pytest

.github/workflows/python-app.yml

@@ -39,4 +39,4 @@ jobs:
         export PATH=$PATH::/__w/proteomics-pipelines/proteomics-pipelines/bin/python:/__w/proteomics-pipelines/proteomics-pipelines/bin/bash:/__w/proteomics-pipelines/proteomics-pipelines/bin/R:/__w/proteomics-pipelines/proteomics-pipelines/bin/perl
         export PYTHONPATH=$PYTHONPATH::/__w/proteomics-pipelines/proteomics-pipelines/lib
         echo $PATH
-        cd cbio-proteogenomics-tests/lib && pytest 
+        cd cbio-proteogenomics-tests/lib && pytest -v

docker/bio/Dockerfile

@@ -122,16 +122,26 @@ WORKDIR /home/bio/
 RUN git clone https://github.com/bmbolstad/preprocessCore.git && cd preprocessCore/ && R CMD INSTALL --configure-args="--disable-threading"  .
 #RUN rm /bin/sh && ln -s /bin/bash /bin/sh
 
+RUN apt-get update && apt-get install -y libssl-dev openssl
+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 jbrowse2  
+RUN conda install emboss  
+RUN yes | conda update --all  
+RUN conda init 
+RUN apt-get update && apt-get install -y software-properties-common build-essential zlib1g-dev  genometools 
 
 
 #ENV PYTHONPATH /root/miniconda3/lib/python3.9/site-packages::$PYTHONPATH
 # testing paths
-ENV PYTHONPATH $PYTHONPATH::/home/testing/proteomics-pipelines/lib
+#ENV PYTHONPATH $PYTHONPATH::/home/testing/proteomics-pipelines/lib
 # production paths
 ENV PYTHONPATH $PYTHONPATH::/home/bio/lib
 
 # testing paths (if files are mounted it will use those
-ENV PATH $PATH::/home/testing/proteomics-pipelines/bin/python:/home/testing/proteomics-pipelines/bin/R:/home/testing/proteomics-pipelines/bin/bash:/home/testing/proteomics-pipelines/bin/python
+#ENV PATH $PATH::/home/testing/proteomics-pipelines/bin/python:/home/testing/proteomics-pipelines/bin/R:/home/testing/proteomics-pipelines/bin/bash:/home/testing/proteomics-pipelines/bin/python
 # production paths
 ENV PATH $PATH::/home/bio/bin/python:/home/bio/bin/R:/home/bio/bin/bash:/home/bio/bin/python
 

docker/bio/build.sh

@@ -2,13 +2,13 @@
 set -e
 
 # Change build context to the root of the directory
-version=v3.0.4
+version=v3.0.5
 name=bio
 docker pull thyscbio/${name}:${version} && echo "version exists" && exit 1 || echo "Gonna build."
 cd ../..
-sudo docker build --build-arg ftp_proxy=$ftp_proxy --build-arg http_proxy=$http_proxy --build-arg https_proxy=$https_proxy -f docker/${name}/Dockerfile  -t thyscbio/${name}:${version} .
-sudo docker login https://index.docker.io/v1/thyscbio
-sudo docker push  thyscbio/${name}:${version} || exit 1
+docker build --build-arg ftp_proxy=$ftp_proxy --build-arg http_proxy=$http_proxy --build-arg https_proxy=$https_proxy -f docker/${name}/Dockerfile  -t thyscbio/${name}:${version} .
+docker login https://index.docker.io/v1/thyscbio
+docker push  thyscbio/${name}:${version} || exit 1
 
-sudo docker tag thyscbio/${name}:${version} thyscbio/${name}:latest
-sudo docker push  thyscbio/${name}:latest
+docker tag thyscbio/${name}:${version} thyscbio/${name}:latest
+docker push  thyscbio/${name}:latest

docker/bio/dev.sh

@@ -1,7 +1,11 @@
 #!/bin/bash
 set -a
-version=v2.3
+version=v3.0.5
 home=/home/$(who -m | awk '{print $1;}')
 config=${home}/.proteomics-pipelines_profile
 source $config
-docker run -it --rm -v ${CBIO_PROTEOGENOMICS_TESTS_PATH}:${CBIO_PROTEOGENOMICS_TESTS_PATH} -v ${PROTEOMICS_PIPELINES_PATH}:${PROTEOMICS_PIPELINES_PATH} thyscbio/bio:${version}  /bin/bash 
+DEV_PYTHONPATH=${PROTEOMICS_PIPELINES_PATH}/lib/
+
+DEV_PATH="$PATH::${PROTEOMICS_PIPELINES_PATH}/bin/python/:${PROTEOMICS_PIPELINES_PATH}/bin/R:${PROTEOMICS_PIPELINES_PATH}/bin/bash/:${PROTEOMICS_PIPELINES_PATH}/bin/perl/"
+
+docker run -it --rm -p 8181:9090 -e PYTHONPATH=${DEV_PYTHONPATH} -e PATH=${DEV_PATH} -v ${CBIO_PROTEOGENOMICS_TESTS_PATH}:${CBIO_PROTEOGENOMICS_TESTS_PATH} -v ${PROTEOMICS_PIPELINES_PATH}:${PROTEOMICS_PIPELINES_PATH} thyscbio/bio:${version}  /bin/bash 

docker/mqproteogenomics/dev.sh

@@ -1,11 +1,12 @@
 #!/bin/bash
 set -a
-version=v2.0.4
+version=v3.0.5
 home=/home/$(who -m | awk '{print $1;}')
 config=${home}/.proteomics-pipelines_profile
 source $config
+
 DEV_PYTHONPATH=${PROTEOMICS_PIPELINES_PATH}/lib/
 
 DEV_PATH="$PATH::${PROTEOMICS_PIPELINES_PATH}/bin/python/:${PROTEOMICS_PIPELINES_PATH}/bin/R:${PROTEOMICS_PIPELINES_PATH}/bin/bash/:${PROTEOMICS_PIPELINES_PATH}/bin/perl/"
 
-docker run -it --rm -p 8181:9090 -e PYTHONPATH=${DEV_PYTHONPATH} -e PATH=${DEV_PATH} -v ${CBIO_PROTEOGENOMICS_TESTS_PATH}:${CBIO_PROTEOGENOMICS_TESTS_PATH} -v ${PROTEOMICS_PIPELINES_PATH}:${PROTEOMICS_PIPELINES_PATH} thyscbio/mqproteogenomics:${version}  /bin/bash 
+docker run -it --rm -p 8181:9090 -e PYTHONPATH=${DEV_PYTHONPATH} -e PATH=${DEV_PATH} -v ${CBIO_PROTEOGENOMICS_TESTS_PATH}:${CBIO_PROTEOGENOMICS_TESTS_PATH} -v ${PROTEOMICS_PIPELINES_PATH}:${PROTEOMICS_PIPELINES_PATH} thyscbio/bio:${version}  /bin/bash