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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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sort: invalid option -- V #9

Closed funnell closed 10 years ago

funnell commented 10 years ago

Hello,

I'm getting an error using vast-tools align:

[vast align]: Mapping reads to the "splice site-based" (aka "a posteriori") EEJ library and Analyzing... sort: invalid option -- V Try sort --help' for more information. [vast align]: Mapping reads to the "transcript-based" (aka "a priori") SIMPLE EEJ library a nd Analyzing... sort: invalid option -- V Trysort --help' for more information. [vast align]: Mapping reads to the "transcript-based" (aka "a priori") MULTI EEJ library an d Analyzing... sort: invalid option -- V Try sort --help' for more information. [vast align]: Mapping reads to microexon EEJ library and Analyzing... sort: invalid option -- V Trysort --help' for more information. [vast align]: Mapping reads to intron retention library... gzip: SA464_A14559_D0R1PACXX_8_1-50.fq.gz: No such file or directory sort: invalid option -- V Try `sort --help' for more information. Warning: Could not find any reads in "-"

$ sort --version sort (GNU coreutils) 5.97 Copyright (C) 2006 Free Software Foundation, Inc. This is free software. You may redistribute copies of it under the terms of the GNU General Public License http://www.gnu.org/licenses/gpl.html. There is NO WARRANTY, to the extent permitted by law.

Written by Mike Haertel and Paul Eggert.

timbitz commented 10 years ago

Hi @funnell Looks like you may have an old verison of GNU sort, when I sort --version I get 8.4... My simplest suggestion is to update. Perhaps there is another option though. @kcha any thoughts? Cheers, -Tim

kcha commented 10 years ago

Thanks @funnell, this is really helpful for us to iron out kinks in our pipeline.

It looks like Mac OS ships with an older version of sort (I have 5.93 on my machine, OS 10.8.5), which doesn't have the -V option. So my guess is that @funnell is running on Mac OS (which is great because we have been almost exclusively testing on Linux)? I think we may have to revisit how we're using sort.

funnell commented 10 years ago

I was testing on an older version of linux (Rocks 5.4). Mac OS 10.9.4 also uses sort 5.93.

timbitz commented 10 years ago

@funnell, OK. So after much deliberation, we decided this did need to change, and as a result I have made some substantial alterations and the version dependency for sort is gone. If you pull the current version it should work on your system. LMK if that is not the case. Cheers

timbitz commented 10 years ago

Hey @funnell, we made one more critical change... please pull before using the tool. I would delete any runs that you made prior to this final pull.