caloger/rsem-bowtie2

The docker rsem-bowtie2 can be run with the following commands:

sudo docker pull docker.io/rcaloger/rsem-bowtie2
sudo docker run -v /host/directory:/container/directory -d docker.io/rcaloger/rsem-bowtie2 sh /host/directory/reference.repository /bin/prepare_ref_bowtie2_ensembl.sh ftp.link.fa.gz ftp.link.gtf.gz n.of.threads 

The above command  is used to create the reference repository using ensembl data.

e.g:
sudo docker run -v /data/scratch/:/data/scratch -d docker.io/rcaloger/rsem-bowtie2 sh /data/scratch/hg19_bowtie2_ensembl75 /bin/prepare_ref_bowtie2_ensembl.sh ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/Homo_sapiens.GRCh37.75.gtf.gz 24