Grinder install on iMac & Python 2.7 install on Edhar

Wrestling with the Grinder install this morning ( ) – had to do this on my iMac because it had the “make” program. The modules weren’t installing in cpan, but I ended up being able to fix this with sudo.

sudo cpan

>cpan: install Bio::SeqIO

>cpan: install Bio::Root::Root

>cpan: install Getopt::Euclid

>cpan: install Math::Random::MT

perl Makefile.PL


make install

And then Grinder worked! Globally installed. Command that Aaron Suggested I run (issue #100 on Github) is as follows:

grinder -read_dist 105 -insert_dist 400 normal 50 -md poly4 3e-3 3.3e-8 -mr 95 5 -genome_file <your genome file> -total_reads XXXXX

-read_dist = length of simulated sequences (bp)

-insert_dist = length of insert between PE reads (bp)

-md = mutation distribution (as stated above this models Illumina errors)

-mr = mutation ratio, % substitutions and indels

-genome_file = reference genome file (B. anthraces in this case)

-total_reads = Total number of simulated reads

Installing Python on Edhar

wget <Python_tarball_URL>

tar -xvf <Python_tarball>



make test

and then add PATH to .profile file :/home/hollybik/Python-2.7

But after all that taxit wouldn’t work – Guillaume seems to think that this is a function of not having root permissions on Edhar. E.g. if users want to use build_marker mode, they’ll have to make sure they have Python-2.7 (installed with root permissions), and then also make sure they have the taxit modules


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