Update mappers

[jaanckae]

Some of the software dependencies in the Docker container are several versions behind a recent version. Would it be possible to update the Dockerfile to work with these updated versions?

At least for some versions of the mappers this would be convenient as not to have to rerun the indexing script.

Software	Website	used_version	latest_release
Scons	http://www.scons.org	3.1.2	4.5.2
Trimmomatic	http://www.usadellab.org/cms/?page=trimmomatic	0.39	0.39
FASTQC	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/	0.11.9	0.12.1
HISAT2	http://ccb.jhu.edu/software/hisat2/index.shtml	2.1.0	2.2.1
STAR	http://github.com/alexdobin/STAR	2.6.1e	2.7.11
BWA	http://bio-bwa.sourceforge.net/	0.7.15-r1140	0.7.17
Bowtie2	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml	2.4.1	2.5.1
Bowtie	http://bowtie-bio.sourceforge.net/index.shtml	1.1.2	1.3.1
TopHat	http://ccb.jhu.edu/software/tophat/index.shtml	2.1.0	2.1.1
Segemehl	http://www.bioinf.uni-leipzig.de/Software/segemehl/	0.3.4	0.3.4
CIRI	http://ciri.sourceforge.io/	2.0.6	2.1.1
CIRCexplorer2	http://github.com/YangLab/CIRCexplorer2	2.3.8	2.3.8
find_circ	http://github.com/marvin-jens/find_circ	1.2	1.2
BEDtools	http://bedtools.readthedocs.io	2.29.2	2.31.0
Samtools	http://www.htslib.org/	1.10	1.18

Thanks in advance Jasper

[egaffo]

Some packages must stay at the version currently implemented in CirComPara2 because of incompatibility issues. F.i. I achieved TopHat2 and Bowtie to work together only with exactly those two versions! In some other tool newer versions, I found bugs that are still unresolved (see f.i. HISAT2 #255). Further, newer versions did not provide improvements for circRNA detection or computation speed (BEDtools, SAMtools, BWA, FASTQC), and CIRI v2.1.1 refers to the CIRI_full algorithm, which actually uses CIRI v2.0.6. Then, I see no reason to spend time updating these packages. Perhaps STAR and Bowtie2 newer versions could give some improvements (as I understand from the release statements), but STAR changed the Chimeric.junction file format that would break the STAR-based detection tools, i.e. circRNA_finder, CIRCexplorer2, and DCC v0.4.8 (DCC v0.5 was indeed released to fix this issue). Unfortunately, you'll have to use a STAR index compatible with v2.6.1e . Making all these tools work together was worse than playing Tetris level 29.