diff --git a/.idea/encodings.xml b/.idea/encodings.xml new file mode 100644 index 0000000..15a15b2 --- /dev/null +++ b/.idea/encodings.xml @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff --git a/.idea/markdown-navigator.xml b/.idea/markdown-navigator.xml new file mode 100644 index 0000000..808794e --- /dev/null +++ b/.idea/markdown-navigator.xml @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/.idea/markdown-navigator/profiles_settings.xml b/.idea/markdown-navigator/profiles_settings.xml new file mode 100644 index 0000000..57927c5 --- /dev/null +++ b/.idea/markdown-navigator/profiles_settings.xml @@ -0,0 +1,3 @@ + + + \ No newline at end of file diff --git a/.idea/misc.xml b/.idea/misc.xml new file mode 100644 index 0000000..28a804d --- /dev/null +++ b/.idea/misc.xml @@ -0,0 +1,6 @@ + + + + + \ No newline at end of file diff --git a/.idea/modules.xml b/.idea/modules.xml new file mode 100644 index 0000000..8148c50 --- /dev/null +++ b/.idea/modules.xml @@ -0,0 +1,8 @@ + + + + + + + + \ No newline at end of file diff --git a/.idea/multiexseq.iml b/.idea/multiexseq.iml new file mode 100644 index 0000000..d6ebd48 --- /dev/null +++ b/.idea/multiexseq.iml @@ -0,0 +1,9 @@ + + + + + + + + + \ No newline at end of file diff --git a/.idea/vcs.xml b/.idea/vcs.xml new file mode 100644 index 0000000..35eb1dd --- /dev/null +++ b/.idea/vcs.xml @@ -0,0 +1,6 @@ + + + + + + \ No newline at end of file diff --git a/Developement.md b/Developement.md deleted file mode 100644 index c4d7faa..0000000 --- a/Developement.md +++ /dev/null @@ -1,11 +0,0 @@ -# Team members for software development - - -# Details for members - -| Name | Email | Site | institute | -|---------------|:------------------------: |-----------------------------: |---------------| -| Qi Zhao | zhaoqi@sysucc.org.cn | https://github.com/likelet | SYSUCC | - - -# to be filled in diff --git a/Development.md b/Development.md new file mode 100644 index 0000000..4791bb4 --- /dev/null +++ b/Development.md @@ -0,0 +1,15 @@ +# Team members for software development + + +# Details for members + +| Name | Email | Site | institute | +|---------------|:------------------------: |-----------------------------: |---------------| +| Qi Zhao | zhaoqi@sysucc.org.cn | https://github.com/likelet | SYSUCC | +| Chengwei Wang | wangchw8@mail2.sysu.edu.cn| https://github.com/Ninomoriaty| SYSU | +| Ziwei Wang | wangzw.edu@gmail.com | https://github.com/ZIWEI-WONG | SYSU | +| Chen Jianyu | 364500513@qq.com | https://github.com/chenjy327 | SYSU | +| Zheng Li | 419125762@qq.com | https://github.com/lizheng141026 | SYSU | +| Xin Wang | wangx555@mail2.sysu.edu.cn| https://github.com/Wangxin555 | SYSU | +| Liu Jie | 1953640796@qq.com | https://github.com/LiuJie1117 | SYSU +# to be filled in diff --git a/Dockerfile b/Dockerfile index 31bb6b8..cde0b33 100644 --- a/Dockerfile +++ b/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"] \ No newline at end of file diff --git a/DockerfileOrigin b/DockerfileOrigin new file mode 100644 index 0000000..278f1bf --- /dev/null +++ b/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"] diff --git a/README.md b/README.md index c4676b6..326261c 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# multiexseq +# MesKit **Analysis pipelie for multi WEX analysis** > this readme was generated by nf-core tools diff --git a/conf/LiuJie.config b/conf/LiuJie.config new file mode 100644 index 0000000..5ab2f8a --- /dev/null +++ b/conf/LiuJie.config @@ -0,0 +1 @@ +Hello \ No newline at end of file diff --git a/conf/chenjy.config b/conf/chenjy.config new file mode 100644 index 0000000..e69de29 diff --git a/conf/wangChengWei.conf b/conf/wangChengWei.conf new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/conf/wangChengWei.conf @@ -0,0 +1 @@ + diff --git a/conf/ziweiwang.config b/conf/ziweiwang.config new file mode 100644 index 0000000..e69de29 diff --git a/environment.yml b/environment1.yml similarity index 79% rename from environment.yml rename to environment1.yml index 9836367..1c3f2fa 100644 --- a/environment.yml +++ b/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 diff --git a/environment2.yml b/environment2.yml new file mode 100644 index 0000000..d9f0b78 --- /dev/null +++ b/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 \ No newline at end of file