:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'indelfixer' .. highlight: bash indelfixer ========== .. conda:recipe:: indelfixer :replaces_section_title: :noindex: A sensitive aligner for 454\, Illumina and PacBio data\, employing a full Smith\-Waterman alignment against a reference. :homepage: https://github.com/cbg-ethz/InDelFixer :license: GNU General Public License v3.0 :recipe: /`indelfixer `_/`meta.yaml `_ .. conda:package:: indelfixer |downloads_indelfixer| |docker_indelfixer| :versions: ``1.1-2``,  ``1.1-1``,  ``1.1-0`` :depends openjdk: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install indelfixer and update with:: mamba update indelfixer To create a new environment, run:: mamba create --name myenvname indelfixer with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/indelfixer: (see `indelfixer/tags`_ for valid values for ````) .. |downloads_indelfixer| image:: https://img.shields.io/conda/dn/bioconda/indelfixer.svg?style=flat :target: https://anaconda.org/bioconda/indelfixer :alt: (downloads) .. |docker_indelfixer| image:: https://quay.io/repository/biocontainers/indelfixer/status :target: https://quay.io/repository/biocontainers/indelfixer .. _`indelfixer/tags`: https://quay.io/repository/biocontainers/indelfixer?tab=tags .. raw:: html Notes ----- InDelFixer is Java program that comes with a custom wrapper shell script. This shell wrapper is called \"InDelFixer\" and is on \$PATH by default. By default \"\-Xms512m \-Xmx1g\" is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have \_JAVA\_OPTIONS set globally this will take precedence. For example run it with \"InDelFixer \-Xms512m \-Xmx1G\" Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/indelfixer/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/indelfixer/README.html