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

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

alignment software-error sequencing • 3.4k views
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9.7 years ago
User 59 13k

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.

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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?

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

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