Samtools from apt

.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: |

.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

.gitignore

@@ -1,3 +1,4 @@
+.env
 /.venv
 *.pyc
 /results

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"]

readme.md

@@ -27,6 +27,8 @@ bash run_analysis.sh
 
 ## Installing
 
+### Python dependencies
+
 To install the dependencies, we used poetry (see [poetry installation instructions](https://python-poetry.org/docs/)).
 
 In the source directory run:
@@ -43,6 +45,31 @@ poetry shell
 
 Now when you call `python`, it will be the one from the `.venv`.
 
+### Other dependencies and setting up transvar
+
+This project uses [transvar](https://github.com/zwdzwd/transvar). This requires to install some binaries.
+
+```bash
+
+# If you have linux and you want to install them globally
+sudo apt install -y samtools tabix
+
+# If you want to install them locally (see the content of the script)
+# > basically downloads the libs and uses make to build the necessary bin files, then deletes all unnecesary source code
+bash install_transvar_dependencies_locally.sh
+
+```
+
+Then, regardless of whether you are using local or global installation of `samtools` and `tabix`:
+
+```bash
+# Env vars (see script)
+. transvar_env_vars.sh
+
+# Build the transvar database, and test that it works
+bash set_up_transvar.sh
+```
+
 ## Getting the data
 
 To download the data from PomBase, run:

set_up_transvar.sh

@@ -4,15 +4,12 @@ set -e
 transvar config -k reference -v "data/pombe_genome.fa" --refversion pombe_genome
 transvar index --ensembl data/pombe_genome.gtf --reference data/pombe_genome.fa
 
-# At this point, we could delete the lib folder, but it's very small
+# Hacky way to use the functions inside another script
+cp $(which transvar) ./transvar_main_script.py
 
 # See whether it works
 transvar panno -i 'SPAC3F10.09:p.E2A' --ensembl data/pombe_genome.gtf.transvardb --reference data/pombe_genome.fa
 transvar ganno -i 'I:g.2832796A>T' --ensembl data/pombe_genome.gtf.transvardb --reference data/pombe_genome.fa
 transvar ganno -i 'I:g.2832795T>A' --ensembl data/pombe_genome.gtf.transvardb --reference data/pombe_genome.fa
-
-# Hacky way to use the functions inside another script
-cp $(which transvar) ./transvar_main_script.py
-
 transvar panno -i 'SPBC1198.04c:p.T566S' --ensembl data/pombe_genome.gtf.transvardb --reference data/pombe_genome.fa
 transvar panno -i 'SPAPB1A10.09:p.S372_N374delinsAAA' --ensembl data/pombe_genome.gtf.transvardb --reference data/pombe_genome.fa  --gseq

transvar_env_vars.sh

@@ -1,4 +1,6 @@
 export TRANSVAR_CFG="$(pwd)/data/transvar.cfg"
 export TRANSVAR_DOWNLOAD_DIR="$(pwd)/data/transvar_download"
+
+# These are only needed if you install transvar locally, but it does not harm to have them
 export PATH="$(pwd)/lib/htslib/bin:$PATH"
 export PATH="$(pwd)/lib/samtools/bin:$PATH"