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Full Discussion: C command not found
Top Forums Shell Programming and Scripting C command not found Post 302916937 by Corona688 on Friday 12th of September 2014 02:59:52 PM
Old 09-12-2014
It builds here without those errors, running mfold gives me

Code:
./mfold: line 7: mfold_datdir: command not found
Usage is
mfold SEQ='file_name' with optional parameters:
    [ AUX='auxfile_name' ] [ RUN_TYPE=text (default) or html ]
    [ NA=RNA (default) or DNA ] [ LC=sequence type (default = linear) ]
    [ T=temperature (default = 37 deg C) ] [ P=percent (default = 5) ]
    [ NA_CONC=Na+ molar concentration (default = 1.0) ]
    [ MG_CONC=Mg++ molar concentration (default = 0.0) ]
    [ W=window parameter (default - set by sequence length) ]
    [ MAXBP=max base pair distance (default - no limit) ]
    [ MAX=maximum number of foldings to be computed (default 100) ]
    [ MAX_LP=maximum bulge/interior loop size (default 30) ]
    [ MAX_AS=maximum asymmetry of a bulge/interior loop (default 30) ]
    [ ANN=structure annotation type: none (default), p-num or ss-count ]
    [ MODE=structure display mode: auto (default), bases or lines ]
    [ LAB_FR=base numbering frequency ] [ ROT_ANG=structure rotation angle ]
    [ START=5' base # (default = 1)] [ STOP=3' base # (default = end) ]
    [ REUSE=NO/YES (default=NO) reuse existing .sav file ]

That first error is just because I didn't bother putting the folder I installed it into, into my PATH.

I don't know what's provoking those 'command not found' errors. Maybe check in config.log.
 

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LEARN ABOUT DEBIAN

ssake

SSAKE(1)						      General Commands Manual							  SSAKE(1)

NAME

       ssake - assembling millions of very short DNA sequences

SYNOPSIS

       Progressive assembly of millions of short DNA sequences by k-mer search through a prefix tree and 3' extension.

OPTIONS

       -f     Fasta file containing all the [paired (-p 1) / unpaired (-p 0)] reads (required) paired reads must now be separated by ":"

       -s     Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)

       -m     Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16)

       -o     Minimum number of reads needed to call a base during an extension (default -o 3)

       -r     Minimum base ratio used to accept a overhang consensus base (default -r 0.7)

       -t     Trim up to -t base(s) on the contig end when all possibilities have been exhausted for an extension (default -t 0)>

       -p     Paired-end reads used? (-p 1=yes, -p 0=no, default -p 0)

       -v     Runs in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional)

       -b     Base name for your output files (optional)

       ============ Options below only considered with -p 1 ============

       -d     Mean distance expected/observed between paired-end reads (default -d 200, optional)

       -e     Error (%) allowed on mean distance   e.g. -e 0.75  == distance +/- 75% (default -e 0.75, optional)

       -k     Minimum number of links (read pairs) to compute scaffold (default -k 2, optional)

       -a     Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.70, optional)

       -z     Minimum contig size to track paired-end reads (default -z 50, optional)

       -g     Fasta file containing unpaired sequence reads (optional)

SEE ALSO

       /usr/share/doc/ssake/SSAKE.readme between

AUTHORS

       This  manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others).  Permission is granted
       to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
       the Free Software Foundation.

       On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.

								   January 2008 							  SSAKE(1)
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