MetaSRA-pipeline

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When installing the pipeline it starts with downloading and preparing the used ontologies. This process fetches the newest versions of them which work perfectly fine. However, when running the pipeline...

dmalzl

Example code couldn't run

6

Got import error at begining

albert-ying

When running the `run_pipeline.py` script I get an import error when it is trying to import `run_sample_type_predictor`. This import is written as ```python from predict_sample_type import run_sample_type_predictor ``` when really...

dmalzl

Hi, I tried to run the pipeline according to the install info but when executing `run_pipeline.py` I found that I still had to install `dill` and `nltk` which are not...

dmalzl

batravarun125

Need to download some data before using ntlk

1

Before run the pipeline, need to down some data using following command ``` import nltk nltk.download('punkt') ```

steves880106

Issue for setting PYTHONPATH when using conda as python environment

2

When using conda environment, python will not search package under PYTHONPATH. A solution may be `conda develop /path/to/MetaSRA-pipeline`.

steves880106

nellore

The CD4+ memory T cell samples should map to term CL:0000897 The CD4+ naive T cell samples should map to term CL:0000895

mbernste

The following maps samples to terms that should be added: ``{"SRS1625126": [ "CL:0008001" ], "SRS1625125": [ "CL:0008001" ], "SRS1625124": [ "CL:0008001" ], "SRS1625123": [ "CL:0008001" ]}``

mbernste