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Bioperl update causing tests to fail #1310

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cmdcolin opened this Issue Feb 6, 2019 · 7 comments

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cmdcolin commented Feb 6, 2019

Need to investigate if this causes actual code in normal use cases to fail via setup.sh

Recent releases here https://metacpan.org/release/BioPerl

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cmdcolin commented Feb 6, 2019

@mortimersebastian

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mortimersebastian commented Feb 8, 2019

I am having this same issue on macOS Sierra.

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cmdcolin commented Feb 8, 2019

@mortimersebastian thanks for reporting. This bioperl update affected quite a few things, there are some basic functions that you can still use in JBrowse though e.g. prepare-refseqs.pl, flatfile-to-json.pl and generate-names.pl should still work

Note that if you want full functionality, you can manually install the older version of BioPerl

Example

rm -rf extlib # inside the jbrowse directory
cpanm https://github.com/bioperl/bioperl-live/archive/release-1-7-2.tar.gz
./setup.sh

I think this will get the older bioperl and keep it through the installation

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keiranmraine commented Feb 14, 2019

FYI, I had to add the following to build the new BioPerl:

   - libxml2-dev
   - libgd-dev
   - libdb-dev

Looks like they've merged some bits back in,

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cmdcolin commented Feb 14, 2019

@keiranmraine which version of bioperl are you referring to? BioPerl 1.7.3+ underwent a big change where many core BioPerl packages were moved into separate ones. see changelog here https://metacpan.org/release/CDRAUG/BioPerl-1.7.3

One module, Bio::DB::SeqFeature::Store which jbrowse depends on had this happen so setup.sh does not get it currently, and actually Bio::DB::SeqFeature::Store still needs uploading to cpan.

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keiranmraine commented Feb 15, 2019

It may have been the change coincided with changes to the underlying travis build hosts, we had lots of things suddenly start failing. It was 1.7.4 though.

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cmdcolin commented Feb 15, 2019

Attempted fix is on dev, pins to Bio::Perl@1.7.2. The method can be fooled but should be better than what's currently there which is just sorta broken

Proper fix would be to upload some modules that were lost in translation but unknown timeline on that

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