From ac964a1bb89b13b795b8c8a95b4c56bb5f3f5e58 Mon Sep 17 00:00:00 2001
From: christine <christine.tranchant@ird.Fr>
Date: Fri, 15 Mar 2024 12:02:39 +0100
Subject: [PATCH] debugg install frangiPANe with update snakemake version
---
frangiPANe/__init__.py | 8 ++++----
frangiPANe/global_variables.py | 2 +-
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/frangiPANe/__init__.py b/frangiPANe/__init__.py
index 7aa23e4..6840e21 100644
--- a/frangiPANe/__init__.py
+++ b/frangiPANe/__init__.py
@@ -4,14 +4,13 @@
from frangiPANe import generate_stats as gs
from .module import FrangiPANe
from pathlib import Path
-from .global_variables import GIT_URL, DOCS, DATATEST_URL_FILES, SINGULARITY_URL_FILES
+from .global_variables import GIT_URL, DOCS, DATATEST_URL_FILES, APPTAINER_URL_FILES
from ._version import version as __version__
from ._version import version_tuple
#TODO SEB : LOGO https://forge.ird.fr/diade/frangipane/-/blob/main/docs/source/_images/frangiPANe.png?ref_type=heads
logo = Path(__file__).parent.resolve().joinpath('frangiPANe.png').as_posix()
-__version__ = Path(__file__).parent.resolve().joinpath("VERSION").open("r").readline().strip()
__doc__ = """frangiPANe was developed as a modular and interactive application to simplify the construction of a panreference
using the map-then-assembly approach. It consists in a Jupyter Notebook application that centralizes code,documentation and interactive visualizations together"""
@@ -52,8 +51,9 @@ dico_tool = {
"url": GIT_URL,
"docs": DOCS,
"description_tool": description_tools,
- "singularity_url_files": SINGULARITY_URL_FILES,
+ "apptainer_url_files": APPTAINER_URL_FILES,
"datatest_url_files": DATATEST_URL_FILES,
"snakefile": Path(__file__).resolve().parent.joinpath("snakefiles", "Snakefile"),
- "snakemake_scripts": Path(__file__).resolve().parent.joinpath("snakemake_scripts")
+ "snakemake_scripts": Path(__file__).resolve().parent.joinpath("snakemake_scripts"),
+ "git_configfile_path": Path(__file__).resolve().parent.joinpath("install_files","configfile.yml")
}
diff --git a/frangiPANe/global_variables.py b/frangiPANe/global_variables.py
index 922cd37..2fd64e7 100644
--- a/frangiPANe/global_variables.py
+++ b/frangiPANe/global_variables.py
@@ -3,7 +3,7 @@ from pathlib import Path
DOCS = "https://frangiPANe.readthedocs.io/en/latest/"
GIT_URL = "https://forge.ird.fr/diade/frangipane"
-SINGULARITY_URL_FILES = [('https://itrop.ird.fr/frangiPANe/',
+APPTAINER_URL_FILES = [('https://itrop.ird.fr/frangiPANe/',
f'INSTALL_PATH/containers/frangiPANe.sif')
]
--
GitLab