From aef754c957a4a745dd0d9c60c26c2b535432ca57 Mon Sep 17 00:00:00 2001 From: Ninomoriaty <31891708+Ninomoriaty@users.noreply.github.com> Date: Mon, 17 Dec 2018 10:23:26 +0800 Subject: [PATCH 01/31] Create wangChengWei.conf --- conf/wangChengWei.conf | 1 + 1 file changed, 1 insertion(+) create mode 100644 conf/wangChengWei.conf 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 @@ + From 8de4d3ef3d8e6c83b337b7bcd3ee127e5999cb02 Mon Sep 17 00:00:00 2001 From: Niinleslie <705172894@qq.com> Date: Mon, 17 Dec 2018 10:41:15 +0800 Subject: [PATCH 02/31] Delete mnliu.config --- conf/mnliu.config | 1 - 1 file changed, 1 deletion(-) delete mode 100644 conf/mnliu.config diff --git a/conf/mnliu.config b/conf/mnliu.config deleted file mode 100644 index 8b13789..0000000 --- a/conf/mnliu.config +++ /dev/null @@ -1 +0,0 @@ - From 9aefe33698cd9b23b46376461d23f498d9610024 Mon Sep 17 00:00:00 2001 From: Niinleslie <705172894@qq.com> Date: Mon, 17 Dec 2018 10:44:18 +0800 Subject: [PATCH 03/31] Create mnliu.config --- conf/mnliu.config | 1 + 1 file changed, 1 insertion(+) create mode 100644 conf/mnliu.config diff --git a/conf/mnliu.config b/conf/mnliu.config new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/conf/mnliu.config @@ -0,0 +1 @@ + From 0c22ae117024532af33a24e3a2f91eac7f94142d Mon Sep 17 00:00:00 2001 From: ZIWEI-WONG Date: Mon, 17 Dec 2018 11:06:28 +0800 Subject: [PATCH 04/31] trying to upload some file --- conf/ziweiwang.config | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 conf/ziweiwang.config diff --git a/conf/ziweiwang.config b/conf/ziweiwang.config new file mode 100644 index 0000000..e69de29 From b41fd674b24490b9cd281cd92baaf444c148e926 Mon Sep 17 00:00:00 2001 From: chenjy327 <364500513@qq.com> Date: Mon, 17 Dec 2018 13:58:36 +0800 Subject: [PATCH 05/31] add chenjy.config --- conf/chenjy.config | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 conf/chenjy.config diff --git a/conf/chenjy.config b/conf/chenjy.config new file mode 100644 index 0000000..e69de29 From f679dce49fbd3bf7be48ddfe6782b1bea64f9858 Mon Sep 17 00:00:00 2001 From: Ninomoriaty <504430784@qq.com> Date: Tue, 18 Dec 2018 18:27:33 +0800 Subject: [PATCH 06/31] wangchw: retry1 information submitted. --- Developement.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Developement.md b/Developement.md index c4d7faa..6970b6f 100644 --- a/Developement.md +++ b/Developement.md @@ -6,6 +6,6 @@ | 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 | # to be filled in From 1da09373648be01f315c004cdbcdf41faa738ab6 Mon Sep 17 00:00:00 2001 From: chenjy327 <364500513@qq.com> Date: Tue, 18 Dec 2018 19:41:22 +0800 Subject: [PATCH 07/31] add Chenjianyu contribution --- Development.md | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 Development.md diff --git a/Development.md b/Development.md new file mode 100644 index 0000000..3ee654a --- /dev/null +++ b/Development.md @@ -0,0 +1,11 @@ +# Team members for software development + + +# Details for members + +| Name | Email | Site | institute | +|---------------|:------------------------: |-----------------------------: |---------------| +| Chen Jianyu | 364500513@qq.com | https://github.com/chenjy327 | SYSU | + + +# to be filled in \ No newline at end of file From f2a13464483e44769f100c998229e6019e81c2e1 Mon Sep 17 00:00:00 2001 From: ZIWEI-WONG Date: Tue, 18 Dec 2018 23:30:26 +0800 Subject: [PATCH 08/31] add personal information --- Developement.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Developement.md b/Developement.md index c4d7faa..2ad6678 100644 --- a/Developement.md +++ b/Developement.md @@ -6,6 +6,6 @@ | Name | Email | Site | institute | |---------------|:------------------------: |-----------------------------: |---------------| | Qi Zhao | zhaoqi@sysucc.org.cn | https://github.com/likelet | SYSUCC | - + Ziwei Wang wangzw.edu@gmail.com https://github.com/ZIWEI-WONG SYSU # to be filled in From 8df09e5eee91cbcde133cc4a0e1a01a39ad7f090 Mon Sep 17 00:00:00 2001 From: Qi ZHAO Date: Wed, 19 Dec 2018 22:50:31 +0800 Subject: [PATCH 09/31] Update Developement.md --- Developement.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Developement.md b/Developement.md index e8cc198..2d1e814 100644 --- a/Developement.md +++ b/Developement.md @@ -8,6 +8,8 @@ | 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 | + # to be filled in From 399633bab1bf5f81579be3c00971e846f57f4a0d Mon Sep 17 00:00:00 2001 From: Qi ZHAO Date: Wed, 19 Dec 2018 22:51:12 +0800 Subject: [PATCH 10/31] Delete Development.md --- Development.md | 11 ----------- 1 file changed, 11 deletions(-) delete mode 100644 Development.md diff --git a/Development.md b/Development.md deleted file mode 100644 index 3ee654a..0000000 --- a/Development.md +++ /dev/null @@ -1,11 +0,0 @@ -# Team members for software development - - -# Details for members - -| Name | Email | Site | institute | -|---------------|:------------------------: |-----------------------------: |---------------| -| Chen Jianyu | 364500513@qq.com | https://github.com/chenjy327 | SYSU | - - -# to be filled in \ No newline at end of file From 756830c91623a3854af879223f4c1f91aa8e2914 Mon Sep 17 00:00:00 2001 From: Qi ZHAO Date: Wed, 19 Dec 2018 22:51:30 +0800 Subject: [PATCH 11/31] fix typos --- Developement.md => Development.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename Developement.md => Development.md (100%) diff --git a/Developement.md b/Development.md similarity index 100% rename from Developement.md rename to Development.md From c4789a9967cb87d8a17b7a6c97161015ad46b0e3 Mon Sep 17 00:00:00 2001 From: Qi ZHAO Date: Thu, 20 Dec 2018 22:34:28 +0800 Subject: [PATCH 12/31] Update Development.md --- Development.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Development.md b/Development.md index 2d1e814..a53b8e5 100644 --- a/Development.md +++ b/Development.md @@ -9,7 +9,7 @@ | 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 | SYSUCC | # to be filled in From fd952ff722be2ed48ea7f565466988c534ab0448 Mon Sep 17 00:00:00 2001 From: Qi ZHAO Date: Sat, 22 Dec 2018 21:20:57 +0800 Subject: [PATCH 13/31] Update Development.md --- Development.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Development.md b/Development.md index a53b8e5..9243977 100644 --- a/Development.md +++ b/Development.md @@ -9,7 +9,7 @@ | 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 | SYSUCC | - +| Zheng Li | 419125762@qq.com | https://github.com/lizheng141026 | SYSU | +| Xin Wang | wangx555@mail2.sysu.edu.cn| https://github.com/Wangxin555 | SYSU | # to be filled in From a2cec4cb23d7205c14c74cf5a940ba862238c6f8 Mon Sep 17 00:00:00 2001 From: LiuJie1117 <1953640796@qq.com> Date: Mon, 24 Dec 2018 00:14:58 +0800 Subject: [PATCH 14/31] create LiuJie.config --- conf/LiuJie.config | 1 + 1 file changed, 1 insertion(+) create mode 100644 conf/LiuJie.config 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 From 9075d804b070c29144571cc198e88de141f2cec1 Mon Sep 17 00:00:00 2001 From: LiuJie1117 <1953640796@qq.com> Date: Wed, 26 Dec 2018 19:53:17 +0800 Subject: [PATCH 15/31] add information of LJ --- Development.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Development.md b/Development.md index 9243977..4791bb4 100644 --- a/Development.md +++ b/Development.md @@ -11,5 +11,5 @@ | 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 From b998ff263ac3fe8a53d5da26ee12d709712780c4 Mon Sep 17 00:00:00 2001 From: Ninomoriaty <504430784@qq.com> Date: Wed, 9 Jan 2019 15:25:59 +0800 Subject: [PATCH 16/31] dockerfile: samtools pyclone but facets control-freec in different environments --- .idea/vcs.xml | 6 ++++++ Dockerfile | 10 ++++++++-- DockerfileOrigin | 28 ++++++++++++++++++++++++++++ environment.yml => environment1.yml | 4 ++++ environment2.yml | 13 +++++++++++++ 5 files changed, 59 insertions(+), 2 deletions(-) create mode 100644 .idea/vcs.xml create mode 100644 DockerfileOrigin rename environment.yml => environment1.yml (79%) create mode 100644 environment2.yml 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/Dockerfile b/Dockerfile index 31bb6b8..483febb 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,6 +2,12 @@ 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 +COPY environment1.yml enviroment2.yml ./ + +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 + ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH diff --git a/DockerfileOrigin b/DockerfileOrigin new file mode 100644 index 0000000..278f1bf --- /dev/null +++ b/DockerfileOrigin @@ -0,0 +1,28 @@ +## images base Ubuntu 16.04 +FROM biocontainers/biocontainers:latest + +## metadata +LABEL base.image="biocontainers:latest" +LABEL version="2" +LABEL about.tags="test1" + +## Enviroment variables + +## runtimes 3 +#ENV PATH /opt/conda/envs/multiexseq_origin/bin:$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/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 From 8fb287b90a736270dca73e4bdf07df27d1109cb7 Mon Sep 17 00:00:00 2001 From: Ninomoriaty <504430784@qq.com> Date: Fri, 18 Jan 2019 16:56:12 +0800 Subject: [PATCH 17/31] dockerfile mytest0 --- .idea/encodings.xml | 4 ++++ .idea/misc.xml | 6 ++++++ .idea/modules.xml | 8 ++++++++ .idea/multiexseq.iml | 9 +++++++++ Dockerfile | 4 +++- 5 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 .idea/encodings.xml create mode 100644 .idea/misc.xml create mode 100644 .idea/modules.xml create mode 100644 .idea/multiexseq.iml 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/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/Dockerfile b/Dockerfile index 483febb..4cf0cea 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ FROM nfcore/base LABEL authors="Qi Zhao" \ description="Docker image containing all requirements for nf-core/multiexseq pipeline" -COPY environment1.yml enviroment2.yml ./ +COPY environment1.yml environment2.yml ./ ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a @@ -11,3 +11,5 @@ ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH RUN conda env create -f /environment2.yml -n multiexseq_freec && conda clean -a ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH + +CMD ["/bin/bash"] \ No newline at end of file From 2e89ef8b3c5df772c3c7885ac667b47fcfdf8067 Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 10:49:48 +0800 Subject: [PATCH 18/31] new dockerfile with annovar --- Dockerfile | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Dockerfile b/Dockerfile index 4cf0cea..5f2c5d4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,6 +4,9 @@ LABEL authors="Qi Zhao" \ COPY environment1.yml environment2.yml ./ +ADD http://www.openbioinfomatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz ./annovar.latest.tar.gz +RUN tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz + ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a From 965270f779911c7528e5bf0e31930253fb0d64e8 Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 11:32:58 +0800 Subject: [PATCH 19/31] new dockerfile with annovar --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 5f2c5d4..68be383 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ LABEL authors="Qi Zhao" \ COPY environment1.yml environment2.yml ./ -ADD http://www.openbioinfomatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz ./annovar.latest.tar.gz +ADD http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.{{version}}.tar.gz ./annovar.latest.tar.gz RUN tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH From f7590de8ae615b04abba122956212b0b0ff0b6fa Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 12:19:37 +0800 Subject: [PATCH 20/31] new dockerfile with annovar --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 68be383..b764e74 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ LABEL authors="Qi Zhao" \ COPY environment1.yml environment2.yml ./ -ADD http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.{{version}}.tar.gz ./annovar.latest.tar.gz +RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.version.tar.gz ./annovar.latest.tar.gz RUN tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH From b12c549af0663372a06c6d9426eb11e0559b43da Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 12:42:48 +0800 Subject: [PATCH 21/31] new dockerfile with annovar --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index b764e74..08c6795 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ LABEL authors="Qi Zhao" \ COPY environment1.yml environment2.yml ./ -RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.version.tar.gz ./annovar.latest.tar.gz +RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.version.tar.gz RUN tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH From bbf1930271042abbb6e6ac17a707c0df6eb9110b Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 13:32:13 +0800 Subject: [PATCH 22/31] new dockerfile with annovar --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 08c6795..5dcd473 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,7 +4,7 @@ LABEL authors="Qi Zhao" \ COPY environment1.yml environment2.yml ./ -RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.version.tar.gz +RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz RUN tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz ENV PATH /opt/conda/envs/multiexseq_facets/bin:$PATH From 7ea60ed321bfecc0df5bb87175d5327be360df06 Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 18:27:03 +0800 Subject: [PATCH 23/31] new dockerfile with annovar db --- Dockerfile | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index 5dcd473..071a643 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,8 +4,7 @@ LABEL authors="Qi Zhao" \ COPY environment1.yml environment2.yml ./ -RUN wget http://www.openbioinformatics.org/annovar/download/0wgxR2rIVP/annovar.latest.tar.gz -RUN tar -xzvf annovar.latest.tar.gz && rm annovar.latest.tar.gz +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:$PATH RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a @@ -13,6 +12,8 @@ RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH RUN conda env create -f /environment2.yml -n multiexseq_freec && conda clean -a -ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH +RUN cd annovar && source activate multiexseq_freec && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ + +# ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH CMD ["/bin/bash"] \ No newline at end of file From 4f36cb4d81c616124d0ba91332ddde11b3c8fadb Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 20:25:23 +0800 Subject: [PATCH 24/31] new dockerfile with annovar db --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 071a643..167669b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,7 +12,7 @@ RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH RUN conda env create -f /environment2.yml -n multiexseq_freec && conda clean -a -RUN cd annovar && source activate multiexseq_freec && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ +RUN cd annovar && conda activate multiexseq_freec && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ # ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH From 34d8eb979a3a4dab0b0aa1c9a2733805ff92cd09 Mon Sep 17 00:00:00 2001 From: Ninomoriaty <504430784@qq.com> Date: Mon, 11 Feb 2019 22:17:44 +0800 Subject: [PATCH 25/31] Merge branch 'LiuJie1117' of https://github.com/Ninomoriaty/multiexseq # Conflicts: # Development.md --- .idea/markdown-navigator.xml | 83 +++++++++++++++++++ .../markdown-navigator/profiles_settings.xml | 3 + Dockerfile | 6 +- 3 files changed, 91 insertions(+), 1 deletion(-) create mode 100644 .idea/markdown-navigator.xml create mode 100644 .idea/markdown-navigator/profiles_settings.xml 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/Dockerfile b/Dockerfile index 167669b..4ce9c27 100644 --- a/Dockerfile +++ b/Dockerfile @@ -12,7 +12,11 @@ RUN conda env create -f /environment1.yml -n multiexseq_facets && conda clean -a ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH RUN conda env create -f /environment2.yml -n multiexseq_freec && conda clean -a -RUN cd annovar && conda activate multiexseq_freec && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ +RUN cd annovar \ + && echo "conda activate" >> ~/.bashrc \ + && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \ + && conda activate multiexseq_freec \ + && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ # ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH From 878f7ff9864a9f1f79fe649552708e80a2f41af3 Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Tue, 12 Feb 2019 09:28:21 +0800 Subject: [PATCH 26/31] new dockerfile with annovar db --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 4ce9c27..c02600d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,8 +13,8 @@ ENV PATH /opt/conda/envs/multiexseq_freec/bin:$PATH RUN conda env create -f /environment2.yml -n multiexseq_freec && conda clean -a RUN cd annovar \ - && echo "conda activate" >> ~/.bashrc \ && echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \ + && echo "conda activate" >> ~/.bashrc \ && conda activate multiexseq_freec \ && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ From 0707bb63ed7b78e3954f799fd7f8e983d1170514 Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Tue, 12 Feb 2019 11:30:35 +0800 Subject: [PATCH 27/31] new dockerfile with annovar db --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index c02600d..03630fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,9 +13,9 @@ ENV PATH /opt/conda/envs/multiexseq_freec/bin:$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 \ + #&& echo "./opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \ + #&& echo "conda activate" >> ~/.bashrc \ + #&& conda activate multiexseq_freec \ && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ # ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH From e30d84468c8066752ce0aa482e3e7cefbdcad8dd Mon Sep 17 00:00:00 2001 From: ninomoriaty <504430784@qq.com> Date: Tue, 12 Feb 2019 13:39:22 +0800 Subject: [PATCH 28/31] new dockerfile with annovar db again --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 03630fe..cde0b33 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,7 +16,7 @@ RUN cd annovar \ #&& echo "./opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc \ #&& echo "conda activate" >> ~/.bashrc \ #&& conda activate multiexseq_freec \ - && annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ + && perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb/ # ENV PATH /opt/conda/envs/nf-core-multiexseq-1.0dev/bin:$PATH From 90ddc6c5e48a7f5bea6b184b29c3009ef842e93b Mon Sep 17 00:00:00 2001 From: Niinleslie <705172894@qq.com> Date: Tue, 30 Apr 2019 09:35:34 +0800 Subject: [PATCH 29/31] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From 145aa75ee71f0c37ab80070290d3a44749bf8f83 Mon Sep 17 00:00:00 2001 From: Niinleslie <705172894@qq.com> Date: Wed, 1 May 2019 08:54:56 +0800 Subject: [PATCH 30/31] Create R --- R | 1 + 1 file changed, 1 insertion(+) create mode 100644 R diff --git a/R b/R new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/R @@ -0,0 +1 @@ + From 34e967b3a5eed7095ceb2e9dfc42bc50e7b93421 Mon Sep 17 00:00:00 2001 From: Niinleslie <705172894@qq.com> Date: Wed, 1 May 2019 08:55:20 +0800 Subject: [PATCH 31/31] Delete R --- R | 1 - 1 file changed, 1 deletion(-) delete mode 100644 R diff --git a/R b/R deleted file mode 100644 index 8b13789..0000000 --- a/R +++ /dev/null @@ -1 +0,0 @@ -