Merge pull request #211 from broadinstitute/run-pipe-config-file-revert

reverted change to run-pipe that allowed passing in the path to a config file

pipes/Broad_LSF/run-pipe.sh

@@ -9,30 +9,10 @@ source /broad/software/scripts/useuse
 reuse -q LSF
 source $SCRIPT_DIRECTORY/../Broad_common/setup_dotkits.sh
 
-# uses the first argument as the config file path, is specified
-if [[ ! -z "$1" && "$1" != " " ]]; then
-    CONFIG_FILE=$1
-else
-    # otherwise the config file is assumed to be "config.yaml" in the cwd
-    CONFIG_FILE="config.yaml"
-fi
-
-# resolve the config file path in full
-CONFIG_FILE=`python -c "import os; print( os.path.realpath(os.path.expanduser(\"$CONFIG_FILE\"))) "`
-
-# if the config file does not exist
-# it is either not in the cwd, or what the user passed in does not exist
-if [[ ! -f $CONFIG_FILE ]]; then
-    echo "Config file does not exist: $CONFIG_FILE"
-    echo "   Usage: $(basename $0) [path/to/config.yaml]"
-    echo "   A file called 'config.yaml' must exist in the current directory, or be passed in."
-    exit 1
-fi
-
 # load config dirs from config.yaml. After using the conda dotkit, we should have PyYAML 
-VENVDIR=`python -c "import yaml, os;f=open(\"$CONFIG_FILE\");print(os.path.realpath(yaml.safe_load(f)['venv_dir']));f.close()"`
-BINDIR=`python -c "import yaml, os;f=open(\"$CONFIG_FILE\");print(os.path.realpath(yaml.safe_load(f)['bin_dir']));f.close()"`
-DATADIR=`python -c "import yaml, os; f=open(\"$CONFIG_FILE\");print(os.path.realpath(yaml.safe_load(f)['data_dir']));f.close()"`
+VENVDIR=`python -c "import yaml, os;f=open(\"config.yaml\");print(os.path.realpath(yaml.safe_load(f)['venv_dir']));f.close()"`
+BINDIR=`python -c "import yaml, os;f=open(\"config.yaml\");print(os.path.realpath(yaml.safe_load(f)['bin_dir']));f.close()"`
+DATADIR=`python -c "import yaml, os; f=open(\"config.yaml\");print(os.path.realpath(yaml.safe_load(f)['data_dir']));f.close()"`
 
 # load Python virtual environment
 source "$VENVDIR/bin/activate"

pipes/Broad_UGER/run-pipe.sh

@@ -9,30 +9,10 @@ source /broad/software/scripts/useuse
 reuse -q UGER
 source $SCRIPT_DIRECTORY/../Broad_common/setup_dotkits.sh
 
-# uses the first argument as the config file path, is specified
-if [[ ! -z "$1" && "$1" != " " ]]; then
-    CONFIG_FILE=$1
-else
-    # otherwise the config file is assumed to be "config.yaml" in the cwd
-    CONFIG_FILE="config.yaml"
-fi
-
-# resolve the config file path in full
-CONFIG_FILE=`python -c "import os; print( os.path.realpath(os.path.expanduser(\"$CONFIG_FILE\"))) "`
-
-# if the config file does not exist
-# it is either not in the cwd, or what the user passed in does not exist
-if [[ ! -f $CONFIG_FILE ]]; then
-    echo "Config file does not exist: $CONFIG_FILE"
-    echo "   Usage: $(basename $0) [path/to/config.yaml]"
-    echo "   A file called 'config.yaml' must exist in the current directory, or be passed in."
-    exit 1
-fi
-
 # load config dirs from config.yaml. After using the conda dotkit, we should have PyYAML 
-VENVDIR=`python -c "import yaml, os;f=open(\"$CONFIG_FILE\");print(os.path.realpath(yaml.safe_load(f)['venv_dir']));f.close()"`
-BINDIR=`python -c "import yaml, os;f=open(\"$CONFIG_FILE\");print(os.path.realpath(yaml.safe_load(f)['bin_dir']));f.close()"`
-DATADIR=`python -c "import yaml, os; f=open(\"$CONFIG_FILE\");print(os.path.realpath(yaml.safe_load(f)['data_dir']));f.close()"`
+VENVDIR=`python -c "import yaml, os;f=open(\"config.yaml\");print(os.path.realpath(yaml.safe_load(f)['venv_dir']));f.close()"`
+BINDIR=`python -c "import yaml, os;f=open(\"config.yaml\");print(os.path.realpath(yaml.safe_load(f)['bin_dir']));f.close()"`
+DATADIR=`python -c "import yaml, os; f=open(\"config.yaml\");print(os.path.realpath(yaml.safe_load(f)['data_dir']));f.close()"`
 
 # load Python virtual environment
 source "$VENVDIR/bin/activate"