correction installation iqtree

.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

for_tests/Dockerfile

@@ -102,9 +102,18 @@ WORKDIR quicktree
 RUN make &&\
     ln -s /tmp/quicktree/quicktree /usr/local/bin
 
+
 # Install iqtree
 WORKDIR /tmp
 RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
 RUN tar -xzf iqtree-1.6.12-Linux.tar.gz &&\
     rm iqtree-1.6.12-Linux.tar.gz &&\
-    l -s /tmp/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
+    ln -s /tmp/iqtree-1.6.12-Linux/bin/iqtree /usr/local/bin
+
+
+# Install iqtree2
+WORKDIR /tmp
+RUN wget https://github.com/Cibiv/IQ-TREE/releases/download/v2.0.6/iqtree-2.0.6-Linux.tar.gz
+RUN tar -xzf iqtree-2.0.6-Linux.tar.gz &&\
+    rm iqtree-2.0.6-Linux.tar.gz &&\
+    ln -s /tmp/iqtree-2.0.6-Linux/bin/iqtree2 /usr/local/bin