search

chanzuckerberg / shasta

[MOVED] Moved to paoloshasta/shasta. De novo assembly from Oxford Nanopore reads
Other
270 stars 57 forks source link

How to specify the output dir ? #269

Closed xiucz closed 2 years ago

xiucz commented 2 years ago

Hi, Aftering reading the document, I still can't get which parameter should I use to specify the output directory.

How to specify the output dir ?

Best, xiucz

paoloczi commented 2 years ago

The option to do that is --assemblyDirectory (default is ShastaRun). That option is described here and here.

To prevent removing existing data, when the assembly starts the specified assembly directory must not exist, or can exist and be empty.

Let us know if additional clarification is needed.

xiucz commented 2 years ago

I am sorry to miss so detailed CommandLineOptions page, my mistake. I will close this issue.

Thank you. xiucz

paoloczi commented 2 years ago

No problem. The documentation is not well organized, which can make it hard to locate the piece of information you need. To alleviate this in the future, keep in mind Shasta documentation is indexed by Google, so you can try a Google search to locate the information you want. For example, for this case searching Google for "shasta output directory" gets to the right place:

image

You can also use shasta --help to get a list of command line options, each listed with a quick description.

In any event, always free to open a new issue if new questions arise or if you are not able to obtain a satisfactory assembly.

xiucz commented 2 years ago

Thank you.