Add references to tracking system
Scripts for managing reference files in tracking system.
Bio-ReferenceManager has the following dependencies:
- dos2unix
- fastaq
- smalt
- bwa
- bowtie2
- samtools
- Picard
- rsync
Details for installing Bio-ReferenceManager are provided below. If you encounter an issue when installing Bio-ReferenceManager please contact your local system administrator. If you encounter a bug please log it here or email us at path-help@sanger.ac.uk.
Clone the repository:
git clone https://github.com/sanger-pathogens/Bio-ReferenceManager.git
Move into the directory and install all dependencies using DistZilla:
cd Bio-ReferenceManager
dzil authordeps --missing | cpanm
dzil listdeps --missing | cpanm
Run the tests:
dzil test
If the tests pass, install Bio-ReferenceManager:
dzil install
The test can be run with dzil from the top level directory:
dzil test
Usage: refman [options] *.fa
Add references to the pipelines.
Options: -o overwrite index files [False]
-p INT number of processors [1]
-r STR reference store directory [/nfs/pathogen/refs]
-d STR production references direcotry [/data/pam.../refs]
-m STR reference metadata filename [metadata.json]
-n use a hash of the file as the reference name [FALSE]
-i STR toplevel index filename [refs.index]
-a Dont annotate with Prokka [FALSE]
-v verbose output to STDOUT
-h this help message
Advanced options:
--java_exec STR java executable [java]
--dos2unix_exec STR dos2unix executable [dos2unix]
--fastaq_exec STR fastaq executable [fastaq]
Bio-ReferenceManager is free software, licensed under GPLv3.
Please report any issues to the issues page or email path-help@sanger.ac.uk.