plachta11b/gfftoolsgx repository overview

FROM alpine/git:latest AS builder

WORKDIR /

# download latest commit (if not change it)
RUN git clone https://github.com/vipints/GFFtools-GX.git
RUN git -C /GFFtools-GX checkout a50cf17206e0465856b1f0156ace95fe392ffa8a

FROM python:2.7

# TODO build wheel and import

COPY --from=builder /GFFtools-GX /GFFtools-GX

RUN python -m pip --no-cache-dir install numpy==1.16.6 biopython==1.76

ADD ./gff2bed /GFFtools-GX

RUN chmod +x /GFFtools-GX/gff2bed

ENV PATH $PATH:/GFFtools-GX

CMD [ "/GFFtools-GX/gff2bed" ]

#!/bin/bash

# THIS WORKS ONLY FOR EXONS CDS :(

tee > temp

python /GFFtools-GX/gff_to_bed.py temp