Changes to reflect the updated to the structure of the mg-process-tes…

…t repo
Multiscale-Genomics · Jun 20, 2018 · eafb674 · eafb674
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/docs/howto/howto_documentation.rst b/docs/howto/howto_documentation.rst
@@ -159,7 +159,7 @@ An example of a pipeline block is as follows:
          :linenos:
 
          cd ${mg-process-test}
-         python process_test.py --config tests/json/process_test.json --in_metadata tests/json/input_test.json --out_metadata tests/results.json --local
+         python mg_process_test/process_test.py --config mg_process_test/tests/json/process_test.json --in_metadata mg_process_test/tests/json/input_test.json --out_metadata mg_process_test/tests/results.json --local
 
       The `--local` parameter should be used if the script is being run within an environment where (py)COMPSs is not installed. It can also be used in an environment where (py)COMPSs is installed, but the script needs to be run locally for testing purposes.
 
@@ -169,7 +169,7 @@ An example of a pipeline block is as follows:
          :linenos:
 
          cd /home/compss/code/mg-process-test
-         runcompss --lang=python process_test.py --config /home/compss/code/mg-process-test/tests/json/process_test.json --in_metadata /home/compss/code/mg-process-test/tests/json/input_test.json --out_metadata /home/compss/code/mg-process-test/tests/results.json
+         runcompss --lang=python mg_process_test/process_test.py --config /home/compss/code/mg-process-test/mg_process_test/tests/json/process_test.json --in_metadata /home/compss/code/mg-process-test/mg_process_test/tests/json/input_test.json --out_metadata /home/compss/code/mg-process-test/mg_process_test/tests/results.json
 
       Methods
       =======

diff --git a/docs/howto/howto_pipeline.rst b/docs/howto/howto_pipeline.rst
@@ -45,7 +45,7 @@ There are 2 ways of calling this function, either directly from another program
    from basic_modules.workflow import Workflow
    from utils import logger
 
-   from tools.testTool import testTool
+   from mg_process_test.tools.testTool import testTool
 
    # ------------------------------------------------------------------------------
 

diff --git a/docs/howto/howto_testing.rst b/docs/howto/howto_testing.rst
@@ -26,7 +26,7 @@ Running the pipeline manually
 .. code-block:: none
    :linenos:
 
-   python process_test.py --config config.json --in_metadata input_files.json --out_metadata output_metadata.json
+   python mg_process_test/process_test.py --config config.json --in_metadata input_files.json --out_metadata output_metadata.json
 
 
 Testing a Tools and Pipelines
@@ -62,7 +62,7 @@ An example pytest for the `test_writer <howto_tool.html>`_ tool:
 
    import os.path
 
-   from tool.testTool import testTool
+   from mg_process_test.tool.testTool import testTool
 
    def test_testTool():
        """
@@ -108,7 +108,7 @@ It is possible to use a local version of the `COMPS virtual machine <https://www
       --library_path=${HOME}/bin                                     \\
       --pythonpath=/<pyenv_virtenv_dir>/lib/python2.7/site-packages/ \\
       --log_level=debug                                              \\
-      process_test.py                                                \\
+      mg_process_test/process_test.py                                \\
          --config <repo>/tool_config/process_test.json               \\
          --in_metadata <repo>/tests/json/input_process_test.json     \\
          --out_metadata <repo>/tests/json/output_process_test.json