FYI: gfold and GNU coreutils conflict as both use "gfold" command
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
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Sounds like this is bad design on the part of the
gfoldgroup. Avoiding name clashes with software is often unavoidable, but clashing with something incoreutilsis a bit of a poor show.The solution would be to softlink the RNAseq suite to a different binary name somewhere in the PATH