Merge pull request #21 from biomedbigdata/bugfix

container bugfix

README.md

@@ -66,6 +66,7 @@ The project is distributed under the [GNU General Public License](https://www.gn
 In order to use our docker container, it is required to have docker installed. The user also needs permission to create and run docker containers (p.r.n., ask your system administrator). Additionally, a Python 3 installation and the command-line tool `curl` are necessary. To make all tools in this repository available in your current terminal session, please first source our installer script. This step needs to be done each time a new terminal session is started. It will only create some lightweight aliases, the actual download will take place only if you actually use one of the tools.
 ```bash
 # install all tools in this repository for the current terminal session
+if command -v shopt > /dev/null 2>&1 ; then shopt -s expand_aliases; fi
 needl_install_sh="$(curl -s https://raw.githubusercontent.com/biomedbigdata/NeEDL/main/run/bash_install.sh)" && eval "$needl_install_sh"
 ```
 

run/NeEDL.py

@@ -128,19 +128,19 @@
 
 if use_singularity:
     volume_string = ' '.join([f'-B "{file}:/mnt/in_{i}:rw"' for i, file in enumerate(input_paths)])
-    external_command = f"{singularity_cmd} exec {volume_string}"
+    external_command = f"{singularity_cmd} exec {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -B "{output_directory}:/mnt/out:rw" '
+        external_command += f'-B "{output_directory}:/mnt/out:rw" '
 
     external_command += "docker://"
 
 else:
     volume_string = ' '.join([f'-v "{file}:/mnt/in_{i}:rw{docker_selinux_flag}"' for i, file in enumerate(input_paths)])
-    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string}"
+    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
+        external_command += f'-v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
 
 
 argument_string = ' '.join(map(lambda a: f'"{a}"', map(lambda b: b.replace('"', '\\"'), arguments)))

run/calculate_scores.py

@@ -113,19 +113,19 @@
 
 if use_singularity:
     volume_string = ' '.join([f'-B "{file}:/mnt/in_{i}:rw"' for i, file in enumerate(input_paths)])
-    external_command = f"{singularity_cmd} exec {volume_string}"
+    external_command = f"{singularity_cmd} exec {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -B "{output_directory}:/mnt/out:rw" '
+        external_command += f'-B "{output_directory}:/mnt/out:rw" '
 
     external_command += "docker://"
 
 else:
     volume_string = ' '.join([f'-v "{file}:/mnt/in_{i}:rw{docker_selinux_flag}"' for i, file in enumerate(input_paths)])
-    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string}"
+    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
+        external_command += f'-v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
 
 
 argument_string = ' '.join(map(lambda a: f'"{a}"', map(lambda b: b.replace('"', '\\"'), arguments)))

run/convert_to_binary.py

@@ -92,19 +92,19 @@
 
 if use_singularity:
     volume_string = ' '.join([f'-B "{file}:/mnt/in_{i}:rw"' for i, file in enumerate(input_paths)])
-    external_command = f"{singularity_cmd} exec {volume_string}"
+    external_command = f"{singularity_cmd} exec {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -B "{output_directory}:/mnt/out:rw" '
+        external_command += f'-B "{output_directory}:/mnt/out:rw" '
 
     external_command += "docker://"
 
 else:
     volume_string = ' '.join([f'-v "{file}:/mnt/in_{i}:rw{docker_selinux_flag}"' for i, file in enumerate(input_paths)])
-    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string}"
+    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
+        external_command += f'-v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
 
 
 argument_string = ' '.join(map(lambda a: f'"{a}"', map(lambda b: b.replace('"', '\\"'), arguments)))

run/epiJSON.py

@@ -105,19 +105,19 @@
 
 if use_singularity:
     volume_string = ' '.join([f'-B "{file}:/mnt/in_{i}:rw"' for i, file in enumerate(input_paths)])
-    external_command = f"{singularity_cmd} exec {volume_string}"
+    external_command = f"{singularity_cmd} exec {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -B "{output_directory}:/mnt/out:rw" '
+        external_command += f'-B "{output_directory}:/mnt/out:rw" '
 
     external_command += "docker://"
 
 else:
     volume_string = ' '.join([f'-v "{file}:/mnt/in_{i}:rw{docker_selinux_flag}"' for i, file in enumerate(input_paths)])
-    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string}"
+    external_command = f"docker run --user='{os.getuid()}':'{os.getgid()}' {volume_string} "
 
     if output_directory is not None:
-        external_command += f' -v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
+        external_command += f'-v "{output_directory}:/mnt/out:rw{docker_selinux_flag}" '
 
 
 argument_string = ' '.join(map(lambda a: f'"{a}"', map(lambda b: b.replace('"', '\\"'), arguments)))