Tools, tool-wrappers and tool dependency packages for Galaxy developed within the Bioinformatics Core Facility at the University of Manchester.
The tools subdirectory contains the following tools which wrap
3rd-party software:
- BLAT
- CEAS
- fastq_screen
- MACS2
- pal_finder
- SOLiD_preprocess_filter_v2.pl
- 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/
The conda-recipes subdirectory contains recipes for building
conda dependencies.
The packages subdirectory contains tool dependency packages:
- package_numpy_1_8
- package_pandaseq_2_8_1
- package_python2_7
The legacy subdirectory contains tools and packages which are
no longer supported, or which are backwardly-incompatible, or where
development is now happening elsewhere.
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.