How to set up and run Mugsy software on Linux 11.04?

Question

[fashiondesignrussian]

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

Answer 1

[User 59]

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.

[fashiondesignrussian]

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?

[User 59]

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

[fashiondesignrussian]

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