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itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
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small bug in runall_sam2cov.pl #18

Closed e-manduchi closed 10 years ago

e-manduchi commented 10 years ago

Need to add a '$shdir/' just before $shfile at line 154

eunjijunekim commented 10 years ago

fixed the bug. just pushed a new version which takes -pgfi instead of -qsub and -pmacs instead of -bsub option.

eunjijunekim commented 10 years ago

forgot to mention this. this new script creates a folder called COV in NORMALIZED_DATA directory and outputs the coverage files there instead of putting them in the same directory as the sam files. i will update the documentation soon.

e-manduchi commented 10 years ago

Thanks. Regarding the option names, -pgfi and -pmacs are Upenn specific, whereas -qsub and -bsub would be more meaningful for a general public, aren't the latter preferred?

eunjijunekim commented 10 years ago

people using LSF and SGE may have different queue names that might clash with the hardcoded options for -bsub and -qsub. so I've added a new option '-other' where people can give commands/options for their cluster.

e-manduchi commented 10 years ago

OK, thx

e-manduchi commented 10 years ago

Note that runall_sam2cov is printing to STDERR information that belongs to STDOUT

khayer commented 10 years ago

Which information would you prefer to be in STDOUT?

e-manduchi commented 10 years ago

I guess everything which is not an actual error that one needs to worry about.

khayer commented 10 years ago

Fixed