1039 lines
54 KiB
Text
1039 lines
54 KiB
Text
perl-blead
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==========
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cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux
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Work directory is /home/ryan/.cpanm/work/1493402765.5542
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You have make /usr/bin/make
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You have LWP 6.26
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You have /bin/tar: tar (GNU tar) 1.29
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Copyright (C) 2015 Free Software Foundation, Inc.
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License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
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This is free software: you are free to change and redistribute it.
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There is NO WARRANTY, to the extent permitted by law.
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Written by John Gilmore and Jay Fenlason.
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You have /usr/bin/unzip
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Searching Bio::DB::GFF::Aggregator::reftranscript () on cpanmetadb ...
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Unpacking GBrowse-2.56.tar.gz
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--> Working on Bio::DB::GFF::Aggregator::reftranscript
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Fetching http://www.cpan.org/authors/id/L/LD/LDS/GBrowse-2.56.tar.gz ... OK
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GBrowse-2.56
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GBrowse-2.56/Build.PL
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GBrowse-2.56/Changes
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GBrowse-2.56/DISCLAIMER
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GBrowse-2.56/INSTALL
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GBrowse-2.56/LICENSE
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GBrowse-2.56/MANIFEST
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GBrowse-2.56/META.json
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GBrowse-2.56/META.yml
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GBrowse-2.56/Makefile.PL
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GBrowse-2.56/README
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GBrowse-2.56/README.IF.GBROWSE.ISNT.WORKING
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GBrowse-2.56/README.fedora_and_selinux
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GBrowse-2.56/README.gff3
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GBrowse-2.56/bin
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GBrowse-2.56/bin/auto_install_databases.pl
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GBrowse-2.56/bin/bed2gff3.pl
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GBrowse-2.56/bin/bp_load_gff.pl
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GBrowse-2.56/bin/gbrowse_aws_balancer.pl
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GBrowse-2.56/bin/gbrowse_change_passwd.pl
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GBrowse-2.56/bin/gbrowse_clean.pl
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GBrowse-2.56/bin/gbrowse_configure_slaves.pl
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GBrowse-2.56/bin/gbrowse_create_account.pl
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GBrowse-2.56/bin/gbrowse_grow_cloud_vol.pl
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GBrowse-2.56/bin/gbrowse_import_ucsc_db.pl
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GBrowse-2.56/bin/gbrowse_metadb_config.pl
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GBrowse-2.56/bin/gbrowse_netinstall.pl
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GBrowse-2.56/bin/gbrowse_netinstall2.pl
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GBrowse-2.56/bin/gbrowse_set_admin_passwd.pl
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GBrowse-2.56/bin/gbrowse_slave
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GBrowse-2.56/bin/gbrowse_slave_start_aws.sh
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GBrowse-2.56/bin/gbrowse_syn_load_alignment_database.pl
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GBrowse-2.56/bin/gbrowse_syn_load_alignments_msa.pl
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GBrowse-2.56/bin/gbrowse_sync_aws_slave.pl
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GBrowse-2.56/bin/gtf2gff3.pl
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GBrowse-2.56/bin/load_genbank.pl
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GBrowse-2.56/bin/make_das_conf.pl
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GBrowse-2.56/bin/process_bamfiles.pl
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GBrowse-2.56/bin/process_gadfly.pl
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GBrowse-2.56/bin/process_ncbi_human.pl
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GBrowse-2.56/bin/process_sgd.pl
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GBrowse-2.56/bin/report_missing_language_tags.pl
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GBrowse-2.56/bin/scan_gbrowse.pl
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GBrowse-2.56/bin/split_wig.pl
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GBrowse-2.56/bin/ucsc_genes2gff.pl
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GBrowse-2.56/bin/wiggle2gff3.pl
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GBrowse-2.56/cgi-bin
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GBrowse-2.56/cgi-bin/das
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GBrowse-2.56/cgi-bin/gbgff
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GBrowse-2.56/cgi-bin/gbrowse
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GBrowse-2.56/cgi-bin/gbrowse_details
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GBrowse-2.56/cgi-bin/gbrowse_gmap
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GBrowse-2.56/cgi-bin/gbrowse_img
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GBrowse-2.56/cgi-bin/gbrowse_key_img
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GBrowse-2.56/cgi-bin/gbrowse_login
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GBrowse-2.56/cgi-bin/gbrowse_syn
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GBrowse-2.56/conf
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GBrowse-2.56/conf/GBrowse.conf
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GBrowse-2.56/conf/aws_balancer.conf
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GBrowse-2.56/conf/detail_select_menu.conf
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GBrowse-2.56/conf/enzymes.txt
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GBrowse-2.56/conf/log4perl.conf
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GBrowse-2.56/conf/pop_demo.conf
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GBrowse-2.56/conf/renderfarm.conf
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GBrowse-2.56/conf/slave_preload.conf
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GBrowse-2.56/conf/submitter_plugin.conf
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GBrowse-2.56/conf/volvox.conf
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GBrowse-2.56/conf/yeast_chr1+2.conf
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GBrowse-2.56/conf/yeast_renderfarm.conf
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GBrowse-2.56/conf/yeast_simple.conf
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GBrowse-2.56/conf/MobyServices
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GBrowse-2.56/conf/MobyServices/GbrowseServices.PMS
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GBrowse-2.56/conf/MobyServices/GbrowseServices.pm
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GBrowse-2.56/conf/MobyServices/b64_encoded_gif_renderer.pm
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GBrowse-2.56/conf/MobyServices/b64_encoded_jpeg_renderer.pm
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GBrowse-2.56/conf/MobyServices/moby.conf
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GBrowse-2.56/conf/MobyServices/text_formatted_renderer.pm
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GBrowse-2.56/conf/MobyServices/text_html_renderer.pm
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GBrowse-2.56/conf/MobyServices/text_plain_renderer.pm
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GBrowse-2.56/conf/MobyServices/text_xml_renderer.pm
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GBrowse-2.56/conf/languages
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GBrowse-2.56/conf/languages/POSIX.pm
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GBrowse-2.56/conf/languages/de.pm
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GBrowse-2.56/conf/languages/en.pm
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GBrowse-2.56/conf/languages/es.pm
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GBrowse-2.56/conf/languages/fr.pm
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GBrowse-2.56/conf/languages/is.pm
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GBrowse-2.56/conf/languages/it.pm
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GBrowse-2.56/conf/languages/ja.pm
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GBrowse-2.56/conf/languages/ko.pm
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GBrowse-2.56/conf/languages/nl.pm
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GBrowse-2.56/conf/languages/pl.pm
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GBrowse-2.56/conf/languages/ru.pm
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GBrowse-2.56/conf/languages/zh.pm
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GBrowse-2.56/conf/languages/zh_cn.pm
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GBrowse-2.56/conf/plugins
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GBrowse-2.56/conf/plugins/AlignTwoSequences.pm
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GBrowse-2.56/conf/plugins/Aligner.pm
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GBrowse-2.56/conf/plugins/AttributeHiliter.pm
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GBrowse-2.56/conf/plugins/BatchDumper.pm
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GBrowse-2.56/conf/plugins/Blat.pm
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GBrowse-2.56/conf/plugins/CMapDumper.pm
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GBrowse-2.56/conf/plugins/CreateBlastDB.pm
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GBrowse-2.56/conf/plugins/FBTableDumper.pm
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GBrowse-2.56/conf/plugins/FastaDumper.pm
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GBrowse-2.56/conf/plugins/FilterTest.pm
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GBrowse-2.56/conf/plugins/GeneFinder.pm
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GBrowse-2.56/conf/plugins/LDAPAuthenticate.pm
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GBrowse-2.56/conf/plugins/OligoFinder.pm
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GBrowse-2.56/conf/plugins/PamAuthenticate.pm
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GBrowse-2.56/conf/plugins/PrimerDesigner.pm
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GBrowse-2.56/conf/plugins/ProteinDumper.pm
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GBrowse-2.56/conf/plugins/RandomGene.pm
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GBrowse-2.56/conf/plugins/RestrictionAnnotator.pm
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GBrowse-2.56/conf/plugins/SequenceDumper.pm
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GBrowse-2.56/conf/plugins/SimpleTrackFinder.pm
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GBrowse-2.56/conf/plugins/SinWave.pm
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GBrowse-2.56/conf/plugins/SourceTrackFinder.pm
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GBrowse-2.56/conf/plugins/Spectrogram.pm
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GBrowse-2.56/conf/plugins/Submitter.pm
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GBrowse-2.56/conf/plugins/TestAuthenticator.pm
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GBrowse-2.56/conf/plugins/TestFinder.pm
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GBrowse-2.56/conf/plugins/TrackDumper.pm
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GBrowse-2.56/conf/plugins/TrackFinder.pm
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GBrowse-2.56/conf/plugins/test.pm
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GBrowse-2.56/conf/synteny
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GBrowse-2.56/conf/synteny/oryza.synconf.disabled.conf
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GBrowse-2.56/conf/synteny/rice_synteny.conf
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GBrowse-2.56/conf/synteny/wild_rice_synteny.conf
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GBrowse-2.56/conf/themes
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GBrowse-2.56/conf/themes/solid_gray_colors
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GBrowse-2.56/conf/themes/transparent_colors
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GBrowse-2.56/conf/themes/warm_colors
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GBrowse-2.56/contrib
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GBrowse-2.56/contrib/README
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GBrowse-2.56/contrib/ace2gff.pl
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GBrowse-2.56/contrib/blast2gff.pl
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GBrowse-2.56/contrib/gdump.pl
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GBrowse-2.56/contrib/import_ncbi_mv_hs.pl
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GBrowse-2.56/contrib/AxtPairwise_convert
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GBrowse-2.56/contrib/AxtPairwise_convert/axt2phy.pl
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GBrowse-2.56/contrib/Coverage
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GBrowse-2.56/contrib/Coverage/INSTALL
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GBrowse-2.56/contrib/Coverage/README
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GBrowse-2.56/contrib/Coverage/plugin
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GBrowse-2.56/contrib/Coverage/plugin/Coverage.pm
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GBrowse-2.56/contrib/GeneFinder
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GBrowse-2.56/contrib/GeneFinder/genefinder
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GBrowse-2.56/contrib/GeneFinder/genefinder/README
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GBrowse-2.56/contrib/GeneFinder/genefinder/gfcode.c
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GBrowse-2.56/contrib/GeneFinder/genefinder/readseq.c
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GBrowse-2.56/contrib/GeneFinder/genefinder/readseq.h
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/cds.hex
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/gftables
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/newnem.atg
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/newnem.codon
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/newnem.gene
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/newnem.intron3
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/newnem.intron5
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/ref.hist
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/zk637.atg
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/zk637.intron3
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/zk637.intron5
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GBrowse-2.56/contrib/GeneFinder/nematode_gftables/zk637.trinuc
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GBrowse-2.56/contrib/SynView
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GBrowse-2.56/contrib/SynView/README
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GBrowse-2.56/contrib/SynView/MAL11
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GBrowse-2.56/contrib/SynView/MAL11/MAL11.conf
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GBrowse-2.56/contrib/SynView/MAL11/MAL11.fa
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GBrowse-2.56/contrib/SynView/MAL11/MAL11.gff3
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GBrowse-2.56/contrib/SynView/cgi-lib
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS/GUS.pm
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS/GUS
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS/GUS/Segment.pm
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS/GUS/Segment
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS/GUS/Segment/Feature.pm
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS/Util
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GBrowse-2.56/contrib/SynView/cgi-lib/DAS/Util/SqlParser.pm
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GBrowse-2.56/contrib/SynView/gbrowse.conf
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GBrowse-2.56/contrib/SynView/gbrowse.conf/plasmodb.conf
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GBrowse-2.56/contrib/SynView/gbrowse.conf/plasmodb.xml
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GBrowse-2.56/contrib/TextDumper
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GBrowse-2.56/contrib/TextDumper/README
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GBrowse-2.56/contrib/TextDumper/TextDumper.pm
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GBrowse-2.56/contrib/conf_files
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GBrowse-2.56/contrib/conf_files/01.yeast.conf
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GBrowse-2.56/contrib/conf_files/02.wormbase.conf
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GBrowse-2.56/contrib/conf_files/03.fly.conf
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GBrowse-2.56/contrib/conf_files/04.human.conf
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GBrowse-2.56/contrib/conf_files/05.embl_proxy.conf
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GBrowse-2.56/contrib/conf_files/06.biosql.conf
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GBrowse-2.56/contrib/conf_files/07.chado.conf
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GBrowse-2.56/contrib/conf_files/08.genbank.conf
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GBrowse-2.56/contrib/conf_files/09.human_karyotype.conf
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GBrowse-2.56/contrib/conf_files/index.html
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GBrowse-2.56/contrib/conf_files/wormbase.syn
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GBrowse-2.56/contrib/install_macosx
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GBrowse-2.56/contrib/install_macosx/BuildConfig.pm
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GBrowse-2.56/contrib/install_macosx/README.html
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GBrowse-2.56/contrib/install_macosx/README.pod
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GBrowse-2.56/contrib/install_macosx/scripts
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GBrowse-2.56/contrib/install_macosx/scripts/build-gbrowse.pl
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GBrowse-2.56/contrib/install_macosx/scripts/build-libraries.pl
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GBrowse-2.56/docs
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GBrowse-2.56/docs/Gbrowse_Color_Palette.pdf
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GBrowse-2.56/docs/README.AWS
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GBrowse-2.56/docs/README.tutorial
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GBrowse-2.56/docs/login.sql
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GBrowse-2.56/docs/developer_notes
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GBrowse-2.56/docs/developer_notes/README.rearchitecture
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GBrowse-2.56/docs/developer_notes/README.sharing_tracks
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GBrowse-2.56/docs/example_remote_configs
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GBrowse-2.56/docs/example_remote_configs/volvox_local.conf
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GBrowse-2.56/docs/example_remote_configs/volvox_remote.conf
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GBrowse-2.56/docs/example_remote_configs/volvox_slave.conf
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GBrowse-2.56/docs/pod
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GBrowse-2.56/docs/pod/BIOSQL_ADAPTER_HOWTO.pod
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GBrowse-2.56/docs/pod/CONFIGURE_HOWTO.pod
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GBrowse-2.56/docs/pod/CONTROLLER.pod
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GBrowse-2.56/docs/pod/DAS_HOWTO.pod
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GBrowse-2.56/docs/pod/FAQ.pod
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GBrowse-2.56/docs/pod/GBROWSE_IMG.pod
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GBrowse-2.56/docs/pod/GENBANK_HOWTO.pod
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GBrowse-2.56/docs/pod/INSTALL.MacOSX.pod
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GBrowse-2.56/docs/pod/INSTALL.pod
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GBrowse-2.56/docs/pod/MAKE_IMAGES_HOWTO.pod
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GBrowse-2.56/docs/pod/ORACLE_AND_POSTGRESQL.pod
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GBrowse-2.56/docs/pod/PLUGINS_HOWTO.pod
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GBrowse-2.56/docs/pod/README-berkeley-gadfly.pod
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GBrowse-2.56/docs/pod/README-chado.pod
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GBrowse-2.56/docs/pod/README-gff-files.pod
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GBrowse-2.56/docs/pod/README-lucegene.pod
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GBrowse-2.56/etc
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GBrowse-2.56/etc/default
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GBrowse-2.56/etc/default/gbrowse-aws-balancer
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GBrowse-2.56/etc/default/gbrowse-slave
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GBrowse-2.56/etc/init.d
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GBrowse-2.56/etc/init.d/gbrowse-aws-balancer
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GBrowse-2.56/etc/init.d/gbrowse-slave
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GBrowse-2.56/htdocs
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GBrowse-2.56/htdocs/annotation_help.html
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GBrowse-2.56/htdocs/cloud_index.html
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GBrowse-2.56/htdocs/gbrowse_karyotype_help.html
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GBrowse-2.56/htdocs/gbrowse_syn_help.html
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GBrowse-2.56/htdocs/general_help.html
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GBrowse-2.56/htdocs/general_help.html.zh
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GBrowse-2.56/htdocs/gmod_cog.jpeg
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GBrowse-2.56/htdocs/index.html
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GBrowse-2.56/htdocs/vbox_index.html
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GBrowse-2.56/htdocs/css
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GBrowse-2.56/htdocs/css/gbrowse.css
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GBrowse-2.56/htdocs/css/gbrowse_autocomplete.css
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GBrowse-2.56/htdocs/css/gbrowse_elements.css
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GBrowse-2.56/htdocs/css/gbrowse_solid.css
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GBrowse-2.56/htdocs/css/gbrowse_transparent.css
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GBrowse-2.56/htdocs/css/gbrowse_warm.css
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GBrowse-2.56/htdocs/css/karyotype.css
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GBrowse-2.56/htdocs/css/menulink.png
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GBrowse-2.56/htdocs/css/menulink_active.png
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GBrowse-2.56/htdocs/css/snapshots.css
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GBrowse-2.56/htdocs/css/subtracktable.css
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GBrowse-2.56/htdocs/css/titlebar-default.css
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GBrowse-2.56/htdocs/css/titlebar-safari.css
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GBrowse-2.56/htdocs/css/tracks.css
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GBrowse-2.56/htdocs/css/dropdown
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GBrowse-2.56/htdocs/css/dropdown/default_theme.css
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GBrowse-2.56/htdocs/css/dropdown/dropdown.css
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GBrowse-2.56/htdocs/css/dropdown/helper.css
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GBrowse-2.56/htdocs/css/dropdown/images
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GBrowse-2.56/htdocs/css/dropdown/images/favicon.ico
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GBrowse-2.56/htdocs/css/dropdown/images/icon.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-down-on.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-down-open.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-down.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-left-on.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-left-open.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-left.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-right-on.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-right-open.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-right.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-up-on.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-up-open.png
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GBrowse-2.56/htdocs/css/dropdown/images/nav-arrow-up.png
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GBrowse-2.56/htdocs/css/dropdown/images/pattern1.png
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GBrowse-2.56/htdocs/css/dropdown/images/pattern2.png
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GBrowse-2.56/htdocs/css/dropdown/images/pattern3.png
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GBrowse-2.56/htdocs/example_scripts
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GBrowse-2.56/htdocs/example_scripts/README
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GBrowse-2.56/htdocs/example_scripts/gbrowse_get_sessionid.pl
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GBrowse-2.56/htdocs/example_scripts/gbrowse_new_sessionid.pl
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GBrowse-2.56/htdocs/example_scripts/gbrowse_upload_data.pl
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GBrowse-2.56/install_util
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GBrowse-2.56/install_util/GBrowseGuessDirectories.pm
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GBrowse-2.56/install_util/GBrowseInstall.pm
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GBrowse-2.56/install_util/InstallUtil.pm
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GBrowse-2.56/install_util/cgi_install.pl
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GBrowse-2.56/install_util/conf_install.pl
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GBrowse-2.56/install_util/gbrowse_ppm_install.pl
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GBrowse-2.56/install_util/htdocs_install.pl
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GBrowse-2.56/install_util/make_clean_add.pl
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GBrowse-2.56/install_util/pod2docs.pl
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GBrowse-2.56/install_util/sync-bioperl.sh
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GBrowse-2.56/install_util/tag.pl
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GBrowse-2.56/lib
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GBrowse-2.56/lib/Bio
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GBrowse-2.56/lib/Bio/DB
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GBrowse-2.56/lib/Bio/DB/Tagger.pm
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GBrowse-2.56/lib/Bio/DB/GFF
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GBrowse-2.56/lib/Bio/DB/GFF/Aggregator
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GBrowse-2.56/lib/Bio/DB/GFF/Aggregator/match_gap.pm
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GBrowse-2.56/lib/Bio/DB/GFF/Aggregator/reftranscript.pm
|
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GBrowse-2.56/lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
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GBrowse-2.56/lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
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GBrowse-2.56/lib/Bio/DB/SeqFeature
|
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GBrowse-2.56/lib/Bio/DB/SeqFeature/Store
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GBrowse-2.56/lib/Bio/DB/SeqFeature/Store/Alias.pm
|
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GBrowse-2.56/lib/Bio/DB/SeqFeature/Store/BedLoader.pm
|
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GBrowse-2.56/lib/Bio/DB/SeqFeature/Store/LoadHelper.pm
|
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GBrowse-2.56/lib/Bio/DB/Tagger
|
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GBrowse-2.56/lib/Bio/DB/Tagger/Tag.pm
|
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GBrowse-2.56/lib/Bio/DB/Tagger/mysql.pm
|
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GBrowse-2.56/lib/Bio/Graphics
|
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GBrowse-2.56/lib/Bio/Graphics/Browser2.pm
|
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GBrowse-2.56/lib/Bio/Graphics/GBrowseFeature.pm
|
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GBrowse-2.56/lib/Bio/Graphics/Karyotype.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Action.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/CAlign.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/CAlign.xs
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GBrowse-2.56/lib/Bio/Graphics/Browser2/CachedTrack.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataBase.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataSource.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/ExternalData.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/GFFhelper.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/I18n.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Markup.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/OptionPick.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/PadAlignment.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Plugin.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/PluginSet.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Realign.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Region.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/RegionSearch.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/RemoteSet.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/RenderPanels.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/SendMail.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Session.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Shellwords.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/SubtrackTable.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/TrackDumper.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/UserDB.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/UserTracks.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Util.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/archive.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/bam.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/bed.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/bigbed.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/featurefile.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/generic.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/gff.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/gff3.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/sam.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/useq.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/wig2bigwig.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/DataLoader/wiggle.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Plugin
|
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Plugin/AuthPlugin.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/HTML.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/Login.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/Slave.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/SnapshotManager.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/TrackConfig.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/HTML
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/HTML/TrackListing.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/HTML/TrackListing
|
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/HTML/TrackListing/Categories.pm
|
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/Slave
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/Slave/AWS_Balancer.pm
|
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GBrowse-2.56/lib/Bio/Graphics/Browser2/Render/Slave/Status.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/TrackDumper
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GBrowse-2.56/lib/Bio/Graphics/Browser2/TrackDumper/RichSeqMaker.pm
|
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GBrowse-2.56/lib/Bio/Graphics/Browser2/UserTracks
|
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GBrowse-2.56/lib/Bio/Graphics/Browser2/UserTracks/Database.pm
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GBrowse-2.56/lib/Bio/Graphics/Browser2/UserTracks/Filesystem.pm
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GBrowse-2.56/lib/CGI
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GBrowse-2.56/lib/CGI/Toggle.pm
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GBrowse-2.56/lib/Legacy
|
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GBrowse-2.56/lib/Legacy/DB
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GBrowse-2.56/lib/Legacy/DB/SyntenyBlock.pm
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GBrowse-2.56/lib/Legacy/DB/SyntenyIO.pm
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GBrowse-2.56/lib/Legacy/Graphics
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GBrowse-2.56/lib/Legacy/Graphics/Browser.pm
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GBrowse-2.56/lib/Legacy/Graphics/Browser
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GBrowse-2.56/lib/Legacy/Graphics/Browser/I18n.pm
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GBrowse-2.56/lib/Legacy/Graphics/Browser/PageSettings.pm
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GBrowse-2.56/lib/Legacy/Graphics/Browser/Synteny.pm
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GBrowse-2.56/lib/Legacy/Graphics/Browser/Util.pm
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GBrowse-2.56/libalign
|
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GBrowse-2.56/libalign/CAlign.pm
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GBrowse-2.56/libalign/CAlign.xs
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GBrowse-2.56/libalign/Changes
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GBrowse-2.56/libalign/README
|
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GBrowse-2.56/libalign/realign.h
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GBrowse-2.56/sample_data
|
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GBrowse-2.56/sample_data/admin_uploads
|
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GBrowse-2.56/sample_data/admin_uploads/README
|
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GBrowse-2.56/sample_data/gbrowse_syn
|
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GBrowse-2.56/sample_data/gbrowse_syn/alignments
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GBrowse-2.56/sample_data/gbrowse_syn/alignments/rice.aln.gz
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GBrowse-2.56/sample_data/gbrowse_syn/rice
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GBrowse-2.56/sample_data/gbrowse_syn/rice/rice.gff3
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GBrowse-2.56/sample_data/gbrowse_syn/wild_rice
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GBrowse-2.56/sample_data/gbrowse_syn/wild_rice/wild_rice.gff3
|
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GBrowse-2.56/sample_data/ideograms
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GBrowse-2.56/sample_data/ideograms/human_cytobands.gff
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GBrowse-2.56/sample_data/ideograms/mouse_cytobands.gff
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GBrowse-2.56/sample_data/ideograms/rat_cytobands.gff
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GBrowse-2.56/sample_data/pop_demo
|
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GBrowse-2.56/sample_data/pop_demo/pop_demo.gff3
|
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GBrowse-2.56/sample_data/yeast_chr1+2
|
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GBrowse-2.56/sample_data/yeast_chr1+2/dummy.fa
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GBrowse-2.56/sample_data/yeast_chr1+2/yeast_chr1+2.gff3
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GBrowse-2.56/sample_data/yeast_scaffolds
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GBrowse-2.56/sample_data/yeast_scaffolds/chr1.fa
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GBrowse-2.56/sample_data/yeast_scaffolds/chr2.fa
|
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GBrowse-2.56/sample_data/yeast_scaffolds/chromosomes.gff3
|
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GBrowse-2.56/t
|
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GBrowse-2.56/t/00.compile.t
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GBrowse-2.56/t/01.yeast.t
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GBrowse-2.56/t/02.rearchitecture.t
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GBrowse-2.56/t/03.render.t
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GBrowse-2.56/t/04.remoteserver.t
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GBrowse-2.56/t/05.deferredrendering.t
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GBrowse-2.56/t/06.featuresearch.t
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GBrowse-2.56/t/07.balancer.t
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GBrowse-2.56/t/07.karyotype.t
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GBrowse-2.56/t/08.calign.t
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GBrowse-2.56/t/Test.pm
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GBrowse-2.56/t/testdata
|
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GBrowse-2.56/t/testdata/TemplateCopy.pm
|
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GBrowse-2.56/t/testdata/conf
|
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GBrowse-2.56/t/testdata/conf/GBrowse.conf
|
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GBrowse-2.56/t/testdata/conf/WHERE_ARE_THE_CONF_FILES.txt
|
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GBrowse-2.56/t/testdata/conf/aws_slave.conf
|
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GBrowse-2.56/t/testdata/conf/enzymes.txt
|
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GBrowse-2.56/t/testdata/conf/languages
|
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GBrowse-2.56/t/testdata/conf/languages/POSIX.pm
|
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GBrowse-2.56/t/testdata/conf/languages/fr.pm
|
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GBrowse-2.56/t/testdata/conf/templates
|
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GBrowse-2.56/t/testdata/conf/templates/volvox_final.conf
|
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GBrowse-2.56/t/testdata/conf/templates/yeast_chr1.conf
|
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GBrowse-2.56/t/testdata/data
|
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GBrowse-2.56/t/testdata/data/volvox
|
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GBrowse-2.56/t/testdata/data/volvox/dummy.fa
|
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GBrowse-2.56/t/testdata/data/volvox/volvox.gff
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GBrowse-2.56/t/testdata/data/volvox2
|
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GBrowse-2.56/t/testdata/data/volvox2/dummy.fa
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GBrowse-2.56/t/testdata/data/volvox2/volvox2.gff
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GBrowse-2.56/t/testdata/data/volvox3
|
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GBrowse-2.56/t/testdata/data/volvox3/dummy.fa
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GBrowse-2.56/t/testdata/data/volvox3/volvox3.gff
|
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GBrowse-2.56/t/testdata/data/volvox4
|
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GBrowse-2.56/t/testdata/data/volvox4/dummy.fa
|
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GBrowse-2.56/t/testdata/data/volvox4/volvox4.gff
|
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GBrowse-2.56/t/testdata/phylo_align
|
|
GBrowse-2.56/t/testdata/phylo_align/phyloalign.fa
|
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GBrowse-2.56/t/testdata/phylo_align/readme.txt
|
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GBrowse-2.56/t/testdata/phylo_align/species.tre
|
|
GBrowse-2.56/t/testdata/phylo_align/volvox_alignment.conf
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GBrowse-2.56/t/testdata/phylo_align/volvox_phyloalign.gff
|
|
Entering GBrowse-2.56
|
|
Checking configure dependencies from META.json
|
|
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
|
|
Checking if you have Module::Build 0.42 ... Yes (0.4222)
|
|
Running Build.PL
|
|
Configuring GBrowse-2.56 ... Checking prerequisites...
|
|
recommends:
|
|
* Bio::DB::BigFile is not installed
|
|
* DB_File::Lock is not installed
|
|
* Net::OpenID::Consumer is not installed
|
|
* Do not worry if some "recommended" prerequisites are missing. You can install *
|
|
* them later if you need the features they provide. Do not proceed with the *
|
|
* install if any of "REQUIRED" prerequisites are missing. *
|
|
* *
|
|
* The optional Safe::World module does not currently run on Perl 5.10 or *
|
|
* higher, and so cannot be installed. *
|
|
|
|
|
|
ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions
|
|
of the modules indicated above before proceeding with this installation
|
|
|
|
**** WARNING *****************************************************************************************
|
|
If you are upgrading from an earlier version of GBrowse and wish to use named user accounts, please
|
|
set "user_accounts" to 1 in /etc/gbrowse2/GBrowse.conf and run bin/gbrowse_metadb_config.pl to
|
|
create/update your user account database.
|
|
|
|
See /etc/gbrowse2/GBrowse.conf.new for suggested settings.
|
|
******************************************************************************************************
|
|
Now run:
|
|
./Build test
|
|
./Build demo (optional)
|
|
./Build install (as superuser/administrator)
|
|
-or-
|
|
./Build install_slave (optional, for slave installations)
|
|
|
|
Other useful targets:
|
|
./Build register (to register your copy of GBrowse)
|
|
./Build reconfig (to reconfigure install locations)
|
|
./Build demostop (to stop the demo)
|
|
Created MYMETA.yml and MYMETA.json
|
|
Creating new 'Build' script for 'GBrowse' version '2.56'
|
|
Checking dependencies from MYMETA.json ...
|
|
Checking if you have CGI::Session 4.02 ... Yes (4.48)
|
|
Checking if you have Time::HiRes 0 ... Yes (1.9741)
|
|
Checking if you have Date::Parse 0 ... Yes (2.30)
|
|
Checking if you have Capture::Tiny 0 ... Yes (0.40)
|
|
Checking if you have Statistics::Descriptive 0 ... Yes (3.0612)
|
|
Checking if you have LWP 0 ... Yes (6.26)
|
|
Checking if you have ExtUtils::CBuilder 0 ... Yes (0.280224)
|
|
Checking if you have parent 0 ... Yes (0.236)
|
|
Checking if you have IO::String 0 ... Yes (1.08)
|
|
Checking if you have GD 2.50 ... Yes (2.66)
|
|
Checking if you have Storable 0 ... Yes (2.51)
|
|
Checking if you have Bio::Root::Version 1.007001 ... Yes (1.007001)
|
|
Checking if you have HTTP::Daemon 0 ... Yes (6.01)
|
|
Checking if you have File::Temp 0 ... Yes (0.2304)
|
|
Checking if you have Term::ReadKey 0 ... Yes (2.33)
|
|
Checking if you have Digest::SHA 0 ... Yes (5.96)
|
|
Checking if you have Text::ParseWords 3.27 ... Yes (3.30)
|
|
Checking if you have JSON 0 ... Yes (2.90)
|
|
Checking if you have Bio::Graphics 2.34 ... Yes (2.40)
|
|
Checking if you have Digest::MD5 0 ... Yes (2.55)
|
|
OK
|
|
Building and testing GBrowse-2.56 ...
|
|
**Beginning interactive configuration**
|
|
Directory for GBrowse's config and support files? [/etc/gbrowse2] /etc/gbrowse2
|
|
Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2] /var/www/html/gbrowse2
|
|
Directory for GBrowse's temporary data [/var/tmp/gbrowse2] /var/tmp/gbrowse2
|
|
Directory for GBrowse's sessions, uploaded tracks and other persistent data [/var/lib/gbrowse2] /var/lib/gbrowse2
|
|
Directory for GBrowse's example databases [/var/lib/gbrowse2/databases] /var/lib/gbrowse2/databases
|
|
Directory for GBrowse's CGI script executables? [/usr/local/apache/cgi-bin/gb2] /usr/local/apache/cgi-bin/gb2
|
|
|
|
******************************WARNING***********************************
|
|
GBrowse is being configured to install in /usr/local/apache, but that
|
|
directory doesn't exist, which means either Apache isn't installed
|
|
or the installer couldn't find it. If you continue with this
|
|
installation there is a good chance it won't work if Apache isn't
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installed.
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******************************WARNING***********************************
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Internet port to run demo web site on (for demo)? [8000] 8000
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Apache loadable module directory (for demo)? [/usr/lib/apache/modules] /usr/lib/apache/modules
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User account under which Apache daemon runs? [www-data] www-data
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Automatically update Apache config files to run GBrowse? [y] y
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Automatically update system config files to run gbrowse-slave? [y] y
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**Interactive configuration done. Run './Build reconfig' to reconfigure**
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Building GBrowse
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cc -I/home/ryan/.cpanm/work/1493402765.5542/GBrowse-2.56/libalign -I/home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux/CORE -DVERSION="2.56" -DXS_VERSION="2.56" -fPIC -c -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -o lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
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ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs')
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cc -shared -O2 -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.so lib/Bio/Graphics/Browser2/CAlign.o
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Performing variable substitutions in blib/conf/aws_balancer.conf
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Performing variable substitutions in blib/conf/detail_select_menu.conf
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Performing variable substitutions in blib/conf/enzymes.txt
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Performing variable substitutions in blib/conf/GBrowse.conf
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Performing variable substitutions in blib/conf/log4perl.conf
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Performing variable substitutions in blib/conf/MobyServices/moby.conf
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Performing variable substitutions in blib/conf/pop_demo.conf
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Performing variable substitutions in blib/conf/renderfarm.conf
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Performing variable substitutions in blib/conf/slave_preload.conf
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Performing variable substitutions in blib/conf/submitter_plugin.conf
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Performing variable substitutions in blib/conf/synteny/oryza.synconf.disabled.conf
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Performing variable substitutions in blib/conf/synteny/rice_synteny.conf
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Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf
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Performing variable substitutions in blib/conf/themes/solid_gray_colors
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Performing variable substitutions in blib/conf/themes/transparent_colors
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Performing variable substitutions in blib/conf/themes/warm_colors
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Performing variable substitutions in blib/conf/volvox.conf
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Performing variable substitutions in blib/conf/yeast_chr1+2.conf
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Performing variable substitutions in blib/conf/yeast_renderfarm.conf
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Performing variable substitutions in blib/conf/yeast_simple.conf
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Performing variable substitutions in blib/htdocs/annotation_help.html
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Performing variable substitutions in blib/htdocs/cloud_index.html
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Performing variable substitutions in blib/htdocs/example_scripts/index.html
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Performing variable substitutions in blib/htdocs/example_scripts/README
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Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html
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Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html
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Performing variable substitutions in blib/htdocs/general_help.html
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|
Performing variable substitutions in blib/htdocs/index.html
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf
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|
Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf
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|
Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf
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Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf
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Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html
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Performing variable substitutions in blib/htdocs/tutorial/tutorial.html
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Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html
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Performing variable substitutions in blib/htdocs/vbox_index.html
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Performing variable substitutions in blib/etc/default/gbrowse-aws-balancer
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Performing variable substitutions in blib/etc/default/gbrowse-slave
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Performing variable substitutions in blib/etc/init.d/gbrowse-aws-balancer
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Performing variable substitutions in blib/etc/init.d/gbrowse-slave
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NOTE: Run ./Build reconfig to change existing configuration.
|
|
t/00.compile.t ............ ok
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t/01.yeast.t .............. ok
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Graphics/FeatureFile.pm line 756.
|
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t/02.rearchitecture.t ..... ok
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Graphics/FeatureFile.pm line 756.
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Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.30), passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){ <-- HERE (.*?)}/ at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Inline/Echo.pm line 25.
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Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.30), passed through in regex; marked by <-- HERE in m/function(\s+)([a-z0-9_]+)(\s*){ <-- HERE (.*?)}/ at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Inline/Nouse.pm line 28.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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t/03.render.t ............. ok
|
|
Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Graphics/FeatureFile.pm line 756.
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|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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Could not open database: Can't call method "seq" on an undefined value at /home/ryan/.cpanm/work/1493402765.5542/GBrowse-2.56/t/../lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 168, <GEN3> line 19.
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Could not open database: Can't call method "seq" on an undefined value at /home/ryan/.cpanm/work/1493402765.5542/GBrowse-2.56/t/../lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 168, <GEN5> line 19.
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Could not open database: Can't call method "seq" on an undefined value at /home/ryan/.cpanm/work/1493402765.5542/GBrowse-2.56/t/../lib/Bio/DB/SeqFeature/Store/LoadHelper.pm line 168, <GEN8> line 19.
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Couldn't open database for Alignments: at /home/ryan/.cpanm/work/1493402765.5542/GBrowse-2.56/t/../lib/Bio/Graphics/Browser2/RenderPanels.pm line 1742.
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File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
t/04.remoteserver.t ....... ok
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Graphics/FeatureFile.pm line 756.
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|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
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|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
t/05.deferredrendering.t .. ok
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Graphics/FeatureFile.pm line 756.
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/DB/GFF.pm line 2000.
|
|
t/06.featuresearch.t ...... ok
|
|
t/07.balancer.t ........... ok
|
|
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Graphics/FeatureFile.pm line 756.
|
|
t/07.karyotype.t .......... ok
|
|
t/08.calign.t ............. ok
|
|
All tests successful.
|
|
Files=10, Tests=460, 16 wallclock secs ( 0.05 usr 0.00 sys + 7.94 cusr 1.20 csys = 9.19 CPU)
|
|
Result: PASS
|
|
NOTE: Run ./Build reconfig to change existing configuration.
|
|
Building GBrowse
|
|
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
|
|
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
ERROR: Can't create '/etc/default'
|
|
Do not have write permissions on '/etc/default'
|
|
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Module/Build/Base.pm line 3559.
|
|
! Installing Bio::DB::GFF::Aggregator::reftranscript failed. See /home/ryan/.cpanm/work/1493402765.5542/build.log for details. Retry with --force to force install it.
|
|
FAIL
|
|
Command [cpanm --reinstall --verbose Bio::DB::GFF::Aggregator::reftranscript] terminated with exit code 1 ($? = 256) under the following perl environment:
|
|
Command terminated with non-zero status.
|
|
|
|
|
|
Current perl:
|
|
Name: perl-blead
|
|
Path: /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl
|
|
Config: -de -Dprefix=/home/ryan/perl5/perlbrew/perls/perl-blead -Dusedevel -Aeval:scriptdir=/home/ryan/perl5/perlbrew/perls/perl-blead/bin
|
|
Compiled at: Mar 30 2017 03:10:09
|
|
|
|
perlbrew:
|
|
version: 0.78
|
|
ENV:
|
|
PERLBREW_ROOT: /home/ryan/perl5/perlbrew
|
|
PERLBREW_HOME: /home/ryan/.perlbrew
|
|
PERLBREW_PATH: /home/ryan/perl5/perlbrew/bin:/home/ryan/perl5/perlbrew/perls/perl-blead/bin
|
|
PERLBREW_MANPATH: /home/ryan/perl5/perlbrew/perls/perl-blead/man
|