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Update README.md
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cbirger authored Aug 12, 2020
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Expand Up @@ -28,6 +28,9 @@ Or download the source and install with setup.py:
Note that if you are installing to a protected location, you may need to preface the `python setup.py install` command with `sudo`.

## Description
(Note: The following description is a bit out of data and does not accurately reflect the current functionalty on the master branch. When I have time I'll
update this.)

Following installation you should be able to run the `genFcWsLoadFiles` command from the command line

```
Expand Down Expand Up @@ -106,4 +109,4 @@ Right now, the two attributes that are created are:

`workspace-column-defaults` - the default order in which the attribute columns should be shown in the table.

Please note that there are instances where multiple files map to the same attribute name. In these situations, fcgdctools attempts to select the "best" file based on metadata stored in the aliquot submitter id (for TCGA, the aliquot barcode). In cases where the aliquot submitter ids are identical fcgdctools makes an arbitrary selection and prints a warning to stdout. Users should search stdout for these warnings and adjust their loadfiles if fcgdctools' choice is incorrect.
Please note that there are instances where multiple files map to the same attribute name. In these situations, fcgdctools attempts to select the "best" file based on metadata stored in the aliquot submitter id (for TCGA, the aliquot barcode). In cases where the aliquot submitter ids are identical fcgdctools makes an arbitrary selection and prints a warning to stdout. Users should search stdout for these warnings and adjust their loadfiles if fcgdctools' choice is incorrect.

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