From 683314ab767327d7837a6700185ccee83ca8bafd Mon Sep 17 00:00:00 2001 From: Matthys Potgieter Date: Fri, 27 Dec 2024 14:32:39 +0000 Subject: [PATCH 1/3] thys --- docker/bio/Dockerfile | 4 ++-- docker/bio/build.sh | 2 +- docker/{mqproteogenomics => progenix}/Dockerfile | 3 ++- docker/{mqproteogenomics => progenix}/build.sh | 4 ++-- docker/{mqproteogenomics => progenix}/dev.sh | 0 docker/{mqproteogenomics => progenix}/run.sh | 0 docker/{mqproteogenomics => progenix}/runtest.sh | 0 7 files changed, 7 insertions(+), 6 deletions(-) rename docker/{mqproteogenomics => progenix}/Dockerfile (95%) rename docker/{mqproteogenomics => progenix}/build.sh (92%) rename docker/{mqproteogenomics => progenix}/dev.sh (100%) rename docker/{mqproteogenomics => progenix}/run.sh (100%) rename docker/{mqproteogenomics => progenix}/runtest.sh (100%) diff --git a/docker/bio/Dockerfile b/docker/bio/Dockerfile index 370a27b..376bb05 100644 --- a/docker/bio/Dockerfile +++ b/docker/bio/Dockerfile @@ -6,7 +6,7 @@ RUN apt-get update && apt-get -y install software-properties-common default-jdk RUN apt-get update && apt-get install -y libssl-dev openssl RUN apt-get update && apt-get install -y curl libssl-dev libxml2-dev libcurl4-openssl-dev libssh2-1-dev openssl curl openssl -RUN apt-get update && apt-get install -f -y libglvnd-dev libglx-dev libgl-dev libgl1-mesa-dev octave liboctave-dev +RUN apt-get update && apt-get install -f -y libglvnd-dev libglx-dev libgl-dev libgl1-mesa-dev octave #liboctave-dev RUN apt-get update && apt-get install -y mesa-common-dev libglu1-mesa-dev freeglut3-dev bwidget libfreetype6-dev RUN apt-get update && apt-get install -y libnetcdf-dev libboost-all-dev RUN apt-get update && apt-get install -y gcc gfortran libnetcdf-dev libnetcdff-dev libhdf5-serial-dev @@ -132,7 +132,7 @@ RUN git clone https://github.com/bmbolstad/preprocessCore.git && cd preprocessCo RUN conda update conda && conda install -c bioconda bcftools minimap2 RUN conda config --add channels bioconda && conda config --add channels conda-forge RUN conda install samtools -RUN conda install tabix +#RUN conda install bioconda/label/cf201901::tabix - should be included in samtools RUN conda install jbrowse2 RUN conda install emboss RUN yes | conda update --all diff --git a/docker/bio/build.sh b/docker/bio/build.sh index e36aafc..1ee1b93 100755 --- a/docker/bio/build.sh +++ b/docker/bio/build.sh @@ -2,7 +2,7 @@ set -e # Change build context to the root of the directory -version=v3.0.19 +version=v4.0.0 name=bio docker pull thyscbio/${name}:${version} && echo "version exists" && exit 1 || echo "Gonna build." cd ../.. diff --git a/docker/mqproteogenomics/Dockerfile b/docker/progenix/Dockerfile similarity index 95% rename from docker/mqproteogenomics/Dockerfile rename to docker/progenix/Dockerfile index 7a317e2..6b5b527 100644 --- a/docker/mqproteogenomics/Dockerfile +++ b/docker/progenix/Dockerfile @@ -18,7 +18,8 @@ FROM thyscbio/bio:v3.0.19 #RUN npm install npm@latest -g && \ # npm install n -g && \ # n latest -#RUN npm install -g @jbrowse/cli +RUN npm install -g @jbrowse/cli +RUN jbrowse --version #RUN npm install -g serve #RUN jbrowse create jbrowse_folder COPY lib /home/bio/lib diff --git a/docker/mqproteogenomics/build.sh b/docker/progenix/build.sh similarity index 92% rename from docker/mqproteogenomics/build.sh rename to docker/progenix/build.sh index ea35019..f57f7c7 100755 --- a/docker/mqproteogenomics/build.sh +++ b/docker/progenix/build.sh @@ -2,8 +2,8 @@ set -e # Change build context to the root of the directory -version=v3.0.19 -name=mqproteogenomics +version=v1.0.0 +name=progenix docker pull thyscbio/${name}:${version} && echo "version exists" && exit 1 || echo "Gonna build." cd ../.. diff --git a/docker/mqproteogenomics/dev.sh b/docker/progenix/dev.sh similarity index 100% rename from docker/mqproteogenomics/dev.sh rename to docker/progenix/dev.sh diff --git a/docker/mqproteogenomics/run.sh b/docker/progenix/run.sh similarity index 100% rename from docker/mqproteogenomics/run.sh rename to docker/progenix/run.sh diff --git a/docker/mqproteogenomics/runtest.sh b/docker/progenix/runtest.sh similarity index 100% rename from docker/mqproteogenomics/runtest.sh rename to docker/progenix/runtest.sh From 54c20cd615a5ce437f2044867e04dd981d940763 Mon Sep 17 00:00:00 2001 From: Matthys Potgieter Date: Fri, 27 Dec 2024 17:01:49 +0200 Subject: [PATCH 2/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8a65445..f815305 100644 --- a/README.md +++ b/README.md @@ -4,4 +4,4 @@ A repo with computational pipelines for pathogen virulence and metaproteome anal ## Pipelines [MetaNovo](MetaNovo.md) -[Progenio](MQProteogenomics.md) +[Progenio](Progenio.md) From b6cfacc4eb54664d224c1cffb7f758ca69edac7a Mon Sep 17 00:00:00 2001 From: Matthys Potgieter Date: Fri, 27 Dec 2024 17:05:45 +0200 Subject: [PATCH 3/3] Update Progenio.md --- Progenio.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Progenio.md b/Progenio.md index 58d68b5..02827a2 100644 --- a/Progenio.md +++ b/Progenio.md @@ -10,7 +10,7 @@ Progenio is an open-source proteogenomics pipeline for multistrain genome annota Ensure singularity is installed, and make sure at least 2 cores and 4 GB of RAM are available. ~~~ -cd proteomics-pipelines/singularity/mqproteogenomics +cd proteomics-pipelines/singularity/progenio ./create_image.sh ~~~ @@ -30,7 +30,7 @@ Run the example: ~~~ cd cbio-proteogenomics-tests/lib/testdata/proteogenomics_sample sixframe.sh genomes/ genomes/config.yaml # create the six frame database used by the next step (genomes/sixframe/combined_prot.fasta) -mqproteogenomics.sh mq_proteogeomics_test.yml # analyze the data using the six frame translated database +Progenio.sh progenio_test.yml # analyze the data using the six frame translated database ~~~ Now adjust the config file for our own data.