Merge branch 'dev' of ssh://git-r3lab-server.uni.lu:8022/shaman.narayanasamy/IMP into dev

Snakefile

@@ -112,12 +112,3 @@ rule MODULE_LOAD_TEST:
         """
         IMPPRL="{config[preload][test]}"; if [[ -n $IMPPRL ]]; then $IMPPRL; fi
         """
-
-if KOOPA:
-    print(KOOPA)
-
-rule T:
-    shell:
-        """
-        echo {MT}
-        """

docker/Dockerfile

@@ -214,7 +214,7 @@ RUN echo "`snakemake --bash-completion`" >> ~/.bashrc \
 ######################
 ENV PATH /home/imp/lib/trinityrnaseq_r20140717:/home/imp/lib/Platypus_0.8.1:/home/imp/lib/megahit:$PATH
 
-VOLUME ["/data", "/config"]
+VOLUME ["/data", "/output"]
 WORKDIR /home/imp/integrated-metaomic-pipeline
 ENTRYPOINT ["snakemake"]
 CMD ["ALL"]

docker/README.md

@@ -11,6 +11,8 @@ For more information about `docker` and how to install and use it, please refers
 * Run latest version of **IMP**. For the first run, it will download all dependencies. It can take some time.
 ```bash
 docker run imp:latest
+... downloading data ...
+Error: Snakefile "Snakefile" not present.
 ```
 
 ## Run IMP on your data

src/config.imp.json

@@ -9,7 +9,7 @@
       "Metatranscriptomics": ""
     },
     "sample": "test",
-    "outputdir": "build",
+    "outputdir": "/output",
     "db_path": "db",
     "preprocessing_filtering": true,
     "trimmomatic": {