build image with prokka and quicktree

.gitlab-ci.yml

@@ -9,35 +9,35 @@ variables:
 before_script:
   - docker login -u gitlab-ci-token -p "$CI_BUILD_TOKEN" registry-gitlab.pasteur.fr
 
-build-test-image:
-  only:
-    - docker
-  stage: build
-  script:
-    - apk update ; apk add git
-    - git checkout master -- requirements.txt
-    - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
-    - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
-
-# build-install-barrnap:
+# build-test-image:
 #   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"
+#     - docker build --pull -t "$CI_REGISTRY_IMAGE/testing-ubuntu" for_tests
+#     - docker push "$CI_REGISTRY_IMAGE/testing-ubuntu"
 
-# build-install-annote-and-quicktree:
+# build-install-barrnap:
 #   only:
 #     - docker
 #   stage: build
 #   script:
 #     - apk update ; apk add git
 #     - git checkout master -- requirements.txt
-#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree" for_build/annote_and_1tree
-#     - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-quicktree"
+#     - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly" for_build/barrnap_only
+#     - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-barrnaponly"
+
+build-install-annote-and-fastme:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update ; apk add git
+    - git checkout master -- requirements.txt
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fastme" for_build/annote_and_1tree
+    - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fastme"
 
 # build-ubuntu:
 #   only:

for_build/annote_and_1tree/Dockerfile

@@ -27,8 +27,9 @@ RUN apt-get install -y\
 
 RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
 
-# Install FastTree
+# Install quicktree
 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
+RUN git clone https://github.com/tseemann/quicktree
+WORKDIR quicktree
+RUN make &&\
+    ln -s /tmp/quicktree/quicktree /usr/local/bin