{"__v":2,"_id":"57618347b65324200072d6ab","category":{"__v":0,"_id":"57618347b65324200072d6a9","project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-15T16:33:11.614Z","from_sync":false,"order":0,"slug":"documentation","title":"Main"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-15T16:33:11.658Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":1,"body":"[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Software requirements\"\n}\n[/block]\n- Mac/UNIX/Linux OS\n- Python 2.7+\n- Matplotlib 2.0 (Python plotting library)\n- Docopt (Python Command-line interface description language)\n- Virtualenv (recommended), see [tutorial](http://docs.python-guide.org/en/latest/dev/virtualenvs/)\n- samtools 1.3 (recommended, required when processing BAM files), see [http://www.htslib.org/download/](http://www.htslib.org/download/)\n- git (recommended)\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Data requirements\"\n}\n[/block]\n- NCBI Taxonomy (names.dmp and nodes.dmp), [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz)\n[block:api-header]\n{\n  \"type\": \"basic\",\n  \"title\": \"Installation\"\n}\n[/block]\n\n[block:code]\n{\n  \"codes\": [\n    {\n      \"code\": \"# install virtualenv and create blobtools env (optional, but recommended)\\npip install virtualenv\\nvirtualenv ~/virtualenvs/blobtools\\nsource ~/virtualenvs/blobtools/bin/activate\\n\\n# download blobtools\\ngit clone https://github.com/DRL/blobtools.git \\n# OR\\nwget https://github.com/DRL/blobtools/releases/latest \\n\\n# install python dependencies\\npip install matplotlib\\npip install docopt\\npip install ujson\\n\\n# download NCBI taxdump\\nwget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz\\ntar zxvf taxdump.tar.gz nodes.dmp names.dmp\\n\\n# run blobtools (and thereby initialise blobtools/data/nodesDB.txt)\\n/blobtools create \\\\\\n-i test_files/assembly.fna \\\\\\n-c test_files/mapping_1.bam.cov \\\\\\n-t test_files/blast.out \\\\\\n--names names.dmp \\\\\\n--nodes nodes.dmp\\n[STATUS]\\t: Parsing FASTA - test_files/assembly.fna\\n[STATUS]\\t: Creating nodesDB from nodes.dmp and names.dmp\\n[STATUS]\\t: Parsing tax0 - /Users/dominik/git/blobtools/test_files/blast.out\\n[STATUS]\\t: Computing taxonomy using taxrule(s) bestsum\\n[PROGRESS]\\t: \\t100%\\n[STATUS]\\t: Parsing cov0 - /Users/dominik/git/blobtools/test_files/mapping_1.bam.cov\\n[PROGRESS]\\t: \\t100%\\n[STATUS]\\t: Generating BlobDB and writing to file blobDB.json\\n# Done\",\n      \"language\": \"shell\",\n      \"name\": \"\"\n    }\n  ]\n}\n[/block]","excerpt":"This page describes how to get blobtools to run on your system.","slug":"getting-started","type":"basic","title":"Installation"}

Installation

This page describes how to get blobtools to run on your system.

[block:api-header] { "type": "basic", "title": "Software requirements" } [/block] - Mac/UNIX/Linux OS - Python 2.7+ - Matplotlib 2.0 (Python plotting library) - Docopt (Python Command-line interface description language) - Virtualenv (recommended), see [tutorial](http://docs.python-guide.org/en/latest/dev/virtualenvs/) - samtools 1.3 (recommended, required when processing BAM files), see [http://www.htslib.org/download/](http://www.htslib.org/download/) - git (recommended) [block:api-header] { "type": "basic", "title": "Data requirements" } [/block] - NCBI Taxonomy (names.dmp and nodes.dmp), [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz) [block:api-header] { "type": "basic", "title": "Installation" } [/block] [block:code] { "codes": [ { "code": "# install virtualenv and create blobtools env (optional, but recommended)\npip install virtualenv\nvirtualenv ~/virtualenvs/blobtools\nsource ~/virtualenvs/blobtools/bin/activate\n\n# download blobtools\ngit clone https://github.com/DRL/blobtools.git \n# OR\nwget https://github.com/DRL/blobtools/releases/latest \n\n# install python dependencies\npip install matplotlib\npip install docopt\npip install ujson\n\n# download NCBI taxdump\nwget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz\ntar zxvf taxdump.tar.gz nodes.dmp names.dmp\n\n# run blobtools (and thereby initialise blobtools/data/nodesDB.txt)\n/blobtools create \\\n-i test_files/assembly.fna \\\n-c test_files/mapping_1.bam.cov \\\n-t test_files/blast.out \\\n--names names.dmp \\\n--nodes nodes.dmp\n[STATUS]\t: Parsing FASTA - test_files/assembly.fna\n[STATUS]\t: Creating nodesDB from nodes.dmp and names.dmp\n[STATUS]\t: Parsing tax0 - /Users/dominik/git/blobtools/test_files/blast.out\n[STATUS]\t: Computing taxonomy using taxrule(s) bestsum\n[PROGRESS]\t: \t100%\n[STATUS]\t: Parsing cov0 - /Users/dominik/git/blobtools/test_files/mapping_1.bam.cov\n[PROGRESS]\t: \t100%\n[STATUS]\t: Generating BlobDB and writing to file blobDB.json\n# Done", "language": "shell", "name": "" } ] } [/block]