Install Request: STAR-related RNA-seq pipeline [IN:04680117]

[heatherkellyucl]

Arriba 2.1.0

Fast and accurate gene fusion detection from RNA-Seq data https://github.com/suhrig/arriba https://arriba.readthedocs.io/en/latest/quickstart/#manual-installation License: MIT/Expat and GNU GPL v3

Requires: STAR version >=2.7.6a recommended (We have star/2.7.3a at present).

STAR-SEQR

RNA Fusion Detection and Quantification using STAR. https://github.com/ExpressionAnalysis/STAR-SEQR License: non-commercial use

Additional Requirements:

• biobambam2(https://github.com/gt1/biobambam2) or conda install -c bioconda biobambam (newer development is at https://gitlab.com/german.tischler/biobambam2 GPLv3)
• STAR(https://github.com/alexdobin/STAR). Must use >2.5.3a. conda install -c bioconda star (see above)
• Velvet(https://github.com/dzerbino/velvet) or conda install -c bioconda velvet (we have velvet/1.2.10 which is current)
• samtools(https://github.com/samtools/samtools) or conda install -c bioconda samtools (we have samtools/1.11/gnu-4.9.2 as our newest)
• Salmon(https://combine-lab.github.io/salmon/) or conda install -c bioconda salmon (GPLv3)
• UCSC utils(http://hgdownload.soe.ucsc.edu/admin/exe/) or conda install -c bioconda ucsc-gtftogenepred (binaries, free for academic, nonprofit, and personal use.)
• gffread(http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.8c.tar.gz) or conda install -c bioconda gffread (http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread)

STAR-Fusion 1.10.0

STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. https://github.com/STAR-Fusion/STAR-Fusion/wiki License: BSD-3-Clause

Requires:

• STAR https://github.com/alexdobin/STAR (see above)
• samtools http://www.htslib.org/download/ (see above)
• possibly some non-standard Perl modules - see below:

  A typical perl module installation may involve:
  perl -MCPAN -e shell
  install DB_File
  install URI::Escape
  install Set::IntervalTree
  install Carp::Assert
  install JSON::XS
  install PerlIO::gzip

FusionInspector

FusionInspector is a component of the Trinity Cancer Transcriptome Analysis Toolkit, and as with the other fusion-transcriptome components of CTAT, FusionInspector leverages the CTAT genome lib data resource, containing a reference genome and corresponding protein-coding gene annotation set, and various metadata. https://github.com/FusionInspector/FusionInspector/wiki/installing-FusionInspector License: Broad (allowing redistribution).

Requires:

• STAR - currently using version 2.6.1a (note Arriba wants newer) you can use a newer version of STAR, but it may not be compatible with the plug-n-play data resource lib described below.
• samtools (modern versions, 1.3+) (see above)
• Perl module: Set::IntervalTree
• Python modules: igv-reports, requests
• Trinity (optional but recommended)
• GMAP (optional but recommended)

TrinityFusion

Fusion and foreign transcript detection via RNA-seq de novo assembly https://github.com/trinityrnaseq/TrinityFusion/wiki License: trinityrnaseq (allowing redistribution)

Requires:

• The Trinity assembler https://github.com/trinityrnaseq/trinityrnaseq/releases
• GMAP version 2017-11-15 http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-11-15.tar.gz
• Bowtie2 aligner https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.3.1/bowtie2-2.3.3.1-linux-x86_64.zip/download (we have earlier version 2.2.5)

Note that Trinity also requires:

• jellyfish http://www.genome.umd.edu/jellyfish.html

Some of these have Singularity containers, not sure if anything has a full pipeline with all of these.

[heatherkellyucl]

Note: EasyBuild has Arriba, STAR-Fusion, Trinity. Does not have STAR-SEQR, FusionInspector, TrinityFusion (unless wrapped into one of the above).

[heatherkellyucl]

Checking what and how much of this is still required as it has been a long time.

[heatherkellyucl]

No longer needed, closing. (If anyone reading this later does need this, or parts of this, let us know at rc-support).