change quicktree to fasttree to see if smaller size of docker image

.gitlab-ci.yml

@@ -9,36 +9,36 @@ 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"
-    - mmseqs
-
-# 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"
+#     - mmseqs
 
-# 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-fasttree:
+  only:
+    - docker
+  stage: build
+  script:
+    - apk update ; apk add git
+    - git checkout master -- requirements.txt
+    - docker build --pull -t "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fasttree" for_build/annote_and_1tree
+    - docker push "$CI_REGISTRY_IMAGE/install-ubuntu-annote-fasttree"
 
 # build-ubuntu:
 #   only:

for_build/annote_and_1tree/Dockerfile

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