nandr0id/galaxy-tools

FLS Galaxy tools and tool-wrappers for in-house and third-party bioinformatic applications.

galaxy-tools

Tools, tool-wrappers and tool dependency packages for Galaxy developed within the Bioinformatics Core Facility at the University of Manchester.

tools

The tools subdirectory contains the following tools which wrap 3rd-party software:

• BLAT
• CEAS
• fastq_screen
• MACS2
• pal_finder
• SOLiD_preprocess_filter_v2.pl
• trimmomatic
• weeder
• weeder2
• bedgraph_to_wig converter

There are also tools wrapping in-house scripts and programs:

• motif_tools
• make_macs_xls
• qc_boxplotter
• RnaChipIntegrator
• SamStats

See the individual README files for information on how to install into a local Galaxy; alternatively where indicated a subset of tools are available from the main toolshed: https://toolshed.g2.bx.psu.edu/

conda-recipes

The conda-recipes subdirectory contains recipes for building conda dependencies.

packages

The packages subdirectory contains tool dependency packages:

• package_numpy_1_8
• package_pandaseq_2_8_1
• package_python2_7

legacy

The legacy subdirectory contains tools and packages which are no longer supported, or which are backwardly-incompatible, or where development is now happening elsewhere.

local_dependency_installers

The local_dependency_installers subdirectory contains shell scripts with installer functions for many of the tool dependencies.

For example:

local_dependency_installers/trimmomatic.sh

contains a function install_trimmomatic_0_36, which will install Trimmomatic v0.36 in a Galaxy-style directory structure (i.e. .../trimmomatic/0.36/ which includes an env.sh which can be sourced to make the installed dependency available.

These functions are used primarily for setting up the test environments for the Planemo tests, but could be recycled e.g. for local tool installations into Galaxy using an appropriately configured galaxy_packages dependency resolver (see e.g. https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html#)

Use e.g. grep ^function local_dependency_installers/*.sh to list the available installer functions.