![]() ![]() rnaSPAdes - a de novo transcriptome assembler from RNA-Seq data (see rnaSPAdes manual).metaplasmidSPAdes - a pipeline for extracting and assembling plasmids from metagenomic data sets (see plasmid options).plasmidSPAdes - a pipeline for extracting and assembling plasmids from WGS data sets (see plasmid options).metaSPAdes - a pipeline for metagenomic data sets (see metaSPAdes options).SPAdes 3.15.5 includes the following additional pipelines: If you have high-coverage data for bacterial/viral isolate or multi-cell organism, we highly recommend to use -isolate option. For such purposes you can use it at your own risk. SPAdes is not intended for larger genomes (e.g. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. Note, that SPAdes was initially designed for small genomes. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Version 3.15.5 of SPAdes supports paired-end reads, mate-pairs and unpaired reads. You can also provide additional contigs that will be used as long reads. The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. The latest SPAdes paper describing various pipelines in a protocol format is available here. SPAdes version 3.15.5 was released under GPLv2 on July 14th, 2022 and can be downloaded from. This manual will help you to install and run SPAdes. Petersburg genome assembler - is an assembly toolkit containing various assembly pipelines. Stand-alone binaries released within SPAdes package.metaplasmidSPAdes and metaviralSPAdes output Assembling long Illumina paired reads (2x150 and 2x250)ģ.8. Downloading and compiling SPAdes source codeģ.4. These optional features are called “extras”. For example, a project might offer optional PDF output if ReportLab is installed, and reStructuredText support if docutils is installed. Sometimes a project has “recommended” dependencies, that are not required for all uses of the project. On the right are the correlated installation commands for these optional sub-packages. On the left in setup.py - extras_require is defined. You can see how this was accomplished in the setup.py script Swe-airflow-tools (0.0.3) - Tools for Apache Airflow ApplicationĪirflow (0.6) - Placeholder for the old Airflow package Pylint-airflow (0.1.0a1) - A Pylint plugin to lint Apache Airflow code. ![]() When we search pypi for apache-airflow note that the optional packages do not show up: pip search 'apache-airflow'Īpache-airflow (1.10.9) - Programmatically author, schedule and monitor data pipelines You can install optional components of airflow with: pip install 'apache-airflow' To install airflow from pip we use this command: pip install 'apache-airflow' Just in case another developer comes along looking to implement this pattern in their own Python package deployment, here's further explanation of the brackets in pip. Solution 2 Brackets in PIP signify optional dependencies Note that it has nothing to do with the django package itself, but is just a string defined by the splinter package for a particular feature set that gets enabled. splinter, on the other hand, installs a variant of the splinter package which contains support for django. Really, you are installing the package named: "splinter".Īn explanation from command pip install splinter django would install two packages named splinter and django. The square brackets ( ) are not specific syntax, just convention. In your case, you are installing the splinter package which has the added support for django. The syntax that you are using is: pip install "project" ![]()
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