Question: How to set up and run Mugsy software on Linux 11.04?
1
gravatar for fashiondesignrussian
4.9 years ago by
Belarus
fashiondesignrussian60 wrote:

How to run Mugsy software on Linux Ubuntu 11.04?

I can`t run it as written in instructions How to set up .sh file with installation path correctly? Here is my effort to set it up:

#!/bin/sh

export MUGSY_INSTALL=./mugsy_x86-64-v1r2.1

export PATH=$PATH:$MUGSY_INSTALL:$MUGSY_INSTALL/mapping

export PERL5LIB=$MUGSY_INSTALL/perllibs

export MUGSY_INSTALL=/media/44D2-B182/Mugsy_BOOKS_Are_Here_July_25/mugsy.

#For testing TBA

#export PATH=$PATH:$MUGSY_INSTALL/../../multiz-tba/trunk/

#export PATH=$PATH:$MUGSY_INSTALL/home/samsung/saitdlyafirmi/mugsy/

#export MUGSY_INSTALL=/home/samsung/saitdlyafirmi/mugsy/

Then I run source mugsyenv.sh in terminal in the appropriate directory and nothing happens

Thank you, Folks

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by fashiondesignrussian60
0
gravatar for Daniel Swan
4.9 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

Nothing will happen when you source the file. When you source the file, all it does is setup the environment variables for mugsy.  Running mugsy is a different step (which you haven't shown that you have tried). When posting code or scripts, please attempt to format your question appropriately, it's almost unreadable as you posted it.

ADD COMMENTlink written 4.9 years ago by Daniel Swan13k

I expected to see something like: 'Now you can run Mugsy, put your .fasta files". Thank you. So can i run it with two or three .gb and .fasta files?

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by fashiondesignrussian60

The instructions are quite clear on what to do next if you read them:

 

  • Run mugsy
  • The input to Mugsy is DNA from two or more genomes in FASTA format. The genomes must be assembled into contigs or scaffolds. For draft genomes, a single multi-FASTA file containing all contigs for the genome should be provided. 
    mugsy --directory /data/output --prefix mygenomes genome1.fasta genome2.fasta genome3.fasta 
    

     

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Daniel Swan13k

Thank you, I`ll try, I seldom use Linux today

ADD REPLYlink written 4.9 years ago by fashiondesignrussian60
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