diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 7031d7cb7b100cba56cf93a57f887e989551d8c5..f4f15f0027abfbaf538a878753ef3816a52c781e 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -22,73 +22,73 @@ build-test-image: tags: - k8s -build-install-barrnap: - only: - - docker - stage: build - script: - - apk update #; apk add git - # - git checkout master -- requirements.txt - - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only - - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" - tags: - - k8s +# build-install-barrnap: +# only: +# - docker +# stage: build +# script: +# - apk update #; apk add git +# # - git checkout master -- requirements.txt +# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only +# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" +# tags: +# - k8s -build-install-annote-and-quicktree: - only: - - docker - stage: build - script: - - apk update #; apk add git - # - git checkout master -- requirements.txt - - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree - - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" - tags: - - k8s +# build-install-annote-and-quicktree: +# only: +# - docker +# stage: build +# script: +# - apk update #; apk add git +# # - git checkout master -- requirements.txt +# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree +# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" +# tags: +# - k8s -build-ubuntu: - only: - - docker - stage: build - script: - - apk update # ; apk add git - # - git checkout master -- requirements.txt - - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu - - docker push "$CI_REGISTRY_IMAGE/install-ubuntu" - tags: - - k8s +# build-ubuntu: +# only: +# - docker +# stage: build +# script: +# - apk update # ; apk add git +# # - git checkout master -- requirements.txt +# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu" for_build/ubuntu +# - docker push "$CI_REGISTRY_IMAGE/install-ubuntu" +# tags: +# - k8s -build-mafft: - only: - - docker - stage: build - script: - - apk update # ; apk add git - # - git checkout master -- requirements.txt - - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft - - docker push "$CI_REGISTRY_IMAGE/install-mafft" - tags: - - k8s +# build-mafft: +# only: +# - docker +# stage: build +# script: +# - apk update # ; apk add git +# # - git checkout master -- requirements.txt +# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mafft" for_build/mafft +# - docker push "$CI_REGISTRY_IMAGE/install-mafft" +# tags: +# - k8s -build-mmseqs_and_fastme: - only: - - docker - stage: build - script: - - apk update # ; apk add git - # - git checkout master -- requirements.txt - - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme - - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" - tags: - - k8s +# build-mmseqs_and_fastme: +# only: +# - docker +# stage: build +# script: +# - apk update # ; apk add git +# # - git checkout master -- requirements.txt +# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" for_build/mmseqs_and_fastme +# - docker push "$CI_REGISTRY_IMAGE/install-mmseqs-fastme" +# tags: +# - k8s -build-install-prodigal: - only: - - docker - stage: build - script: - - apk update - - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal - - docker push "$CI_REGISTRY_IMAGE/install-prodigal" - tags: - - k8s +# build-install-prodigal: +# only: +# - docker +# stage: build +# script: +# - apk update +# - docker build --pull -t "$CI_REGISTRY_IMAGE/install-prodigal" for_build/prodigal +# - docker push "$CI_REGISTRY_IMAGE/install-prodigal" +# tags: +# - k8s diff --git a/for_tests/Dockerfile b/for_tests/Dockerfile index 935987407ef46eb610ea9f8ceb1beb1e5e2e6ba6..2f9547b4b8ede19820c325ad71f2d54402c708ca 100644 --- a/for_tests/Dockerfile +++ b/for_tests/Dockerfile @@ -5,15 +5,22 @@ RUN apt-get update &&\ apt-get -y upgrade -# Install package needed and update pip +# Install packages needed and update pip RUN apt-get install -y \ wget \ python3-pip \ python3 - RUN pip3 install --upgrade pip +# Update makeblastdb +WORKDIR /tmp +RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.9.0+-x64-linux.tar.gz &&\ + tar zxvpf ncbi-blast-2.9.0+-x64-linux.tar.gz &&\ + cp /tmp/ncbi-blast-2.9.0+/bin/makeblastdb /usr/local/bin/ &&\ + rm ncbi-blast-2.9.0+-x64-linux.tar.gz + + # Install mash WORKDIR /tmp RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\ @@ -41,21 +48,20 @@ RUN apt-get install -y\ libdigest-md5-perl \ git \ default-jre \ - bioperl &&\ - git clone https://github.com/tseemann/prokka.git + bioperl +RUN git clone https://github.com/tseemann/prokka.git RUN /tmp/prokka/bin/prokka --setupdb &&\ ln -s /tmp/prokka/bin/prokka /usr/local/bin -# Install mmseqs2 +# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e WORKDIR /tmp -RUN apt-get install -y cmake &&\ - wget https://mmseqs.com/latest/mmseqs-static_sse41.tar.gz &&\ - tar xf mmseqs-static_sse41.tar.gz &&\ - rm mmseqs-static_sse41.tar.gz &&\ +RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ + tar xvfz mmseqs-linux-sse41.tar.gz &&\ + rm mmseqs-linux-sse41.tar.gz &&\ mv /tmp/mmseqs2/bin/mmseqs /usr/local/bin &&\ # remove useless files - rm -r /tmp/mmseqs2 + rm -r /tmp/mmseqs # Install mafft 7.313 @@ -70,26 +76,27 @@ RUN make clean &&\ make install -# Install FastTree -WORKDIR /tmp -RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\ - gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\ - ln -s /tmp/FastTreeMP /usr/local/bin - - -# Install FastME -WORKDIR /tmp -RUN apt-get install -y automake &&\ - git clone https://gite.lirmm.fr/atgc/FastME.git -WORKDIR /tmp/FastME -RUN ./configure &&\ - make &&\ - make install - - -# Install quicktree -WORKDIR /tmp -RUN git clone https://github.com/tseemann/quicktree -WORKDIR quicktree -RUN make &&\ - ln -s /tmp/quicktree/quicktree /usr/local/bin +## Install FastTree +#WORKDIR /tmp +#RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\ +# gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP #FastTree.c -lm &&\# +# ln -s /tmp/FastTre#eMP /usr/local/bin# +# +# +## Install FastME +#WORKDIR /tmp +#RUN apt-get install -y automake &&\ +# git clone https://gite.lirmm.fr/atgc/FastME.git +#WORKDIR /tmp/FastME +#RUN ./configure &&\ +# make &&\ +# make install +# +# +## Install quicktree +#WORKDIR /tmp +#RUN git clone https://github.com/tseemann/quicktree +#WORKDIR quicktree +#RUN make &&\ +# ln -s /tmp/quicktree/quicktree /usr/local/bin +# \ No newline at end of file