tseemann
commented
7 years ago Perl is not the issue. Those pipelines have lots of dependencies, some of which may not be in Conda yet. Plus it seems a lot of it is based around a web server setup, which isn't really what Conda is designed for.
JAMg (and any gene annotation) really shines for species for which you have raw RNA-Seq (or other transcriptome) data but it can work without it too.
These software are core to the way JAMg works:
HHblits used to identify transposable elements and domains not captured by transcriptomes (i.e. not expressed)
Augustus our de-novo gene predictor of choice
RepeatMasker
WebApollo
And our other software:
PASA2 (unpublished version 2): incorporate transcriptome information
Trinity RNA-Seq: Arguably, the best de-novo RNA-seq assembler out there.
TransDecoder: protein prediction from RNA-Seq assemblies, bundled in PASA2 so no need to install it separately.
aatpackage: a simple and fast way to align proteins to a genome
EvidenceModeller: constructs consensus gene sets
Just_Preprocess_My_reads: a simple way of pre-processing and QCing RNA-Seq
JAMp: functional annotation of your predicted proteins
These dependencies exist due to the above software (on Ubuntu you can install them with apt-get):
GMAP and GSNAP
bedtools
samtools
blat
Tomcat and Apache webserver
Further, we currently support these optional components:
GeneMark: de-novo predictor without any training
geneid: no longer supported by authors
snap: SNAP from Ian Korf
Glimmer: no longer supported by authors
Hi, Is anyone working on these below workflows?
Some of the steps are written in Perl. Will it still be possible to install them?
Thank you in advance.
Michal