creat a .config file

Development.md

@@ -0,0 +1,15 @@
+# Team members for software development 
+
+
+# Details for members    
+
+|   Name     	|         Email         	|           Site             	| institute 	|
+|---------------|:------------------------:	|-----------------------------:	|---------------|
+| Qi Zhao   	| [email protected]  	| https://github.com/likelet 	| SYSUCC    	|
+| Chengwei Wang | [email protected]| https://github.com/Ninomoriaty| SYSU          |
+|  Ziwei Wang   |  [email protected]    |   https://github.com/ZIWEI-WONG |   SYSU |
+| Chen Jianyu  	| [email protected]  	| https://github.com/chenjy327 	| SYSU    	|
+| Zheng Li   	| [email protected]  	| https://github.com/lizheng141026 	| SYSU    	|
+| Xin Wang      | [email protected]| https://github.com/Wangxin555 | SYSU          |
+| Liu Jie       | [email protected]      | https://github.com/LiuJie1117 | SYSU
+# to be filled in 

Dockerfile

@@ -2,6 +2,22 @@ FROM nfcore/base
 LABEL authors="Qi Zhao" \
       description="Docker image containing all requirements for nf-core/multiexseq pipeline"
 
-COPY environment.yml /
-RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH
+COPY environment1.yml environment2.yml ./
+
+RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz && tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz
+
+ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH
+RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a
+
+ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH
+RUN conda env create -f /environment2.yml -n multiexseq_freec && conda clean -a
+
+RUN cd annovar \
+    #&& echo "./opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \
+    #&& echo "conda activate" >> ~/.bashrc \
+    #&& conda activate multiexseq_freec \
+    && perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/
+
+# ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH
+
+CMD ["/bin/bash"]

DockerfileOrigin

@@ -0,0 +1,28 @@
+## images base Ubuntu 16.04
+FROM biocontainers/biocontainers:latest
+
+## metadata
+LABEL base.image="biocontainers:latest"
+LABEL version="2"
+LABEL about.tags="test1"
+
+## Enviroment variables
+
+## runtimes 3
+#ENV PATH /opt/conda/envs/multiexseq_origin/bin:$PATH
+#RUN conda create -c aroth85 --name multiexseq_origin samtools pyclone
+
+RUN conda config --add channels bioconda &&\
+    conda config --add channels aroth85
+
+ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH
+RUN conda create --name multiexseq_facets samtools pyclone r-facets 
+
+ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH
+RUN conda create --name multiexseq_freec samtools pyclone control-freec
+
+# annovar* (it seems that annovar could always be used as .pl documents so I just copy it..) 
+# RUN conda install perl
+# ADD annovar.latest.tar.gz .
+
+CMD ["/bin/bash"]

README.md

@@ -1,4 +1,4 @@
-# multiexseq  
+# MesKit 
 
 **Analysis pipelie for multi WEX analysis** 
 > this readme was generated by nf-core tools 

conf/LiuJie.config

@@ -0,0 +1 @@
+Hello

conf/wangChengWei.conf

@@ -0,0 +1 @@
+

environment.yml → environment1.yml

@@ -3,7 +3,11 @@ channels:
   - conda-forge
   - bioconda
   - defaults
+  - aroth85
 dependencies:
   # TODO nf-core: Add required software dependencies here
   - fastqc=0.11.8
   - multiqc=1.6
+  - samtools
+  - pyclone
+  - r-facets

environment2.yml

@@ -0,0 +1,13 @@
+name: nf-core-multiexseq-1.0dev
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+  - aroth85
+dependencies:
+  # TODO nf-core: Add required software dependencies here
+  - fastqc=0.11.8
+  - multiqc=1.6
+  - samtools
+  - pyclone
+  - control-freec