Central repo for all Brinkman Lab maintained Galaxy Tools
Do not edit README.rst, edit README.header.rst and regenerate README.rst using ./generate_readme
See CONTRIBUTING.md for information on contributing to this repo.
- Clone this repo into the Galaxy server
- Add the full ./tool_conf.xml path to the Galaxy config tool_config_file: list
- Use Galaxies Manage dependencies admin panel to install all tool dependencies
See tool xml files for more information
| Name | Desc | ID | Path |
|---|---|---|---|
| SigiHMM | Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models | sigihmm | colombo/SigiHMM.xml |
| GFF/GTF Feature Merge | Merge GFF features based on a variety of criteria | feature-merge | feature_merge/feature_merge.xml |
| IslandPath | predict genomic islands in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes | islandpath | islandpath/IslandPath.xml |
| MASH | Fast genome and metagenome distance estimation using MinHash | mash | mash/mash.xml |
| ParSNP | Efficient microbial core genome alignment and SNP detection | parsnp | parsnp/ParSNP.xml |
| MCL | The Markov Cluster Algorithm, a cluster algorithm for graphs | mcl | mcl/mcl.xml |
| BioPython SeqIO Converter | Interconvert between the various sequence file formats that BioPython supports | biopython-convert | biopython-convert/biopython-convert.xml |
| BioPython Phylo Parse Newick Leaf Order | Convert a newick tree to an ordered list of its leaves | extract-tree-order | extract_tree_order/extract_tree_order.xml |
| Mauve Contig Mover | Reorder a multi-contig dataset against a reference genome | mauve-contig-mover | mauve_contig_mover/mauve_contig_mover.xml |
| Mauve Contig Mover - Stitch | Concatenate multiple contigs, complementing reversed sequences and rewriting all feature coordinates | mauve-contig-mover-stitch | mauve_contig_mover/mcm_stitch.xml |
| BioPython Make Unique ID | Makes all record ids unique across all input data | make-unique-id | make_unique_id/make_unique_id.xml |
| Send Email | Send mail using templates and include information about datasets | sendmail | sendmail/sendmail.xml |
| Coreutils sha256sum | Generate or check SHA256 (256-bit) checksums | sha256sum | hash/sha256sum.xml |
| Coreutils base64 encode/decode | Base64 encode/decode data | base64 | base64/base64.xml |
| AWK Script | Transform, modify, or generate data | awkscript | awkscript/awkscript.xml |
| Inspect | Dump Cheetah tool template environment. Useful for writing advanced tools. DO NOT INSTALL ON A PUBLIC SERVER | inspect | inspect/inspect.xml |