RNA-Seq Example |

Let’s walk through using the container that is provided by this repository. As a reminder, here is how we built it:

docker pull vanessa/example.scif
docker build -t vanessa/example.scif .

Now let’s review examples of how to run each of the applications using SCIF with the container. For the following steps, scif ensures that /scif/data exists in the container, so we can use it as a working directory (to mount from the hose) if needed. The weird name is chosen specifically to ensure that the same path doesn’t exist on the host you are mounting from.

Bowtie

Here is what we are starting with: this is dat in the repository.

ls data/ggal
ggal_1_48850000_49020000.bed.gff               ggal_gut_1.fq  ggal_liver_1.fq
ggal_1_48850000_49020000.Ggal71.500bpflank.fa  ggal_gut_2.fq  ggal_liver_2.fq

and let’s define what these paths will look like in the container. The /scif/data folder that we know to exist with scif we will map to “data” in the present working directory.

genome=/scif/data/ggal_1_48850000_49020000.Ggal71.500bpflank.fa
genomeIndex=${genome}.index

docker run -v $PWD/data/ggal:/scif/data vanessa/example.scif exec bowtie bowtie2-build --threads 1 $genome $genomeIndex
singularity run -B $PWD/data/ggal:/scif/data rnatoy exec bowtie bowtie2-build --threads 1 $genome $genomeIndex

In the above, notice that I am:

defining a genome and index output to be in the /scif/data folder in the container
which is mapped to my host $PWD/data folder that has the data files

The output is verbose, but I get the result on my local machine!

ls data/ggal/
ggal_1_48850000_49020000.bed.gff                           ggal_1_48850000_49020000.Ggal71.500bpflank.fa.index.3.bt2      ggal_gut_1.fq
ggal_1_48850000_49020000.Ggal71.500bpflank.fa              ggal_1_48850000_49020000.Ggal71.500bpflank.fa.index.4.bt2      ggal_gut_2.fq
ggal_1_48850000_49020000.Ggal71.500bpflank.fa.index.1.bt2  ggal_1_48850000_49020000.Ggal71.500bpflank.fa.index.rev.1.bt2  ggal_liver_1.fq
ggal_1_48850000_49020000.Ggal71.500bpflank.fa.index.2.bt2  ggal_1_48850000_49020000.Ggal71.500bpflank.fa.index.rev.2.bt2  ggal_liver_2.fq

Tophat

Now let’s do the next step, and we will do the same sort of deal. Note I’m not sure if I am executing this correctly, I’ve never used tophat.

reads="/scif/data/ggal_gut_1.fq /scif/data/ggal_gut_2.fq /scif/data/ggal_liver_1.fq /scif/data/ggal_liver_2.fq"
annot=/scif/data/ggal_1_48850000_49020000.bed.gff

docker run -v $PWD/data/ggal:/scif/data vanessa/example.scif exec tophat tophat2 -p 1 --GTF $annot $genomeIndex $reads
singularity run -B $PWD/data/ggal:/scif/data example.simg exec tophat tophat2 -p 1 --output-dir /scif/data --GTF $annot $genomeIndex $reads