Implement support for --init option.

Makefile.am

@@ -16,6 +16,7 @@ dist_pkglibexec_scripts_SCRIPTS =					\
   scripts/validate_input.py
 
 dist_pkgdata_DATA =									\
+  etc/sample_sheet.csv.example								\
   etc/settings.yaml									\
   etc/pretty.txt									\
   images/Logo_PiGx.png

etc/sample_sheet.csv.example

@@ -0,0 +1,7 @@
+name,reads,reads2,sample_type
+HBR_Rep1,HBR_Rep1.read1.fastq.gz,HBR_Rep1.read2.fastq.gz,HBR
+HBR_Rep2,HBR_Rep2.read1.fastq.gz,HBR_Rep2.read2.fastq.gz,HBR
+HBR_Rep3,HBR_Rep3.read1.fastq.gz,HBR_Rep3.read2.fastq.gz,HBR
+UHR_Rep1,UHR_Rep1.read1.fastq.gz,UHR_Rep1.read2.fastq.gz,UHR
+UHR_Rep2,UHR_Rep2.read1.fastq.gz,UHR_Rep2.read2.fastq.gz,UHR
+UHR_Rep3,UHR_Rep3.read1.fastq.gz,UHR_Rep3.read2.fastq.gz,UHR

pigx-rnaseq.in

@@ -61,13 +61,16 @@ parser = argparse.ArgumentParser(description=description,
 parser.add_argument('-v', '--version', action='version',
                     version=version)
 
-parser.add_argument('samplesheet',
+parser.add_argument('sample_sheet', nargs='?', default='sample_sheet.csv',
                     help="""\
 The sample sheet containing sample data in CSV format.\
 """)
 
-parser.add_argument('-s', '--settings', dest='settings', required=True,
-                    help='A YAML file for settings that deviate from the defaults.')
+group = parser.add_mutually_exclusive_group(required=True)
+group.add_argument('--init', dest='init', choices=['settings', 'sample-sheet', 'both'], const='both', nargs='?',
+                   help='Generate a template SETTINGS file, a SAMPLE-SHEET.  Leave empty for both.')
+group.add_argument('-s', '--settings', dest='settings',
+                   help='A YAML file for settings that deviate from the defaults.')
 
 parser.add_argument('-c', '--configfile', dest='configfile', default='./config.json',
                     help="""\
@@ -116,38 +119,11 @@ def bail(msg):
     exit(1)
 
 
-def generate_config(configfile, samplesheet, settingsfile):
+def generate_config(configfile, sample_sheet, settingsfile, dirs):
     """Generate a new configuration file CONFIGFILE using SAMPLESHEET and
-SETTINGSFILE as inputs."""
-    dirs = {}
-    if os.getenv('PIGX_UNINSTALLED'):
-        here = os.getenv('srcdir') if os.getenv('srcdir') else os.getcwd()
-        dirs['locations'] = {
-            'prefix'       : here,
-            'exec_prefix'  : here,
-            'libexecdir'   : here,
-            'pkglibexecdir': here,
-            'datarootdir'  : here,
-            'pkgdatadir'   : here
-        }
-    else:
-        # Expand and store autoconf directory variables
-        prefix = '@prefix@'
-        exec_prefix = '@exec_prefix@'[1:].format(prefix=prefix)
-        libexecdir = '@libexecdir@'[1:].format(exec_prefix=exec_prefix)
-        pkglibexecdir = '{libexecdir}/@PACKAGE@'.format(libexecdir=libexecdir)
-        datarootdir = '@datarootdir@'[1:].format(prefix=prefix)
-        pkgdatadir = '@datadir@/@PACKAGE@'[1:].format(datarootdir=datarootdir)
-
-        dirs['locations'] = {
-            'prefix'       : '@prefix@',
-            'exec_prefix'  : exec_prefix,
-            'libexecdir'   : libexecdir,
-            'pkglibexecdir': pkglibexecdir,
-            'datarootdir'  : datarootdir,
-            'pkgdatadir'   : pkgdatadir
-        }
-
+SETTINGSFILE as inputs.  Use the locations in DIRS to find default
+settings.
+    """
     # Load defaults
     if os.getenv('PIGX_UNINSTALLED'):
         where = os.getenv('srcdir') if os.getenv('srcdir') else '.'
@@ -168,14 +144,14 @@ SETTINGSFILE as inputs."""
     settings['locations'].update(dirs['locations'])
 
     # Resolve relative paths in the locations section
-    root = path.dirname(samplesheet)
+    root = path.dirname(sample_sheet)
     here = os.getenv('srcdir') if os.getenv('srcdir') else os.getcwd()
 
     for key in settings['locations']:
         settings['locations'][key] = path.normpath(path.join(here, root, settings['locations'][key]))
 
     # Record the location of the sample sheet.
-    settings['locations']['sample-sheet'] = path.abspath(samplesheet)
+    settings['locations']['sample-sheet'] = path.abspath(sample_sheet)
 
     # Write the config file
     with open(configfile, 'w') as outfile:
@@ -258,10 +234,74 @@ def display_logo():
 
 
 
+# Determine locations
+dirs = {}
+if os.getenv('PIGX_UNINSTALLED'):
+    here = os.getenv('srcdir') if os.getenv('srcdir') else os.getcwd()
+    dirs['locations'] = {
+        'prefix'       : here,
+        'exec_prefix'  : here,
+        'libexecdir'   : here,
+        'pkglibexecdir': here,
+        'datarootdir'  : here,
+        'pkgdatadir'   : here
+    }
+else:
+    # Expand and store autoconf directory variables
+    prefix = '@prefix@'
+    exec_prefix = '@exec_prefix@'[1:].format(prefix=prefix)
+    libexecdir = '@libexecdir@'[1:].format(exec_prefix=exec_prefix)
+    pkglibexecdir = '{libexecdir}/@PACKAGE@'.format(libexecdir=libexecdir)
+    datarootdir = '@datarootdir@'[1:].format(prefix=prefix)
+    pkgdatadir = '@datadir@/@PACKAGE@'[1:].format(datarootdir=datarootdir)
+
+    dirs['locations'] = {
+        'prefix'       : '@prefix@',
+        'exec_prefix'  : exec_prefix,
+        'libexecdir'   : libexecdir,
+        'pkglibexecdir': pkglibexecdir,
+        'datarootdir'  : datarootdir,
+        'pkgdatadir'   : pkgdatadir
+    }
+
+# Init?
+if args.init:
+    init_settings = False
+    init_sample_sheet = False
+    if os.getenv('PIGX_UNINSTALLED'):
+        base = os.getcwd() + '/etc/'
+    else:
+        base = dirs['locations']['pkgdatadir']
+
+    if args.init == 'both':
+        init_settings = True
+        init_sample_sheet = True
+
+    if args.init == 'settings' or init_settings:
+        name = 'settings.yaml'
+        if path.exists(name):
+            print('Refusing to overwrite existing {}.'.format(name))
+        else:
+            with open(name, 'w') as outfile:
+                with open(path.join(base, name), 'r') as infile:
+                    for line in infile:
+                        outfile.write('# ' + line)
+            print('Generated {} template.'.format(name))
+
+    if args.init == 'sample-sheet' or init_sample_sheet:
+        name = 'sample_sheet.csv'
+        if path.exists(name):
+            print('Refusing to overwrite existing sample_sheet.csv.')
+        else:
+            shutil.copy(path.join(base, name + '.example'), name)
+            print('Generated {} template.'.format(name))
+    exit(0)
+
 # Run snakemake!
 generate_config(args.configfile,
-                args.samplesheet,
-                args.settings)
+                args.sample_sheet,
+                args.settings,
+                dirs)
 
 config = json.load(open(args.configfile, 'r'))