FILES_FOR_R

[s4251484]

Hi

thanks for developing this tool! i encouter an error as such: line 710: $((${#FILES_FOR_R} - 1)): substring expression < 0

when i run SequelTools.sh -t Q -u /Users/s4251484/Desktop/sequeltool.txt

Please enlighten!

[aseetharam]

Thanks for trying SequelTools! It looks like the shell you are using doesn't support Command Substitutions. Can you let us know what environment you're using for running SequelTools?

[s4251484]

HI!

Thanks for your prompt reply! I’m running it on local mac terminal env with R Samtools and Python and even the bash files in SequelTools/Script folder in the path.

[aseetharam]

Hi Chian,

Can you try running this in a native Linux environment (non-Mac)? Quick look upon that error tells me that Mac doesn't support something required for SequelTools. https://superuser.com/q/1033273

Thank you for reporting this, we will try to fix this by converting the expression to something generic in the next version.

Thanks,

[s4251484]

Hi Dr Seetharam

Wow! I think you detected the problem. Here are the run results on two of my systems:

PBS cluster (linus) – no R installed

s4251484@fl102:/30days/s4251484/bwa_bcf> STR="Hello World" s4251484@fl102:/30days/s4251484/bwa_bcf> echo ${STR:6:-1} Worl s4251484@fl102:/30days/s4251484/bwa_bcf> echo ${STR:6:$((${#STR} - 6 - 1))} Worl

Local Mac Unix d-i89-241-70:~ s4251484$ STR="Hello World" d-i89-241-70:~ s4251484$ echo ${STR:6:-1} -bash: -1: substring expression < 0 d-i89-241-70:~ s4251484$ echo ${STR:6:$((${#STR} - 6 - 1))} Worl