diff --git a/README.md b/README.md index 2aa95bed..8758123b 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,38 @@ Mikado can be installed with singularity. If you don't have singularity, please VERSION=2.3.5rc2 singularity exec docker://gemygk/mikado:v${VERSION} mikado -h ``` +Or, we can build and run a singularity image +```console +# 1. Create a Singularity definition file + +$ cat mikado-2.3.5rc2.def +bootstrap: docker +from: gemygk/mikado:v2.3.5rc2 + +# Build the Singularity image +$ sudo singularity build mikado-2.3.5rc2.sif mikado-2.3.5rc2.def + +# Execute Mikado +$ singularity exec mikado-2.3.5rc2_CBG.sif mikado -h +usage: Mikado [-h] [--version] {configure,prepare,serialise,pick,compare,util} ... + +Mikado is a program to analyse RNA-Seq data and determine the best transcript for each locus in accordance to user-specified criteria. + +optional arguments: + -h, --help show this help message and exit + --version Print Mikado current version and exit. + +Components: + {configure,prepare,serialise,pick,compare,util} + These are the various components of Mikado: + configure This utility guides the user through the process of creating a configuration file for Mikado. + prepare Mikado prepare analyses an input GTF file and prepares it for the picking analysis by sorting its transcripts and performing some simple consistency checks. + serialise Mikado serialise creates the database used by the pick program. It handles Junction and ORF BED12 files as well as BLAST XML results. + pick Mikado pick analyses a sorted GTF/GFF files in order to identify its loci and choose the best transcripts according to user-specified criteria. It is dependent on files produced by the "prepare" and "serialise" + components. + compare Mikado compare produces a detailed comparison of reference and prediction files. It has been directly inspired by Cufflinks's cuffcompare and ParsEval. + util Miscellaneous utilities +``` ### Conda/Mamba/Manual Installation Mikado can be installed with conda. If you don't have conda, please install [mamba](https://github.com/conda-forge/miniforge?tab=readme-ov-file#miniforge-pypy3) first. Then you can create a new environment with mikado installed.