add container

zhangrengang · Sep 28, 2023 · dde7037 · dde7037
1 parent 15efcd6
commit dde7037
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Showing 3 changed files with 25 additions and 12 deletions.
diff --git a/README.md b/README.md
@@ -23,6 +23,7 @@ bash test_wheat.sh
    * [Introduction](#introduction)
    * [Inputs](#Inputs)
    * [Run SubPhaser](#Run-SubPhaser)
+   * [Run SubPhaser through Singularity/Apptainer](#Run-SubPhaser-through-Singularity/Apptainer)
    * [Outputs](#Outputs)
    * [When SubPhaser do not work](#When-SubPhaser-do-not-work)
    * [Citation](#Citation)
@@ -133,7 +134,17 @@ Input custom feature (e.g. transposable element, gene) sequences for subgenome-s
 ```
 subphaser -i genome.fasta.gz -c sg.config -custom_features TEs.fasta genes.fasta
 ```
+### Run SubPhaser through Singularity/Apptainer ###
+Alternatively, you can run `subphaser` through Singularity/Apptainer container:
+```
+# install
+apptainer remote add --no-login SylabsCloud cloud.sylabs.io
+apptainer remote use SylabsCloud
+apptainer pull subphaser.sif library://shang-hongyun/collection/subphaser.sif:1.2.6
 
+# run
+./subphaser.sif subphaser -h
+```
 ### Outputs ###
 ```
 phase-results/

diff --git a/subphaser/RunCmdsMP.py b/subphaser/RunCmdsMP.py
@@ -24,12 +24,12 @@
 	import drmaa    # for grid
 	GRID = True
 	from tempfile import NamedTemporaryFile
-except (RuntimeError,ImportError,AttributeError) as e:
-#	if "DRMAA_LIBRARY_PATH" in format(e):
-#		logger.warning('Grid computing is not available because DRMAA not configured properly: {}'.format(e))
-#	else:
-#		logger.warning('Grid computing is not available because DRMAA not installed: {}'.format(e))
-#		logger.info('No DRMAA, Switching to local/cluster mode.')
+except (RuntimeError,ImportError,AttributeError,OSError) as e:
+	if "DRMAA_LIBRARY_PATH" in format(e):
+		logger.warning('Grid computing is not available because DRMAA not configured properly: {}'.format(e))
+	else:
+		logger.warning('Grid computing is not available because DRMAA not installed: {}'.format(e))
+	logger.info('No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode.')
 	GRID = False
 
 __version__ = '1.1'
@@ -149,6 +149,7 @@ def which_grid(self):
 			return 'slurm'
 		else:
 			logger.warn('Please provide your grid system `{}` to auther'.format(name))
+		return 'sge'
 def run_tasks(cmd_list, tc_tasks=None, mode='grid', grid_opts='', cpu=1, mem='1g', cont=1,
 			retry=1, script=None, out_path=None, completed=None, cmd_sep='\n', **kargs):
 	if not cmd_list:

diff --git a/subphaser/api/TEsorter/modules/RunCmdsMP.py b/subphaser/api/TEsorter/modules/RunCmdsMP.py
@@ -24,12 +24,12 @@
 	import drmaa    # for grid
 	GRID = True
 	from tempfile import NamedTemporaryFile
-except (RuntimeError,ImportError,AttributeError) as e:
-#	if "DRMAA_LIBRARY_PATH" in format(e):
-#		logger.warning('Grid computing is not available because DRMAA not configured properly: {}'.format(e))
-#	else:
-#		logger.warning('Grid computing is not available because DRMAA not installed: {}'.format(e))
-#		logger.info('No DRMAA, Switching to local/cluster mode.')
+except (RuntimeError,ImportError,AttributeError,OSError) as e:
+	if "DRMAA_LIBRARY_PATH" in format(e):
+		logger.warning('Grid computing is not available because DRMAA not configured properly: {}'.format(e))
+	else:
+		logger.warning('Grid computing is not available because DRMAA not installed: {}'.format(e))
+	logger.info('No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode.')
 	GRID = False
 
 __version__ = '1.1'
@@ -149,6 +149,7 @@ def which_grid(self):
 			return 'slurm'
 		else:
 			logger.warn('Please provide your grid system `{}` to auther'.format(name))
+		return 'sge'
 def run_tasks(cmd_list, tc_tasks=None, mode='grid', grid_opts='', cpu=1, mem='1g', cont=1,
 			retry=1, script=None, out_path=None, completed=None, cmd_sep='\n', **kargs):
 	if not cmd_list: