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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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syntax error in kronotools install.pl #142

Closed jffkm closed 10 years ago

jffkm commented 10 years ago

I wanted to give you a heads up that I found an error in the install.pl script for kronatools install.pl which causes a test suite error in the latest release and install from source.

It's missing a set of parentheses on line 37 In Praline Brownie, it is missing a bracket before "qw" and after the list of scripts. The appropriate changes are below.

foreach my $script (qw( ClassifyBLAST GetContigMagnitudes GetLibPath GetTaxIDFromGI ImportBLAST ImportDiskUsage ImportEC ImportFCP ImportGalaxy ImportMETAREP-BLAST ImportMETAREP-EC ImportMGRAST ImportPhymmBL ImportRDP ImportRDPComparison ImportTaxonomy ImportText ImportXML ))

skoren commented 10 years ago

Hi,

Thanks, this looks like it is fixed in the latest version of KronaTools on sourceforge (KronaTools is an external package to metAMOS). Not sure why it builds on my system without issues, I'm guessing a difference in perl versions/options. We should update metAMOS to use KronaTools 2.4 instead of 2.2 after testing the new release.

ondovb commented 10 years ago

Yes, this was due to a Perl syntax change, I think in Perl 5.14, and was fixed in KronaTools 2.4.

skoren commented 10 years ago

Leaving open until we update metAMOS to KronaTools 2.4

skoren commented 10 years ago

KronaTools version has been updated.