From 21e05d982610a76cf24d46ee8aff102d5a7310c8 Mon Sep 17 00:00:00 2001
From: "christine.tranchant_ird.fr" <christine.tranchant@ird.fr>
Date: Thu, 28 Nov 2024 09:14:14 +0000
Subject: [PATCH] Update .gitlab-ci.yml
---
.gitlab-ci.yml | 171 +++++--------------------------------------------
1 file changed, 17 insertions(+), 154 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 19e33ac..b8ef50b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,10 +1,11 @@
-image: registry.forge.ird.fr/diade/culebront_pipeline/podman/gitlab-runner:0.0.1 # docker image used
+image: python:3.10 # docker image use
####################
# TAG stages: we define 3 test steps called install, test, deploy
stages:
- install
- test
- - deploy
+# - deploy
+
#variables:
# CI_DEBUG_TRACE: "true"
@@ -12,162 +13,24 @@ stages:
# TAG before_script : we list all the commands required before running any test. eg.: clone repo, install soft
before_script:
- echo ${CI_PROJECT_DIR}
- - export PATH=$PATH:/root/.local/bin
- - export APPTAINER_BINDPATH="${CI_PROJECT_DIR}:${CI_PROJECT_DIR},/root:/root"
- #- python3 -m pip install -U snakemake setuptools build pip
- - python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
- - python3 -m pip install --user culebrONT@git+https://forge.ird.fr/diade/culebront_pipeline.git@$CI_COMMIT_REF_NAME
- - culebrONT --install_env
- - bash -ec 'CPDIR="/root/.local/lib/python3.10/site-packages/culebrONT/containers"; DIR="/usr/local/culebrONT/Containers"; if [[ -d $DIR ]]; then ls $DIR; echo "copy Containers files in $DIR to $CPDIR"; ln -sf $DIR/* $CPDIR; fi'
- - culebrONT install_local
+ - export PATH=$PATH:/root/.local/bin
+ # CD 28/11 Frangipane ? - export APPTAINER_BINDPATH="${CI_PROJECT_DIR}:${CI_PROJECT_DIR},/root:/root"
+ - python3 -m pip install -U snakemake setuptools build pip
+ #- python3 -m pip install snakecdysis@git+https://forge.ird.fr/phim/sravel/snakecdysis.git@main
+ - python3 -m pip install --user frangiPANe@git+https://forge.ird.fr/diade/frangiPANe_snake.git@$CI_COMMIT_REF_NAME
+# - culebrONT --install_env
+# - bash -ec 'CPDIR="/root/.local/lib/python3.10/site-packages/culebrONT/containers"; DIR="/usr/local/culebrONT/Containers"; if [[ -d $DIR ]]; then ls $DIR; echo "copy Containers files in $DIR to $CPDIR"; ln -sf $DIR/* $CPDIR; fi'
+# - culebrONT install_local
####### COMMON (Install) #######
-culebrONT:installing:
+frangiPANe:installing:
stage: install # Put the name of stage defined previously
script: # shell commands executed by the runner
- - culebrONT --install_env
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_quick
-culebrONT:Test_config_quick.yaml:
- stage: test
- artifacts:
- name: culebrONT-config_quick
- paths:
- - test/CulebrONT_OUTPUT
- - /root/.local/lib/python3.10/site-packages/culebrONT
- script:
- - culebrONT --install_env
- - culebrONT test_install -d test
- - culebrONT run_local -t 22 -c ./culebrONT/install_files/config_test/config_quick.yaml;
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-
-# @Description TEST config_A
-culebrONT:Test_config_A.yaml:
- stage: test
- artifacts:
- name: culebrONT-logs
- paths:
- - test/CulebrONT_OUTPUT
- script:
- - culebrONT --install_env
- - culebrONT test_install -d test
- - culebrONT run_local -t 22 -c ./culebrONT/install_files/config_test/config_A.yaml
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_AC
-culebrONT:Test_config_AC.yaml:
- stage: test
- artifacts:
- name: culebrONT-logs-AC
- paths:
- - test/CulebrONT_OUTPUT
- script:
- - culebrONT test_install -d test
- - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_AC.yaml
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_AP
-culebrONT:Test_config_AP.yaml:
- stage: test
- artifacts:
- name: culebrONT-logs-AP
- paths:
- - test/CulebrONT_OUTPUT
- script:
- - culebrONT test_install -d test
- - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_AP.yaml
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_APC
-culebrONT:Test_config_APC.yaml:
- stage: test
- artifacts:
- name: culebrONT-logs-APC
- paths:
- - test/CulebrONT_OUTPUT
- script:
- - culebrONT test_install -d test
- - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APC.yaml
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_APCQ-CIRQ
-culebrONT:Test_config_APCQ-CIRQ.yaml:
- stage: test
- artifacts:
- name: culebrONT-logs-APCQ-CIRQ
- paths:
- - test/CulebrONT_OUTPUT
- script:
- - culebrONT test_install -d test
- - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APCQ-CIRQ.yaml
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-
-
-# @Description TEST config_APCQ
-culebrONT:Test_config_APCQ.yaml:
- stage: test
- artifacts:
- name: culebrONT-logs-APCQ
- paths:
- - test/CulebrONT_OUTPUT
- script:
- - culebrONT test_install -d test
- - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APCQ.yaml
+ - frangiPANNe --version
tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
+ - VM # quel runner sur lequel on tourne
+ #rules: # Condition if the test is run or not
+ # - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit tag start with v.
+ # - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
-# @Description TEST config_APQ
-culebrONT:Test_config_APQ.yaml:
- stage: test
- artifacts:
- name: culebrONT-logs-APQ
- paths:
- - test/CulebrONT_OUTPUT
- script:
- - culebrONT test_install -d test
- - culebrONT run_local -t 14 -c ./culebrONT/install_files/config_test/config_APQ.yaml
- tags:
- - VM
- rules: # Condition if the test is run or not
- - if: $CI_COMMIT_TAG =~ "/^v.*rc/" # Tests ran if commit message start with v.
- - if: $CI_COMMIT_MESSAGE =~ "/.*-TEST.*/i"
--
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