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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Document abbreviated options #144

Open nmanik opened 11 years ago

nmanik commented 11 years ago

This is a minor one. It seems like RUM will accept both --index and --index-dir (or any abbrev that is uniquely identifiable). The wiki uses --index, while "rum_runner help align" uses --index-dir, and may be mentioning about abbreviated options or using the same option string in all documentations would be easier for first-time users.

mdelaurentis commented 11 years ago

Before the next release we'll try to make sure those options are consistently represented in the documentation.

nmanik commented 11 years ago

Thanks!

Another minor doc suggestion: While RUM works fine with usual .gz files, there are certain .gz files with multiple members in them (cf. Advanced Usage in "man gunzip") that causes issues with RUM. It might be useful to mention this in documentation (as a sample split in multiple lanes to increase seq-coverage could be combined this way into a single *.gz file with multiple members like so: cat lane[123].fastq.gz > combined.fastq.gz ).

mdelaurentis commented 11 years ago

Thanks very much for all of your suggestions! If you make changes (as I think you did for the qsub call), would you mind forking the repository and putting in pull requests, so we can incorporate your changes back into RUM? If you're not familiar with that process, you can read about forking here ( https://help.github.com/articles/fork-a-repo) and pull requests here ( https://help.github.com/articles/using-pull-requests).

Thanks again,

Mike

On Wed, Oct 17, 2012 at 7:12 PM, nmanik notifications@github.com wrote:

Thanks!

Another minor doc suggestion: While RUM works fine with usual .gz files, there are certain .gz files with multiple members in them (cf. Advanced Usage in "man gunzip") that causes issues with RUM. It might be useful to mention this in documentation (as a sample split in multiple lanes to increase seq-coverage could be combined this way into a single *.gz file with multiple members like so: cat lane[123].fastq.gz > combined.fastq.gz ).

— Reply to this email directly or view it on GitHubhttps://github.com/PGFI/rum/issues/144#issuecomment-9547651.

nmanik commented 11 years ago

Good idea, but the patches I did are very specific to my system.

For instance, I don't know if bash is in /bin/bash for every system (so my edit to qsub to include "-S /bin/bash" won't work as such for others) and I am not knowledgeable enough with perl to automatically retrieve bash's location from RUM's config files. Similarly, my fix of var-length reads by changing reads_temp.fa from 50,001 to 50,000 lines might work for my fastq files, but not sure for others (as fastq files are not required to have multiple of 4 lines). Anyways, I will definitely commit any generic patches I may come up in future. Thanks!