add --init-new-pipeline

README.rst

@@ -147,8 +147,7 @@ Initiate a project (Sequana pipeline) with cookiecutter
 
 You can start a Sequana pipeline skeleton as follows::
 
-    pip install cookiecuter
-    cookiecutter https://github.com/sequana/sequana_pipeline_template -o . --overwrite-if-exists
+    sequana_pipetools --init-new-pipeline
 
 and then follow the instructions. You will be asked some questions such as the name of your pipeline (eg. variant), a description, keywords and the *project_slug* (just press enter).
 
@@ -313,6 +312,10 @@ Changelog
 ========= ======================================================================
 Version   Description
 ========= ======================================================================
+1.1.1     * symlink creation on apptainers skipped if permission error (file
+            is probably already present and created by another users e.g.
+            the admin system)
+          * add --init-new-pipeline argument in sequana_pipetools standalone
 1.1.0     * add exclude_pattern in input data section
 1.0.6     * add py3.12, slight updates wrt slurm
 1.0.5     * introspect slurm files to extract stats

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "poetry.core.masonry.api"
 #maintainer ?#maintainer email
 [tool.poetry]
 name = "sequana_pipetools"
-version = "1.1.0"
+version = "1.1.1"
 description = "A set of tools to help building or using Sequana pipelines"
 authors = ["Sequana Team"]
 license = "BSD-3"
@@ -49,6 +49,7 @@ charset-normalizer = ">=2"
 versionix = ">=0.2.0"
 rich-click = "^1.7.1"
 docutils = "^0.20"
+cookiecutter = "^2.6.0"
 
 [tool.poetry.scripts]
 sequana_pipetools = "sequana_pipetools.scripts.main:main"

sequana_pipetools/options.py

@@ -216,7 +216,7 @@ def deps_callback(ctx, param, value):
         data = data.split()
         data = "\n".join(sorted(data))
         click.echo(
-            f"sequana_{ctx.NAME} will need one or more of these software to work correctly. We recommend you to use --apptainer option so that you do not need to install them manually:\n\n{data}\n"
+            f"sequana_{ctx.NAME} will need one or more of these software to work correctly. We recommend you to use --use-apptainer and --apptainer-prefix options so that you do not need to install them manually:\n\n{data}\n"
         )
         ctx.exit(0)
 

sequana_pipetools/scripts/main.py

@@ -12,25 +12,27 @@
 ##############################################################################
 import importlib
 import os
+import subprocess
 import sys
 import tempfile
-import subprocess
 
 import rich_click as click
 
 from sequana_pipetools import version
 from sequana_pipetools.misc import url2hash
+from sequana_pipetools.snaketools.dot_parser import DOTParser
 from sequana_pipetools.snaketools.errors import PipeError
 from sequana_pipetools.snaketools.pipeline_utils import get_pipeline_statistics
 from sequana_pipetools.snaketools.sequana_config import SequanaConfig
-from sequana_pipetools.snaketools.dot_parser import DOTParser
 
 click.rich_click.USE_MARKDOWN = True
 click.rich_click.SHOW_METAVARS_COLUMN = False
 click.rich_click.APPEND_METAVARS_HELP = True
 click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"
 click.rich_click.SHOW_ARGUMENTS = True
-click.rich_click.FOOTER_TEXT = "Authors: Thomas Cokelaer, Dimitri Desvillechabrol -- http://github.com/sequana/sequana_pipetools"
+click.rich_click.FOOTER_TEXT = (
+    "Authors: Thomas Cokelaer, Dimitri Desvillechabrol -- http://github.com/sequana/sequana_pipetools"
+)
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 
 
@@ -174,7 +176,9 @@ def set_option_file(self, option_name):
 
 @click.command(context_settings=CONTEXT_SETTINGS)
 @click.option("--version", is_flag=True)
-@click.option("--dot2png", type=click.STRING, help="convert the input.dot into PNG file. Output name is called INPUT.sequana.png")
+@click.option(
+    "--dot2png", type=click.STRING, help="convert the input.dot into PNG file. Output name is called INPUT.sequana.png"
+)
 @click.option(
     "--completion",
     type=click.STRING,
@@ -194,6 +198,11 @@ def set_option_file(self, option_name):
 )
 @click.option("--slurm-diag", is_flag=True, help="Scans slurm files and get summary information")
 @click.option("--url2hash", type=click.STRING, help="For developers. Convert a URL to hash mame. ")
+@click.option(
+    "--init-new-pipeline",
+    is_flag=True,
+    help="Give name of new pipeline and this will create full structure for a new sequana pipeline",
+)
 def main(**kwargs):
     """Pipetools utilities for the Sequana project (sequana.readthedocs.io)
 
@@ -216,7 +225,7 @@ def main(**kwargs):
         return
     elif kwargs["url2hash"]:
         click.echo(url2hash(kwargs["url2hash"]))
-    elif kwargs['dot2png']:
+    elif kwargs["dot2png"]:
         name = kwargs["dot2png"]
         assert name.endswith(".dot")
         outname = name.replace(".dot", ".sequana.png")
@@ -262,7 +271,10 @@ def main(**kwargs):
         click.echo("Looking for slurm files")
         p = PipeError()
         p.status(".")
+    elif kwargs["init_new_pipeline"]:  # pragma: no cover
+        cmd = "cookiecutter https://github.com/sequana/sequana_pipeline_template -o . --overwrite-if-exists"
+        subprocess.run(cmd.split(), capture_output=False)
 
 
 if __name__ == "__main__":
-    main() #pragma: no cover
+    main()  # pragma: no cover

sequana_pipetools/sequana_manager.py

@@ -309,7 +309,7 @@ def teardown(self, check_schema=True, check_input_files=True):
         self.config.save(self.workdir / f".sequana/{config_name}")
         try:
             os.symlink(f".sequana/{config_name}", f"{self.workdir}/{config_name}")
-        except FileExistsError:  # pragma: no cover
+        except (FileExistsError, PermissionError):  # pragma: no cover
             pass
 
         # the final command