Specifying Non-local Output Dir

snijderlab / stitch

Template-based assembly of proteomics short reads for de novo antibody sequencing and repertoire profiling

MIT License

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Specifying Non-local Output Dir #204

Closed kostrouc closed 1 year ago

kostrouc commented 1 year ago

Hi,

I noticed that the building requires stitch be installed on a local directory using mklink. Is there any way to specify an output directory with dotnet run --project stitch? I didn't see anything listed under --help.

kostrouc commented 1 year ago

Ah I believe this is specified in the batch file that is provided.

From batchfiles\basic.txt:


Report ->
    HTML ->
        Path    : ../results/{datetime} {name}/report-basic.html
    <-
<-
``

douweschulte commented 1 year ago

It is indeed specified there. If you take a look at the manual that is also bundled with the program you will be able to find the full definition of what you can do with this setting. You can find this here. Keep in mind that all paths in the whole batchfile are seen relative to the location of the batchfile itself.