From ca6f0fa21184d97617e354b0c2ea8f37790806d3 Mon Sep 17 00:00:00 2001
From: Samuel Mondal <samuel.mondal@unibas.ch>
Date: Tue, 13 Dec 2022 23:08:47 +0100
Subject: [PATCH] dockerfile addition

---
 .gitlab-ci.yml             | 23 +++++++++++++++++++++++
 Dockerfile                 |  9 +++++++++
 tests/test_files/test_1.fa |  8 ++++++++
 tests/test_files/test_2.fa |  7 +++++++
 4 files changed, 47 insertions(+)
 create mode 100644 .gitlab-ci.yml
 create mode 100644 Dockerfile
 create mode 100644 tests/test_files/test_1.fa
 create mode 100644 tests/test_files/test_2.fa

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..a723cb2
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,23 @@
+default:         # Set default
+  tags:
+    - docker
+  image: python:3.10-slim-buster
+
+stages:          # List of employment runs, starts with build ends with deploy.
+  - build
+  - test
+
+build-job:       # First stage deployment and installation of dependencies.
+  stage: build   # Build Stage
+  script:
+    - pip install -r requirements.txt
+    - pip install -r requirements_dev.txt
+    - pip install -e .
+    - echo "Dependencies successfully deployed."
+
+lint-test-job:   # Test Stage
+  stage: test    # Deploys and runs all 3 linters.
+  script:
+    - flake8 --docstring-convention google sequence_extractor/ gtf_processing/
+    - pylint sequence_extractor/ gtf_processing/
+    - mypy sequence_extractor/ gtf_processing/
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..9665293
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,9 @@
+FROM python:3.10-slim-buster
+
+MAINTAINER Samuel Mondal
+
+ENV PATH=$PATH:/usr/local/
+
+COPY . .
+
+RUN pip install -e .
diff --git a/tests/test_files/test_1.fa b/tests/test_files/test_1.fa
new file mode 100644
index 0000000..f92bb2b
--- /dev/null
+++ b/tests/test_files/test_1.fa
@@ -0,0 +1,8 @@
+>ENST00000673477::1:1471765-1472089
+TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGCTCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGGCGGCGGTAGCGGCGGCGGCGGTGCGAGCATGTCGTGGCTCTTCGGCGTTAACAAGGGCCCCAAGGGTGAAGGCGCGGGGCCGCCGCCGCCTTTGCCGCCCGCGCAGCCCGGGGCCGAGGGCGGCGGGGACCGCGGTTTGGGAGACCGGCCGGCGCCCAAGGACAAATGGAGCAACTTCGACCCCACCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAGCACTCGC
+>ENST00000673477::1:1477274-1477350
+TTACGCCAAGGAGGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAACAGTCCAAGCTCAAA
+>ENST00000378391::1:3244087-3244137
+AAATACTGACGGACGTGGAAGTGTCGCCCCAGGAAGGCTGCATCACAAAG
+>ENST00000378391::1:3385152-3385286
+TCTCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGGCTGGCAGCTGGCTCAAGTACATCCGTGTGGCGTGCTCCTGCGATGACCAGAACCTCACCATGTGTCAGATCAGTGAGCAG
diff --git a/tests/test_files/test_2.fa b/tests/test_files/test_2.fa
new file mode 100644
index 0000000..7b8ebb2
--- /dev/null
+++ b/tests/test_files/test_2.fa
@@ -0,0 +1,7 @@
+>ENST00000673477::1:1482545-1482614
+ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGACAGCCACG
+>ENST00000673477::1:1485016-1485171
+TGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAGAATGCGACAGCCGTCACTGGCCGCTTCATCGAGGCTCGGCTGGGGAAGCCGTCCCTAGTGAGGGAGACGTCCCGCATCACGGTGCTGGAGGCGCTGCGGCACCCCATCCAG
+>ENST00000673477::1:1485782-1485838
+TCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGTTGTGCTTAGT
+>ENST00000673477::1:1486110-1486235
-- 
GitLab