Fixed unit tests

README.md

@@ -34,7 +34,9 @@
 
 ### Pulling the Docker image (recommended)
 
-Please follow the instruction [here](https://docs.docker.com/get-docker/) to download and install Docker based on your operating system before running the Docker image. This is **recommended** as it is compatible with most common operating systems including Linux, macOS and Windows.
+Please follow the instruction [here](https://docs.docker.com/get-docker/) to download and install Docker based on your operating system before running the Docker image. **For Windows users**, please check [here](https://github.com/yangwu91/r2g/wiki/Install-and-configure-Docker-on-Windows) to configure the Docker if it is your first time to use it. 
+
+This installation method is **recommended** as it is compatible with most common operating systems including Linux, macOS and Windows.
 
 Then, pull the r2g Docker image with all required software packages installed and configured by one command as follows:
 

tests/test_assemblers.py

@@ -34,7 +34,7 @@ def test_trinity_paired(self):
         paired = True
         app_json = utils.preflight(self.args)
         trinity = assemblers.Trinity(self.args, app_json, self.fastq_list, paired)
-        trinity_dir = trinity.run()
+        trinity_dir, trinity_log_file = trinity.run()
         result = "{}/Trinity.fasta".format(trinity_dir)
         if os.path.isfile(result):
             trinity.copyto("{}/final_assembly.fasta".format(self.output_dir))
@@ -49,7 +49,7 @@ def test_trinity_singled_trimmed(self):
         self.args['trim'] = True
         app_json = utils.preflight(self.args)
         trinity = assemblers.Trinity(self.args, app_json, self.fastq_list, paired)
-        trinity_dir = trinity.run()
+        trinity_dir, trinity_log_file = trinity.run()
         # result = "{}/{}.Trinity.fasta".format(self.output_dir, os.path.split(trinity_dir)[1])
         result = "{}/{}/Trinity.fasta".format(self.output_dir, os.path.split(trinity_dir)[1])
         if os.path.isfile(result) and os.stat(result).st_size > 1000:
@@ -64,7 +64,7 @@ def test_trinity_customtrimmed(self):
         del self.fastq_list['2']
         app_json = utils.preflight(self.args)
         trinity = assemblers.Trinity(self.args, app_json, self.fastq_list, paired)
-        trinity_dir = trinity.run()
+        trinity_dir, trinity_log_file = trinity.run()
         result = "{}/{}/Trinity.fasta".format(self.output_dir, os.path.split(trinity_dir)[1])
         print(result)
         print(os.stat(result).st_size)
@@ -79,7 +79,7 @@ def test_trinity_stage(self):
             self.args['stage'] = stage
             app_json = utils.preflight(self.args)
             trinity = assemblers.Trinity(self.args, app_json, self.fastq_list, paired)
-            trinity_dir = trinity.run()
+            trinity_dir, trinity_log_file = trinity.run()
             if stage == "jellyfish":
                 result = "{}/jellyfish.kmers.fa".format(trinity_dir)
             elif stage == "inchworm":

tests/test_r2g.py

@@ -51,7 +51,7 @@
 class TestR2g(unittest.TestCase):
 
     def test_utils_parse_argument(self):
-        online_raw_args = "-o RPS7 -s SRX5138669 -q aae_RPS7.fa --cut 50,20 -r 5 --CPU 4".split()
+        online_raw_args = "r2g -o RPS7 -s SRX5138669 -q aae_RPS7.fa --cut 50,20 -r 5 --CPU 4".split()
         globals()['args_dict']['query'] = "aae_RPS7.fa"
         self.assertEqual(utils.parse_arguments(online_raw_args), globals()['args_dict'])
 

tests/test_utils.py

@@ -48,7 +48,7 @@ def setUp(self):
 
     def test_parse_args(self):
         utils.log("Testing r2g.utils.utils _parse_args")
-        raw_args = "-o OUTPUT -s SRXNNNNNN -q ATGC --cut 80,50 -p blastn --CPU 4 --retry"
+        raw_args = "r2g -o OUTPUT -s SRXNNNNNN -q ATGC --cut 80,50 -p blastn --CPU 4 --retry"
         raw_args = raw_args.split()
         parsed_args = utils.parse_arguments(raw_args)
         self.assertEqual(parsed_args, self.args)