Question

FYI: gfold and GNU coreutils conflict as both use "gfold" command

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4.3 years ago

nathan bowen ▴ 20

Just an FYI if you are using gfold

installation of GNU coreutils will call the fold command of GNU coreutils when gfold is issued at the command line

gfold --version fold (GNU coreutils) 8.31 Copyright (C) 2019 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later https://gnu.org/licenses/gpl.html. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

Written by David MacKenzie.

as opposed to calling the local installation of gfold

/Users/XYZ/bioinf/gfold.V1.1.4/gfold ERROR: argument Job is required

  =============================================================================== 
      gfold    :   Generalized fold change for ranking differentially expressed   
                   genes from RNA-seq data.

      Author   :   Jianxing Feng (jianxing.tongji@gmail.com)
        Date   :   Sun May 24 07:42:36 CST 2015
      Version  :   V1.1.4
  =============================================================================== 

  USAGE:   Please go to the source code directory and use command 'man doc/gfold.man' 
           or open doc/gfold.html to find documentation.

  Quick Examples: 
           gfold count -ann hg19Ref.gtf -tag sample1.sam -o sample1.read_cnt          
           gfold count -ann hg19Ref.gtf -tag sample2.sam -o sample2.read_cnt          
           gfold diff -s1 sample1 -s2 sample2 -suf .read_cnt -o sample1VSsample2.diff

RNA-Seq • 839 views

ADD COMMENT • link 4.3 years ago by nathan bowen ▴ 20

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Sounds like this is bad design on the part of the gfold group. Avoiding name clashes with software is often unavoidable, but clashing with something in coreutils is a bit of a poor show.

The solution would be to softlink the RNAseq suite to a different binary name somewhere in the PATH

ADD REPLY • link 4.3 years ago by Joe 21k