Merge pull request #583 from maxplanck-ie/config_fix

snakePipes config fix

.ci_stuff/test_dag.sh

@@ -54,6 +54,9 @@ mkdir -p allelic_input
 mkdir -p allelic_input/Ngenome
 touch allelic_input/file.vcf.gz allelic_input/snpfile.txt
 
+# Ensure an empty snakePipes config doesn't muck anything up
+snakePipes config
+
 # DNA mapping
 WC=`DNA-mapping -i PE_input -o output .ci_stuff/organism.yaml --snakemakeOptions " --dryrun --conda-prefix /tmp" | tee >(cat 1>&2) | grep -v "Conda environment" | wc -l`
 if [ ${PIPESTATUS[0]} -ne 0 ] || [ $WC -ne 886 ]; then exit 1 ; fi

bin/snakePipes

@@ -100,6 +100,11 @@ def parse_arguments():
                                    "(Default: %(default)s)",
                               default=defaults['tempDir'])
 
+    configParser.add_argument('--noToolsVersion',
+                              dest='toolsVersion',
+                              help="By default, tool versions are printed to a workflow-specific file. Specifying this disables that behavior.",
+                              action="store_false")
+
     email = configParser.add_argument_group(title="Email/SMTP options", description="These options are only used if/when --emailAddress is used.")
     email.add_argument('--smtpServer',
                        help="SMTP server address. (Default: %(default)s)",
@@ -302,9 +307,13 @@ def updateConfig(args):
          'onlySSL': args.onlySSL,
          'emailSender': args.emailSender,
          'smtpUsername': args.smtpUsername,
-         'smtpPassword': args.smtpPassword
+         'smtpPassword': args.smtpPassword,
+         'toolsVersion': args.toolsVersion
         }
     baseDir = os.path.dirname(snakePipes.__file__)
+    # Load, update and rewrite the default dictionary
+    currentDict = cof.load_configfile(os.path.join(baseDir, "shared", "defaults.yaml"), False)
+    cof.merge_dicts(currentDict, d)
     cof.write_configfile(os.path.join(baseDir, "shared", "defaults.yaml"), d)
 
 

docs/content/News.rst

@@ -1,6 +1,11 @@
 snakePipes News
 ===============
 
+snakePipes 2.0.1
+----------------
+
+ * Fixed a bug in `snakePipes config` that caused the `toolsVersion` variable to be removed from `defaults.yaml`. This is likely related to issue #579.
+
 snakePipes 2.0.0
 ----------------
 

snakePipes/__init__.py

@@ -1 +1 @@
-__version__ = '2.0.0'
+__version__ = '2.0.1'