Download link not displayed for MACS2 tabular output file

[hackdna]

Commit f48b57f.

Steps to reproduce

Run a MACS2 workflow

Observed results

• Download links are displayed for 'MACS2_plot' and 'MACS2_bigwig' output files but not for 'MACS2_bed' file.
• The 'MACS2_bed' output file is successfully downloaded from Galaxy and exists on disk but has the type of <FileType: DAT file>.

Expected results

• Download links should be displayed for all successfully downloaded workflow outputs.
• The 'MACS2_bed' output file should have the type of <FileType: BED file> or <FileType: Tabular file>.

Notes

This may be due to the change of output file format in the latest version of MACS2 from 'bed' to 'tabular'.

[hackdna]

[ngehlenborg]

@scottx611x: Do you have any spare cycles to look into this?

[scottx611x]

@ngehlenborg Definitely, I'll check it out today!

[scottx611x]

This issue will most likely be addressed with PR #908 but needs to be tested

[hackdna]

Still a problem in commit 0b896f6:

2016-03-04 15:35:59 WARNING  file_store:237 get_item() - FileStoreItem with UUID 'None' does not exist
2016-03-04 15:35:59 WARNING  data_set_manager.search_indexes:141 prepare() - Unable to get file store item None. No file type available.
2016-03-04 15:35:59 INFO     data_set_manager.utils:502 _index_annotated_nodes() - 3 nodes indexed in 0.237416028976
2016-03-04 15:35:59 DEBUG    core.models:1189 rename_results() - Renaming analysis results
2016-03-04 15:35:59 DEBUG    file_store:469 rename_datafile() - Renaming datafile 7d/3f/display to 1_MACS2_bed.tabular
2016-03-04 15:35:59 DEBUG    file_store:712 _rename_file_on_disk() - Renamed /data/media/file_store/7d/3f/display to /data/media/file_store/9c/bd/1_MACS2_bed.tabular
2016-03-04 15:35:59 INFO     file_store:484 rename_datafile() - Datafile renamed
2016-03-04 15:35:59 DEBUG    file_store:469 rename_datafile() - Renaming datafile 7d/3f/display_U6pBI13 to 1_MACS2_plot.pdf
2016-03-04 15:35:59 DEBUG    file_store:712 _rename_file_on_disk() - Renamed /data/media/file_store/7d/3f/display_U6pBI13 to /data/media/file_store/38/6e/1_MACS2_plot.pdf
2016-03-04 15:35:59 INFO     file_store:484 rename_datafile() - Datafile renamed
2016-03-04 15:35:59 DEBUG    file_store:469 rename_datafile() - Renaming datafile 7d/3f/display_lKoev0u to 1_MACS2_bigwig.bigwig
2016-03-04 15:35:59 DEBUG    file_store:712 _rename_file_on_disk() - Renamed /data/media/file_store/7d/3f/display_lKoev0u to /data/media/file_store/56/fc/1_MACS2_bigwig.bigwig
2016-03-04 15:35:59 INFO     file_store:484 rename_datafile() - Datafile renamed

[scottx611x]

@hackdna I'm not seeing an issue with the output that you've commented. Is there something I'm not seeing?

[hackdna]

This is simply part of the log that might be relevant to the error.

[scottx611x]

This issue actually stems from the MACS2 tool annotations. Changing the annotations like shown below addresses the issue.

Original:

{
    "output_tabular": {
--      "name": "MACS2_bed",
        "description": "",
--      "type": "bed"
    },
    "output_plot": {
        "name": "MACS2_plot",
        "description": "",
        "type": "pdf"
    }
}

Edited:

{
    "output_tabular": {
++      "name": "MACS2_tabular",
        "description": "",
++     "type": "tabular"
    },
    "output_plot": {
        "name": "MACS2_plot",
        "description": "",
        "type": "pdf"
    }
}

Working in Refinery:

[hackdna]

OK but this is strange because the output file name is arbitrary. If this is not the case, we should update the wiki.

[scottx611x]

@hackdna can I close this after updating?

[hackdna]

I'd like to test this before we close.

[hackdna]

Test importing MACS2 workflow results

[hackdna]

Successfully tested using commit 657b619 with MACS2 revision 6d4babad010f. Only "type" needs to be changed to "tabular".