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MUGSY install troubleshoot

Hello everyone

I am trying to install mugsy, but when I try to run it, I get the next error message:

-directory must be a directory at ./mugsy line 246

How can I solve this? Thanks in advance.

mugsy alignment
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updated by Ram Ram • written by bpz • bpz

You don't give much info but it looks like you're not giving a valid directory to the --directory option.

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written by Jean-Karim Heriche Jean-Karim Heriche

I don know if it is an installation issue, or a problem with the command line. The whole error message is the next:

ERROR: MUGSY_INSTALL environment variable not set. Set using export MUGSY_INSTALL=/somepath/to/mugsy
5 genomes
Starting Nucmer: jue dic 24 18:56:57 CST 2015
.sh: 1: /MUMmer3.20/delta-filter: not found
sh: 1: /MUMmer3.20/delta2maf: not found
sh: 1: /fixMAFnames.pl: not found
.sh: 1: /MUMmer3.20/delta-filter: not found
sh: 1: /MUMmer3.20/delta2maf: not found
sh: 1: /fixMAFnames.pl: not found
.sh: 1: /MUMmer3.20/delta-filter: not found
sh: 1: /MUMmer3.20/delta2maf: not found
sh: 1: /fixMAFnames.pl: not found
.sh: 1: /MUMmer3.20/delta-filter: not found
sh: 1: /MUMmer3.20/delta2maf: not found
sh: 1: /fixMAFnames.pl: not found

Finished Nucmer jue dic 24 18:56:57 CST 2015
Starting MUGSYWGA: jue dic 24 18:56:57 CST 2015
sh: 1: /maf2fasta.pl: not found
sh: 1: /maf2fasta.pl: not found
sh: 1: /maf2fasta.pl: not found
sh: 1: /maf2fasta.pl: not found
Final output (MAF format): /home/bernardo/mugsy_x86-64-v1r2.2/Results/mygenomes.maf
Finished jue dic 24 18:56:57 CST 2015
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updated by Ram Ram • written by bpz • bpz

Do not post comments as an answer to your question, use add comment instead.

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updated by Ram Ram • written by h.mon h.mon

Was a solution ever found to this problem? I am getting the same error even though I have 'run source mugsyenv.sh' and echo $MUGSY_INSTALL returns the path to my mugsy executable.

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updated by Ram Ram • written by mmacd • mmacd

1 answer

The error message is clear, and if you read the README.install file from Mugsy distribution you would:

Edit MUGSY_INSTALL in mugsyenv.sh and set to absolute path of the installation directory
In bash, run  source mugsyenv.sh

That is, before running Mugsy, you have to set some environment variables:

source mugsyenv.sh

Then you run mugsy.

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updated by Ram Ram • written by h.mon h.mon

Hello. I have done this already, and it is not working. Thanks

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written by bpz • bpz

What does echo $MUGSY_INSTALL returns?

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written by h.mon h.mon

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