how to add a bed track

[qwzhang0601]

I am trying to add a track for my bed file, I used the command "flatfile-to-json.pl --bed ./data.input/bed/i4_i5.bed --tracklabel i4i5 --out ./data.apollo", but get following errors. I can prepare gff track successfully. Not clear what's wrong. Do you have any suggestions? thanks.

#errors
Can't locate Bio/FeatureIO.pm in @inc (you may need to install the Bio::FeatureIO module) (@inc contains: /Users/qwzhang/Documents/tools/Apollo/jbrowse/bin/../src/perl5 /Users/qwzhang/Documents/tools/vcftools_0.1.13/perl /Users/qwzhang/Library/ActivePerl-5.26/lib /usr/local/ActivePerl-5.26/site/lib /usr/local/ActivePerl-5.26/lib) at /Users/qwzhang/Documents/tools/Apollo/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 158.
at /Users/qwzhang/Documents/tools/Apollo/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.
Bio::JBrowse::ConfigurationManager::ANON("Can't locate Bio/FeatureIO.pm in @inc (you may need to instal"...) called at /Users/qwzhang/Documents/tools/Apollo/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 158
Bio::JBrowse::Cmd::FlatFileToJson::make_bed_stream(Bio::JBrowse::Cmd::FlatFileToJson=HASH(0x7fa77d8030a0)) called at /Users/qwzhang/Documents/tools/Apollo/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 118
Bio::JBrowse::Cmd::FlatFileToJson::run(Bio::JBrowse::Cmd::FlatFileToJson=HASH(0x7fa77d8030a0)) called at /Users/qwzhang/Documents/tools/Apollo/jbrowse/bin/flatfile-to-json.pl line 9

#My bed file
Contig25 10847917 10847543 i4.1 100 -
Contig25 10850493 10850351 i4.2 100 -
Contig25 10841461 10840918 i5.1 99 -
Contig25 10850686 10850351 i5.2 99 -
Contig25 10854061 10853736 i5.3 97 -
Contig25 10854358 10854150 i5.4 100 -
Contig25 10847018 10846971 i5.5 100 -
Contig25 10847917 10847868 i5.6 98 -

[cmdcolin]

@qwzhang0601 sorry for the delay, this is the jbrowse 2 forum technically

this appears to be somewhat an Apollo issue, since it appears to suggest that at the least jbrowse's dependencies were not installed correctly by the apollo installation

I might recommend to download jbrowse by itself, run setup.sh in jbrowse, so you can use jbrowse tools. That way you are not bound by possible issues with Apollo's installation of the jbrowse tools.