/bootstrap-rnascape

Script to bootstrap the complete installation of CRISP and CODAC

Primary LanguageShellGNU General Public License v3.0GPL-3.0

RNAScape bootstrap procedure

The following procedure will result in the creation of a working RNAScape installation.

In that process these steps will be executed:

  • download all required reference files, images, and code
  • build a docker image capable of executing RNAScape
  • build indices/caches for samtools, STAR, Minimap2, and GMAP
  • install CRISP and CODAC
  • test CRISP and CODAC

The process will take approx. 8h to finish. The final output is a large "refs" folder which contains all the references, software, libraries etc. and a docker image gx${USER}. The recommended hardware has at least 8 cores and 96GB of RAM, although very rarely (<<1%) more than 64GB is needed.

  1. Make sure the following dependencies are installed:
- bash
- git
- wget
- pigz (important not always installed!)
- docker
- tar
  1. The user shoud have also full permissions to use docker tested on version 1.13.1 and 17.05.0-ce

RNAScape bundles great software by other people:

- STAR
- featureCounts
- samtools
- Bioconductor core
- data.table
- stringr
- Inchworm
- Minimap2
- GMAP
- sambamba
- MiXCR
- Jellyfish
- bbmap
- FastQC
- bedtools
- seqtk

Installation instructions

  1. Clone this repository:
git clone https://github.com/mcieslik-mctp/bootstrap-rnascape
cd bootstrap-rnascape
  1. Configure/edit settings bootstra_rnascape.sh:
## build parameters
## by default the current user name and id is embedded into the image change if necessary
export USER=$USER
export USERID=`id -u`
## number of cpu-cores
export NCORES=64
## release tag
export BUILD_TAG=relx
export BUILD_NAME=build_$BUILD_TAG
## select which steps to execute (all are needed for 
export BUILD_GXUSER=true
export BUILD_REFS=true
export BUILD_TOOLS=true
export BUILD_INDICES=true
export BUILD_BIOC=true
export BUILD_CRISP=true
export BUILD_CODAC=true
export BUILD_RELEASE=true
export BUILD_TESTCRISP=true
  1. Build (6-8h)
bash bootstrap_rnascape.sh
  1. Inspect the output of the build_$BUILD_TAG directory:
#### final output needed to run RNAscape
## the customized docker image
gx${USER}_docker_1.6.5.tar.gz
## the complete "refs" folder
rnascape_relx.tar.gz # tared 
refs # un-tared
## example CRISP/CODAC test-runs 
test.codac
test.crisp

The following files can be deleted:

## downloaded FASTQ files for test
repo
## downloaded files (can be removed)
refs_$VER.tar.gz
bioc_$VER.tar.gz
codac_$VER.tar.gz
crisp_$VER.tar.gz