7.tgz","fileCount":15,"unpackedSize":5776661,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\n6ASk\r\n=tNpA\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCIFQdXercNXcXaP5v6VboBxTWI/OJIHczZ1t3I6BkTMUGAiEA+MpIwEonBXxsxEDDjSpmKNkj+ttfuq1cSS8bfoPBct4="}]},"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0-alpha.7_1604613803587_0.8190627962075276"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. The latest information and installation instructions are available: in Nextclade Web application: https://clades.nextstrain.org/, in official documentation: https://docs.nextstrain.org/projects/nextclade/en/stable/, on GitHub: https://github.com/nextstrain/nextclade"},"0.7.8":{"name":"@neherlab/nextclade","version":"0.7.8","description":"Clade assignment, mutation calling, and sequence quality checks","homepage":"https://clades.nextstrain.org","repository":{"type":"git","url":"git+https://github.com/nextstrain/nextclade.git"},"keywords":["nextstrain","nextclade","phylogenetics","clade","mutations","qc"],"bugs":{"url":"https://github.com/nextstrain/nextclade/issues"},"bin":{"nextclade":"dist/nextclade.js","nextclade.js":"dist/nextclade.js"},"engines":{"node":">=10"},"main":"dist/nextclade.js","module":"src/cli/cli.ts","license":"MIT","publishConfig":{"access":"public"},"readme":"# Nextclade\n\nClade assignment, mutation calling, and sequence quality checks\n\n---\n\n

\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge beta version:\n\n```bash\nnpm install --global @neherlab/nextclade@beta\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.7.8","_nodeVersion":"14.15.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-c3Z8n2Q258iaunskcj9/aaE8gNk161Qe1DU1/hT9rHFCW727l6I3VWDq1M5HtqmHvgDA0nIfuOT0L7xKv60+Aw==","shasum":"db6d934e83c603ff60da3574d2da36a5dc92ae2d","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.7.8.tgz","fileCount":4,"unpackedSize":2509897,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\nM9iU\r\n=3KJw\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCIQDdOHVBz2paYcv6o0de8z2F5C806+F+bWfc0m10eDQnVQIgJRxfiFN0zBnnrTa+o2JgxQmUNGByTwA4la2gg+5Rhgw="}]},"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.7.8_1604626300913_0.16089380261273978"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. 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It means that we no longer recommend to use it. Please upgrade to the most recent version, containing latest bug fixes and new features. Make sure you remove the old version to avoid conflicts. 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\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge alpha version:\n\n```bash\nnpm install --global @neherlab/nextclade@alpha\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.0","_nodeVersion":"14.15.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-B9ONXZNLWmIc4G+tHN4Rg3igWoQJG5b99JlEQIuWPhzDWzCFKsbcRsfbonOh5zIJGUzr0lN/cLiDe9ojHBoXyw==","shasum":"1b69f2eaa90a756e99176eeb7d719e47a7b2bab2","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.0.tgz","fileCount":15,"unpackedSize":5776909,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\nFDDr\r\n=dkbd\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEYCIQC+Ipn4qU6+XDuifm1/ekO03dLZkIkNjrrIGAHK+KN6iwIhAK8ezAj4vEBY3aKHsiD1sK2ItoSTBSU3MLfbsbWh04qP"}]},"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.0_1605035202284_0.6646541261132015"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. 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\n Try our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 10.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nyou may also try the cutting-edge alpha version:\n\n```bash\nnpm install --global @neherlab/nextclade@alpha\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nAdditionally, Nextclade can output a new Nextstrain tree (in the same Auspice JSON v2 format), with the user-provided sequences placed on it, with `--output-tree`. Note that this simplified tree placement is to give a rough idea of where the sequences may end up, and this does not substitute the full Nextstrain build.\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade)\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull.\n - `nextclade.js --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we previously mounted our local directory with sequences to.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\n## Build\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe bundled npm script will appear as `nextclade/packages/cli/dist/nextclade.js`.\nThe script is standalone, does not require any local dependencies and can be moved.\n\nIf Node.js >= 10 is available locally, the tool can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. \n\n\n## Publish\n\nThis describes how to publish a new version of the package on NPM.\nAfter build step above, increment the version in `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nand run:\n\n```bash\ncd nextclade/packages/cli\nnpm publish\n```\n\nIf you need to re-publish the same version (which npm disallows), append an index of the re-release after a dash,\n using the following format: `${x.y.z}-{k}`, for example: \n\n```json\n{\n \"version\": \"0.4.0-1\"\n}\n```\n\nIn order to publish a beta version, name the version in `nextclade/packages/cli/package.json` using\n`${x.y.z}-beta.${k}`, format where `${x.y.z}` is the semantic version of the corresponding future release and `${k}`,\nis the numeric index of the current beta version, for example: \n\n```json\n{\n \"version\": \"0.4.0-beta.1\"\n}\n```\n\nand run publish with a `beta` tag:\n\n```bash\nnpm publish --tag=beta\n```\n\nThis allows users to install the latest beta version with \n\n\nwhile releases (`latest` tag) are still installed by default.\n\n## Development\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds.\nThe build result will appear `nextclade/packages/cli/dist/nextclade.js` and can be run similarly to the production version.\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.8.1-alpha.1","_nodeVersion":"14.15.0","_npmVersion":"6.14.8","dist":{"integrity":"sha512-4aZqLVGIAIONEI8isgnJJE10amu0Mrg9MANEr83Thda2dg8Aa7BQqD83IF/DOnQw4cv+SqpQXScedZ6oPgRTig==","shasum":"b036b0ba20e6163e2ab0c4b29dc8d3fde3e5986c","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.8.1-alpha.1.tgz","fileCount":15,"unpackedSize":5775839,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\nNbZu\r\n=sadF\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCIHYWZq37PhsAFpInuMV/kbBj9NuAoOm34FlznrtfDtIJAiEApDaCcrgCZDTq+aXzQeJ8yRChNKs0Z+4DC7C3e4pnjBA="}]},"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"maintainers":[{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},{"name":"rneher","email":"richard.neher@unibas.ch"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.8.1-alpha.1_1605176990772_0.12374288387829013"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. 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\n You can also yry our web application at: \n \n clades.nextstrain.org\n \n

\n\n\n\n## Getting started\n\n### Locally\n\nIn order to run locally, you need Node.js and npm installed.\nIt is recommended to use [`nvm`](https://github.com/nvm-sh/nvm) or [`nvm-windows`](https://github.com/coreybutler/nvm-windows) to install and manage Node.js versions. Nextclade CLI supports Node.js versions >= 12, version >= 14.15.0 LTS is recommended.\n\nHaving Node.js and npm available, install the latest release of the [`nextclade` npm package](https://www.npmjs.com/package/@neherlab/nextclade) globally:\n\n```bash\nnpm install --global @neherlab/nextclade\n```\n\nExplore available options:\n\n```bash\nnextclade --help\n```\n\nRun, given a .fasta file with sequences\n\n```bash\nnextclade --input-fasta 'sequences.fasta' --output-json 'results.json'\n```\n\nor, shorter:\n\n```bash\nnextclade -i 'sequences.fasta' -o 'results.json'\n```\n\nGenerated file `results.json` will contain the results in JSON format.\nSimilarly, results can be generated in .csv or .tsv format, or in multiple formats (by passing multiple `--output-=` flags)\nAll files have the same format as exports from the [Nextclade web application](https://clades.nextstrain.org).\n\nNextclade can accept a custom Auspice JSON v2 reference tree through `--input-tree` and it's root sequence through `--input-root-seq` flags. It is user's responsibility to ensure that the root sequence corresponds to the root node of the tree - Nextclade has no possibility to enforce that requirement. The results will be incorrect if it isn't.\n\nWith `--output-tree` flag you can output a new Nextstrain tree, with the analyzed sequences placed on it (in the same Auspice JSON v2 format). The tree produced is the same which you would see in Nextclade web application on tree page. This file can be used for further processing and visualization (for example with [auspice.us](https://auspice.us)). Note that Nextclade implements a fast but also very simplified tree placement algorithm. Its purpose is to give a rough idea of where the sequences may end up on the tree, and it is not a substitute for a full Nextstrain build.\n\nNextclade is currently in active development stage. If you encounter problems with the latest version, or if you need to use the same version to produce consistent, comparable experiments, you can install a specific version as follows:\n\n```\nnpm install --global @neherlab/nextclade@0.8.1\n```\n\nSee the list of all versions released on NPM: [www.npmjs.com/package/@neherlab/nextclade?activeTab=versions](https://www.npmjs.com/package/@neherlab/nextclade?activeTab=versions). Note that only versions from the `latest` channel are officially supported. Version marked `alpha` and `beta` versions are for development and internal testing. We release them publicly, but discourage using them for any serious purposes. You can find out which version you are currently using by running `nextclade --version`.\n\n\n### With docker\n\nDocker images with Nextclade CLI are hosted in docker hub repository [`neherlab/nextclade`](https://hub.docker.com/r/neherlab/nextclade). They contain everything needed to run Nextclade, including the currently recommended version of Node.js. The only requirement is to have [Docker installed](https://docs.docker.com/get-docker/).\n\nYou can pull the latest image and run the container as follows\n\n```bash\ndocker run -it --rm -u 1000 --volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\" neherlab/nextclade nextclade --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json'\n```\n\nExplanation:\n\n - `-it` - runs inside an interactive instance of tty. Optional.\n - `--rm` - deletes the container after usage. Optional.\n - `-u 1000`. Runs container as a user with UID `1000`. Substitute `1000` with your local user's UID. UID of the current user can be found by running `id -u`. On single-user machines it is typically `1000` on Linux and `501` on Mac. If this parameter is not present, output files will be written on behalf of the root user, making them harder to operate on. Optional, but recommended.\n - `--volume=\"${ABSOLUTE_PATH_TO_SEQUENCES}:/seq\"`. Substitute `${ABSOLUTE_PATH_TO_SEQUENCES}` with your *absolute* path to a directory containing input fasta sequences on your computer. This is necessary in order for docker container to have access to this directory. In this example, it will be available as `/seq` inside the container.\n - `neherlab/nextclade` name of the image to pull. In Unix-like environments you can use the variable `${PWD}` to get the absolute path to the current directory, for example: `--volume=\"${PWD}/data:/seq\"`.\n - `nextclade --input-fasta '/seq/sequences.fasta' --output-json '/seq/results.json` the usual invocation of the tool. Note that in this example we read and write from `/seq` directory inside the container, which we mounted using Docker's `--volume=` parameter.\n\n\nThe default (`latest`) tag uses Node.js image based on Debian stretch. It is also possible to use smaller Alpine Linux-based images by appending `:alpine` tag after the repo name: \n\n```\ndocker run ... neherlab/nextclade:alpine ...\n```\n\nSee the list of all tags on Docker Hub: [hub.docker.com/r/neherlab/nextclade/tags](https://hub.docker.com/r/neherlab/nextclade/tags)\n\n\n### Tips and tricks\n\n#### Memory consumption\n\nIn the current implementation, Nextclade may consume large amounts of memory. By default, Nextclade currently detects the number of logical threads available on the machine and runs this number of sequence analyses in parallel - one input sequence per thread. It might happen that you have a machine with many cores/threads but limited amount of memory. In this case, many Nextclade threads will run concurrently, and it might run out of heap space and become very slow and unstable.\n\nAdditionally, while processing sequences, Nextclade accumulates information for the output tree construction. When there are many sequences, it may also lead to the excessive memory consumption, even in low-parallelism scenarios.\n\n\nIt is recommended to monitor the memory consumption, especially in automated workflows. To tune the memory consumption you could also:\n \n - limit the parallelism of Nextclade with `--jobs=n` flag\n\n - run completely sequentially (1 thread) with `--jobs=1`\n\n - process fewer sequences, by filtering/subsampling the data before passing to Nextclade\n \n - process fewer sequences at a time, by batching the input data before passing it into multiple Nextclade runs, and then merging the results for every run\n\n\nWe are planning:\n\n - algorithmic improvements which should reduce the memory footprint of Nextclade\n \n - streaming and batching of inputs\n \nContributions are welcome!\n\n\n## Developer's guide\n\n### Build: production version\n\nThis will build a production version of the command-line tool:\n\n```bash\ngit clone https://github.com/nextstrain/nextclade\n# Optionally checkout a branch or a tag: git checkout -b 0.8.1\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:prod:build\n```\n\nThe build results - the main executable script, and a set of webworker modules, along with their source maps - will appear in `nextclade/packages/cli/dist/`.\n\nIf Node.js >= 12 is available locally, the freshly built Nextclade can be ran as\n\n```bash\nnode nextclade.js\n```\n\nor simply \n\n```bash\nnextclade.js\n```\n\n### Build: standalone executables\n\nA standalone executable (without dependency on Node.js) can be created with\n\n```bash\ncd nextclade/packages/web\nyarn cli:prod:build:exe\n```\n\nThe native executables for various platforms will appear in `nextclade/packages/cli/dist/`.\nThis uses [`pkg`](https://github.com/vercel/pkg) tool to wrap the script together with Node.js runtime into one standalone file. Currently, these are neither officially released nor supported.\n\n### Publish a new version to NPM and Docker Hub\n\nIncrement the version in both, `nextclade/packages/web/package.json` and `nextclade/packages/cli/package.json`:\n\n```json\n{\n \"version\": \"x.y.z\"\n}\n```\n\nThe version formats accepted:\n \n - `x.y.z` - semantic version for stable releases (will be published to `latest` channel on NPM and with no tag prefix on Docker Hub)\n\n - `x.y.z-beta.n` - semantic version and a mandatory suffix for beta releases (will be published to `beta` channel on NPM and with `beta` tag prefix on Docker Hub)\n\n - `x.y.z-alpha.n` - semantic version and a mandatory suffix for alpha releases (will be published to `alpha` channel on NPM and with `alpha` tag prefix on Docker Hub) \n\n\nrebuild:\n\n```bash\ncd packages/web\nyarn cli:prod:build\n```\n\npublish:\n\n```bash\ncd packages/cli\n./release.sh\n```\n\nThis will:\n - publish a new version on NPM to the appropriate channel\n - build and push Docker images to Docker Hub\n\n### Run in development mode\n\nFor development purposes run\n\n```\ngit clone https://github.com/nextstrain/nextclade\ncd nextclade/packages/web\ncp .env.example .env\nyarn cli:dev\n\n```\n\nThis will start webpack in watch mode and all changes will trigger partial rebuilds, which is convenient for continuous development. The build results will appear in `nextclade/packages/cli/dist/` and can be run similarly to the production version (see above).\n\n\n## License\n\nMIT License\n","readmeFilename":"README.md","_id":"@neherlab/nextclade@0.11.0-alpha.1","_nodeVersion":"14.15.4","_npmVersion":"6.14.10","dist":{"integrity":"sha512-a99Z6tuCH/n3GvfjoGSkfTGyFjMwWQkHQkT7c3blIRk45dI+JQFQ1wLOQNWsse/48WP5Hedplp/a75oyKsblVg==","shasum":"8e7d14ae36048553b6d587de13b705e8f1d21856","tarball":"https://registry.npmjs.org/@neherlab/nextclade/-/nextclade-0.11.0-alpha.1.tgz","fileCount":15,"unpackedSize":5762387,"npm-signature":"-----BEGIN PGP SIGNATURE-----\r\nVersion: OpenPGP.js v3.0.13\r\nComment: https://openpgpjs.org\r\n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\n6zr3\r\n=F0J/\r\n-----END PGP SIGNATURE-----\r\n","signatures":[{"keyid":"SHA256:jl3bwswu80PjjokCgh0o2w5c2U4LhQAE57gj9cz1kzA","sig":"MEUCIGKKHnAB5kClYzNgTQFbj5dtOfWa4bglK1bRV9oueQiPAiEA7i0LVBbZUVmhnIozMSuvOWcWvmLenHAACdeszkawZ4U="}]},"_npmUser":{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"},"directories":{},"maintainers":[{"name":"rneher","email":"richard.neher@unibas.ch"},{"name":"ivan-aksamentov","email":"ivan.aksamentov+npm@gmail.com"}],"_npmOperationalInternal":{"host":"s3://npm-registry-packages","tmp":"tmp/nextclade_0.11.0-alpha.1_1609942583005_0.1841989288061503"},"_hasShrinkwrap":false,"deprecated":"Nextclade version 0.x is deprecated. 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