Merge branch 'master' of https://github.com/uct-cbio/proteomics-pipel…

…ines

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.

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)

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  

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 ../..

docker/progenio/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 

docker/progenio/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 ../..