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INCATools / biosample-analysis

analysis of biosamples in INSDC
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Perl modules required by Makefile recipes #57

Closed turbomam closed 7 months ago

turbomam commented 3 years ago 
make target/harmonized-attributes-only-eav.tsv

gzip -dc downloads/biosample_set.xml.gz | ./util/harmonized-attributes-only-eav.pl > target/harmonized-attributes-only-eav.tsv Can't locate Text/Trim.pm in @INC (you may need to install the Text::Trim module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at ./util/harmonized-attributes-only-eav.pl line 2. BEGIN failed--compilation aborted at ./util/harmonized-attributes-only-eav.pl line 2. make: *** [target/harmonized-attributes-only-eav.tsv] Error 2

perl -MCPAN -e'install Text::Trim' with "mostly automatic CPAN configuration" solved the problem for me.

I have been closing and restarting my shell after these CPAN installations. Is that really necessary?

turbomam commented 3 years ago 
make target/harmonized-attribute-value.ttl

gzip -dc target/harmonized-values-eav.tsv.gz | ./util/harmonized-eav-to-rdf.pl > target/harmonized-attribute-value.ttl Can't locate String/Util.pm in @INC (you may need to install the String::Util module) (@INC contains: /Users/MAM/perl5/lib/perl5/5.18.4/darwin-thread-multi-2level /Users/MAM/perl5/lib/perl5/5.18.4 /Users/MAM/perl5/lib/perl5/darwin-thread-multi-2level /Users/MAM/perl5/lib/perl5 /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at ./util/harmonized-eav-to-rdf.pl line 2. BEGIN failed--compilation aborted at ./util/harmonized-eav-to-rdf.pl line 2. make: *** [target/harmonized-attribute-value.ttl] Error 2

Note

'YAML' not installed, will not store persistent state