recipe indelfixer

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

package indelfixer

(downloads) docker_indelfixer

Versions

1.1-11.1-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install indelfixer

and update with:

conda update indelfixer

or use the docker container:

docker pull quay.io/biocontainers/indelfixer:<tag>

(see indelfixer/tags for valid values for <tag>)

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"