Install samtools/htslib from APT (#99)

* Install samtools/htslib from APT ... instead of compiling * Install samtools/htslib from APT for workflows * Use sudo when installing with APT
pombase · Aug 17, 2023 · 15b6620 · 15b6620
1 parent 3ef4c14
commit 15b6620
Show file tree

Hide file tree

Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/.github/workflows/run_pipeline.yml b/.github/workflows/run_pipeline.yml
@@ -29,7 +29,7 @@ jobs:
       - name: Install and set up transvar
         run: |
           . transvar_env_vars.sh
-          bash install_transvar_dependencies.sh
+          sudo apt install -y samtools tabix
           bash set_up_transvar.sh
       - name: Update file
         run: |

diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -23,7 +23,7 @@ jobs:
       - name: Install and set up transvar
         run: |
           . transvar_env_vars.sh
-          bash install_transvar_dependencies.sh
+          sudo apt install -y samtools tabix
           bash set_up_transvar.sh
       - name: Run tests
         # -W because of transvar

diff --git a/Dockerfile b/Dockerfile
@@ -21,6 +21,6 @@ COPY ./*.sh /api/
 COPY ./config.json /api/
 COPY ./data /api/data
 
-RUN bash install_transvar_dependencies.sh
+RUN apt install -y samtools tabix
 
 CMD ["bash", "docker_start.sh"]