Refactor to use upstream script in isatools-galaxy

Dockerfile

@@ -3,14 +3,21 @@ FROM isatools/isatools:3.6-alpine-0.9.4
 LABEL maintainer="PhenoMeNal-H2020 Project ( phenomenal-h2020-users@googlegroups.com )"
 LABEL Description="Convert MWTab to ISA-Tab"
 LABEL software="mw2isa"
-LABEL software.version="0.9.5"
+LABEL software.version="0.9.4"
 LABEL version="0.5"
 
+RUN apk add --no-cache --virtual git-deps git openssh \
+    && git clone --depth 1 --single-branch -b develop https://github.com/ISA-tools/isatools-galaxy /files/galaxy \
+    && apk del git-deps \
+    && rm -rf /var/cache/apk/* \
+    && rm -rf /tmp/* /var/tmp/*
+
+ENV PATH=$PATH:/files/galaxy
 
 ADD run_test1.sh /usr/local/bin/run_test1.sh
 RUN chmod a+x /usr/local/bin/run_test1.sh
 
-ADD mw2isatab.py /usr/local/bin/mw2isatab.py
+RUN cp /files/galaxy/tools/other/mw2isatab.py /usr/local/bin/mw2isatab.py
 RUN chmod a+x /usr/local/bin/mw2isatab.py
 
 ENTRYPOINT ["mw2isatab.py"]

README.md

@@ -53,13 +53,13 @@ On a PhenoMeNal Cloud Research Environment Galaxy environment, go to ISA tools t
 From docker:
 
 ```bash
-docker run docker-registry.phenomenal-h2020.eu/phnmnl/container-mw2isa <MW_STUDY_ID>
+docker run docker-registry.phenomenal-h2020.eu/phnmnl/mw2isa <MW_STUDY_ID> <output directory>
 ```
 
 e.g.
 
 ```bash
-docker run docker-registry.phenomenal-h2020.eu/phnmnl/container-mw2isa ST000110
+docker run docker-registry.phenomenal-h2020.eu/phnmnl/mw2isa ST000110 /
 ```
 
 ## Future Developments