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LieberInstitute / RNAseq-pipeline

Original version of the RNA-seq pipeline implemented in SPEAQeasy at https://github.com/LieberInstitute/SPEAQeasy.
http://research.libd.org/SPEAQeasy/
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More flexible and robust option specification #16

Closed lcolladotor closed 7 years ago

lcolladotor commented 7 years ago

Hi,

I know that we have been adding lots of changes to the shell scripts recently. Some of these additions change the order of the options and/or the number of them. I think that it'll be cool if we make the shell scripts more robust. See http://www.bahmanm.com/blogs/command-line-options-how-to-parse-in-bash-using-getopt for an idea.

If you like this, I can implement it.

Best, Leo

andrewejaffe commented 7 years ago

What about using flags instead of hard-to-remember positions of the argument string? Like: --build hg19 --paired TRUE etc

On Tue, Jan 24, 2017 at 2:48 PM, Leonardo Collado-Torres < notifications@github.com> wrote:

Hi,

I know that we have been adding lots of changes to the shell scripts recently. Some of these additions change the order of the options and/or the number of them. I think that it'll be cool if we make the shell scripts more robust. See http://www.bahmanm.com/blogs/command-line-options-how-to- parse-in-bash-using-getopt for an idea.

If you like this, I can implement it.

Best, Leo

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lcolladotor commented 7 years ago

That's what getopt will allow us to do.

andrewejaffe commented 7 years ago

Haha sounds good, I skipped immediately to "option strings" and the code example when skimming that site...now I see what you're talking about -a

On Tue, Jan 24, 2017 at 5:17 PM, Leonardo Collado-Torres < notifications@github.com> wrote:

That's what getopt will allow us to do.

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