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GMOD / jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
http://jbrowse.org
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Deals with ACLs #1558

Open FredericBGA opened 3 years ago

FredericBGA commented 3 years ago

-d and -w test operators do not seem to respect the acls. use filetest pragma

rbuels commented 3 years ago

@FredericBGA will this affect the minimum version of Perl that the tools require?

cmdcolin commented 3 years ago

this also is only applied to IndexNames e.g. generate-names...is it something that needs distributing more widely?

more reading on filetest here https://perldoc.perl.org/filetest

cmdcolin commented 3 years ago

I also wonder: what was the error before this change was added? Was it unable to write things it should have been able to write to?

FredericBGA commented 3 years ago

The error was:

Output directory '.' is not writable. at /softs/bioinfo/jbrowse-1.16.10-release/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7. Bio::JBrowse::ConfigurationManager::ANON("Output directory '.' is not writable.\x{a}") called at /softs/bioinfo/jbrowse-1.16 .10-release/bin/../src/perl5/Bio/JBrowse/Cmd/IndexNames.pm line 73 Bio::JBrowse::Cmd::IndexNames::run(Bio::JBrowse::Cmd::IndexNames=HASH(0x2624f30)) called at /softs/bioinfo/jbrowse/bin/generate- names.pl line 8

but the directory was indeed writable due to ALCs. I don't know if this should be applied more widely. We use JBrowse a lot and we didn't notice anything else that looks related. Regarding the Perl minimun version, I don't know... We have v5.10.1. filetest seems to exist since Perl 5.6.0: https://metacpan.org/pod/release/GSAR/perl-5.6.0/lib/filetest.pm

cmdcolin commented 3 years ago

seems like this should be ok. it does say in the docs here https://perldoc.perl.org/filetest to consider this carefully, but if it helps and doesn't have side effects then it seems good