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ugeneunipro / ugene

UGENE is free open-source cross-platform bioinformatics software
http://ugene.net
GNU General Public License v2.0
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ugene-37.0: No plugins listed in the GUI #293

Closed mmokrejs closed 3 years ago

mmokrejs commented 3 years ago

Hi, where is ugene looking for the plasmid files? I don't see any. Please make this configurable in the Settings too. Users would hence laso know where they are stored.

no_plugins

The logfile should have recognized this as well.

/usr
/usr/bin
/usr/bin/ugene
/usr/lib
/usr/lib/ugene
/usr/lib/ugene/libQSpec.so
/usr/lib/ugene/libU2Algorithm.so
/usr/lib/ugene/libU2Core.so
/usr/lib/ugene/libU2Designer.so
/usr/lib/ugene/libU2Formats.so
/usr/lib/ugene/libU2Gui.so
/usr/lib/ugene/libU2Lang.so
/usr/lib/ugene/libU2Private.so
/usr/lib/ugene/libU2Script.so
/usr/lib/ugene/libU2Test.so
/usr/lib/ugene/libU2View.so
/usr/lib/ugene/libbreakpad.so
/usr/lib/ugene/libugenedb.so
/usr/lib/ugene/plugins
/usr/lib/ugene/plugins/libCoreTests.so
/usr/lib/ugene/plugins/libGUITestBase.so
/usr/lib/ugene/plugins/libannotator.so
/usr/lib/ugene/plugins/libapi_tests.so
/usr/lib/ugene/plugins/libball.so
/usr/lib/ugene/plugins/libbiostruct3d_view.so
/usr/lib/ugene/plugins/libchroma_view.so
/usr/lib/ugene/plugins/libcircular_view.so
/usr/lib/ugene/plugins/libclark_support.so
/usr/lib/ugene/plugins/libdbi_bam.so
/usr/lib/ugene/plugins/libdiamond_support.so
/usr/lib/ugene/plugins/libdna_export.so
/usr/lib/ugene/plugins/libdna_flexibility.so
/usr/lib/ugene/plugins/libdna_graphpack.so
/usr/lib/ugene/plugins/libdna_stat.so
/usr/lib/ugene/plugins/libdotplot.so
/usr/lib/ugene/plugins/libenzymes.so
/usr/lib/ugene/plugins/libexternal_tool_support.so
/usr/lib/ugene/plugins/libgenome_aligner.so
/usr/lib/ugene/plugins/libgor4.so
/usr/lib/ugene/plugins/libhmm2.so
/usr/lib/ugene/plugins/libkalign.so
/usr/lib/ugene/plugins/libkraken_support.so
/usr/lib/ugene/plugins/liblinkdata_support.so
/usr/lib/ugene/plugins/libmetaphlan2_support.so
/usr/lib/ugene/plugins/libngs_reads_classification.so
/usr/lib/ugene/plugins/libopencl_support.so
/usr/lib/ugene/plugins/liborf_marker.so
/usr/lib/ugene/plugins/libpcr.so
/usr/lib/ugene/plugins/libperf_monitor.so
/usr/lib/ugene/plugins/libphylip.so
/usr/lib/ugene/plugins/libprimer3.so
/usr/lib/ugene/plugins/libpsipred.so
/usr/lib/ugene/plugins/libptools.so
/usr/lib/ugene/plugins/libquery_designer.so
/usr/lib/ugene/plugins/libremote_blast.so
/usr/lib/ugene/plugins/librepeat_finder.so
/usr/lib/ugene/plugins/libsitecon.so
/usr/lib/ugene/plugins/libsmith_waterman.so
/usr/lib/ugene/plugins/libtest_runner.so
/usr/lib/ugene/plugins/libumuscle.so
/usr/lib/ugene/plugins/libvariants.so
/usr/lib/ugene/plugins/libweight_matrix.so
/usr/lib/ugene/plugins/libwevote_support.so
/usr/lib/ugene/plugins/libworkflow_designer.so
/usr/lib/ugene/plugins_checker
/usr/lib/ugene/transl_en.qm
/usr/lib/ugene/transl_ru.qm
/usr/lib/ugene/ugene
/usr/lib/ugene/ugenecl
/usr/lib/ugene/ugenem
/usr/lib/ugene/ugeneui
/usr/share
/usr/share/applications
/usr/share/applications/ugene.desktop
/usr/share/doc
/usr/share/doc/ugene-37.0-r1
/usr/share/doc/ugene-37.0-r1/README.md.bz2
/usr/share/icons
/usr/share/icons/hicolor
/usr/share/icons/hicolor/32x32
/usr/share/icons/hicolor/32x32/mimetypes
/usr/share/icons/hicolor/32x32/mimetypes/application-x-ugene-ext.png
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/ugene.1.bz2
/usr/share/mime
/usr/share/mime/packages
/usr/share/mime/packages/application-x-ugene.xml
/usr/share/pixmaps
/usr/share/pixmaps/ugene.png
/usr/share/pixmaps/ugene.xpm
/usr/share/ugene
/usr/share/ugene/data
/usr/share/ugene/data/DBXRefRegistry.txt
/usr/share/ugene/data/adapters
/usr/share/ugene/data/adapters/adapters.fasta
/usr/share/ugene/data/adapters/illumina
/usr/share/ugene/data/adapters/illumina/NexteraPE-PE.fa
/usr/share/ugene/data/adapters/illumina/TruSeq2-PE.fa
/usr/share/ugene/data/adapters/illumina/TruSeq2-SE.fa
/usr/share/ugene/data/adapters/illumina/TruSeq3-PE-2.fa
/usr/share/ugene/data/adapters/illumina/TruSeq3-PE.fa
/usr/share/ugene/data/adapters/illumina/TruSeq3-SE.fa
/usr/share/ugene/data/back_translation
/usr/share/ugene/data/back_translation/Bacteria
/usr/share/ugene/data/back_translation/Bacteria/Arthrobacter_aurescens_TC1.cut
/usr/share/ugene/data/back_translation/Bacteria/Bacillus_subtilis.cut
/usr/share/ugene/data/back_translation/Bacteria/Escherichia_coli.cut
/usr/share/ugene/data/back_translation/Bacteria/Haemophilus_influenzae.cut
/usr/share/ugene/data/back_translation/Bacteria/Helicobacter_pylori.cut
/usr/share/ugene/data/back_translation/Bacteria/Listeria_monocytogenes.cut
/usr/share/ugene/data/back_translation/Bacteria/Neisseria_meningitidis.cut
/usr/share/ugene/data/back_translation/Bacteria/Salmonella_typhimurium_LT2.cut
/usr/share/ugene/data/back_translation/Bacteria/Streptomyces_coelicolor_A3(2).cut
/usr/share/ugene/data/back_translation/Bacteria/Sulfolobus_solfataricus_P2.cut
/usr/share/ugene/data/back_translation/Invertebrates
/usr/share/ugene/data/back_translation/Invertebrates/Apis_mellifera_(honey_bee).cut
/usr/share/ugene/data/back_translation/Invertebrates/Caenorhabditis_elegans.cut
/usr/share/ugene/data/back_translation/Invertebrates/Drosophila_melanogaster_(fruit_fly).cut
/usr/share/ugene/data/back_translation/Invertebrates/Plasmodium_falciparum_(malaria_parasite_P._falciparum).cut
/usr/share/ugene/data/back_translation/Invertebrates/mitochondrion_Caenorhabditis_elegans.cut
/usr/share/ugene/data/back_translation/Invertebrates/mitochondrion_Drosophila_melanogaster_(fruit_fly).cut
/usr/share/ugene/data/back_translation/Mammalia
/usr/share/ugene/data/back_translation/Mammalia/Bos_taurus_(cow).cut
/usr/share/ugene/data/back_translation/Mammalia/Canis_familiaris_(dog).cut
/usr/share/ugene/data/back_translation/Mammalia/Sus_scrofa_(pig).cut
/usr/share/ugene/data/back_translation/Mammalia/mitochondrion_Bos_taurus_(cow).cut
/usr/share/ugene/data/back_translation/Mammalia/mitochondrion_Sus_scrofa_(pig).cut
/usr/share/ugene/data/back_translation/Plants
/usr/share/ugene/data/back_translation/Plants/Arabidopsis_thaliana_(thale_cress).cut
/usr/share/ugene/data/back_translation/Plants/Oryza_sativa.cut
/usr/share/ugene/data/back_translation/Plants/Zea_mays.cut
/usr/share/ugene/data/back_translation/Primates
/usr/share/ugene/data/back_translation/Primates/Homo_sapiens_(human).cut
/usr/share/ugene/data/back_translation/Primates/Pan_troglodytes_(chimpanzee).cut
/usr/share/ugene/data/back_translation/Primates/mitochondrion_Homo_sapiens_(human).cut
/usr/share/ugene/data/back_translation/Primates/mitochondrion_Pan_troglodytes_(chimpanzee).cut
/usr/share/ugene/data/back_translation/Rodents
/usr/share/ugene/data/back_translation/Rodents/Mus_musculus_(house_mouse).cut
/usr/share/ugene/data/back_translation/Rodents/Rattus_norvegicus_(Norway_rat).cut
/usr/share/ugene/data/back_translation/Vertebrates
/usr/share/ugene/data/back_translation/Vertebrates/Gallus_gallus_(chicken).cut
/usr/share/ugene/data/back_translation/Vertebrates/Takifugu_rubripes_(Fugu_rubripes).cut
/usr/share/ugene/data/back_translation/Vertebrates/Xenopus_laevis_(African_clawed_frog).cut
/usr/share/ugene/data/back_translation/Vertebrates/mitochondrion_Gallus_gallus_(chicken).cut
/usr/share/ugene/data/back_translation/Vertebrates/mitochondrion_Takifugu_rubripes_(Fugu_rubripes).cut
/usr/share/ugene/data/back_translation/Viruses
/usr/share/ugene/data/back_translation/Viruses/Human_immunodeficiency_virus_1_(HIV-1).cut
/usr/share/ugene/data/back_translation/Viruses/Influenza_A_virus.cut
/usr/share/ugene/data/back_translation/Yeast
/usr/share/ugene/data/back_translation/Yeast/Saccharomyces_cerevisiae_(baker's_yeast).cut
/usr/share/ugene/data/back_translation/tables.xml
/usr/share/ugene/data/biostruct3d_plugin
/usr/share/ugene/data/biostruct3d_plugin/BioStruct3DLinks.txt
/usr/share/ugene/data/cmdline
/usr/share/ugene/data/cmdline/align-clustalo.uwl
/usr/share/ugene/data/cmdline/align-clustalw.uwl
/usr/share/ugene/data/cmdline/align-kalign.uwl
/usr/share/ugene/data/cmdline/align-mafft.uwl
/usr/share/ugene/data/cmdline/align-tcoffee.uwl
/usr/share/ugene/data/cmdline/align-to-reference.uwl
/usr/share/ugene/data/cmdline/align.uwl
/usr/share/ugene/data/cmdline/convert-msa.uwl
/usr/share/ugene/data/cmdline/convert-seq.uwl
/usr/share/ugene/data/cmdline/extract-sequence.uwl
/usr/share/ugene/data/cmdline/extract_consensus_sequence.uwl
/usr/share/ugene/data/cmdline/extract_consensus_string.uwl
/usr/share/ugene/data/cmdline/extract_coverage.uwl
/usr/share/ugene/data/cmdline/fetch-sequence.uwl
/usr/share/ugene/data/cmdline/find-orfs.uwl
/usr/share/ugene/data/cmdline/find-repeats.uwl
/usr/share/ugene/data/cmdline/find-sw.uwl
/usr/share/ugene/data/cmdline/gene-by-gene.uwl
/usr/share/ugene/data/cmdline/generate-dna.uwl
/usr/share/ugene/data/cmdline/hmm2-build.uwl
/usr/share/ugene/data/cmdline/hmm2-search.uwl
/usr/share/ugene/data/cmdline/hmm3-build-and-search.uwl
/usr/share/ugene/data/cmdline/join-quality.uwl
/usr/share/ugene/data/cmdline/local-blast+.uwl
/usr/share/ugene/data/cmdline/pfm-build.uwl
/usr/share/ugene/data/cmdline/pfm-search.uwl
/usr/share/ugene/data/cmdline/pwm-build.uwl
/usr/share/ugene/data/cmdline/pwm-search.uwl
/usr/share/ugene/data/cmdline/query.uwl
/usr/share/ugene/data/cmdline/remote-request.uwl
/usr/share/ugene/data/cmdline/revcompl.uwl
/usr/share/ugene/data/cmdline/sitecon-build.uwl
/usr/share/ugene/data/cmdline/sitecon-search.uwl
/usr/share/ugene/data/cmdline/snp.uwl
/usr/share/ugene/data/custom_annotations
/usr/share/ugene/data/custom_annotations/plasmid_features.txt
/usr/share/ugene/data/enzymes
/usr/share/ugene/data/enzymes/2013_08_01.bairoch.gz
/usr/share/ugene/data/genome_lengths
/usr/share/ugene/data/genome_lengths/danRer7.genome
/usr/share/ugene/data/genome_lengths/ecoli.genome
/usr/share/ugene/data/genome_lengths/hg18.genome
/usr/share/ugene/data/genome_lengths/hg19.genome
/usr/share/ugene/data/genome_lengths/mm10.genome
/usr/share/ugene/data/genome_lengths/mm8.genome
/usr/share/ugene/data/genome_lengths/mm9.genome
/usr/share/ugene/data/genome_lengths/test.genome
/usr/share/ugene/data/license
/usr/share/ugene/data/position_weight_matrix
/usr/share/ugene/data/position_weight_matrix/JASPAR
/usr/share/ugene/data/position_weight_matrix/JASPAR/all_jaspar.csv
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0265.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0266.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0267.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0268.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0269.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0270.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0271.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0272.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0273.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0274.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0275.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0276.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0277.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0278.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0279.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0283.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0284.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0289.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0290.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0291.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0292.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0293.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0294.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0295.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0296.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0300.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0301.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0302.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0303.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0313.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0314.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0315.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0316.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0317.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0318.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0319.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0320.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0321.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0322.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0323.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0324.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0325.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0326.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0327.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0328.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0329.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0330.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0332.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0334.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0335.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0336.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0337.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0338.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0339.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0340.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0342.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0343.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0345.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0347.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0350.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0352.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0354.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0355.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0357.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0359.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0360.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0361.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0362.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0363.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0364.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0366.1.pfm
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/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0370.1.pfm
/usr/share/ugene/data/position_weight_matrix/JASPAR/fungi/MA0371.1.pfm
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/usr/share/ugene/data/sitecon_models/eukaryotic/srf_all.sitecon.gz
/usr/share/ugene/data/sitecon_models/eukaryotic/yy1.sitecon.gz
/usr/share/ugene/data/sitecon_models/prokaryotic
/usr/share/ugene/data/sitecon_models/prokaryotic/AgaR.sitecon.gz
/usr/share/ugene/data/sitecon_models/prokaryotic/AraC.sitecon.gz
/usr/share/ugene/data/sitecon_models/prokaryotic/ArcA.sitecon.gz
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/usr/share/ugene/data/sitecon_models/prokaryotic/CysB.sitecon.gz
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/usr/share/ugene/data/sitecon_models/prokaryotic/DeoR.sitecon.gz
/usr/share/ugene/data/sitecon_models/prokaryotic/DnaA.sitecon.gz
/usr/share/ugene/data/sitecon_models/prokaryotic/FUR.sitecon.gz
/usr/share/ugene/data/sitecon_models/prokaryotic/FadR.sitecon.gz
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/usr/share/ugene/data/sitecon_models/prokaryotic/Fnr.sitecon.gz
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/usr/share/ugene/data/sitecon_models/prokaryotic/RcsB_1core.sitecon.gz
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/usr/share/ugene/data/sitecon_models/prokaryotic/Rob2.sitecon.gz
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/usr/share/ugene/data/sitecon_models/prokaryotic/fis_new1.sitecon.gz
/usr/share/ugene/data/sitecon_models/prokaryotic/soxS.sitecon.gz
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/usr/share/ugene/data/weight_matrix/pam120.txt
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/usr/share/ugene/data/weight_matrix/pam140.txt
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/usr/share/ugene/data/weight_matrix/pam170.txt
/usr/share/ugene/data/weight_matrix/pam180.txt
/usr/share/ugene/data/weight_matrix/pam190.txt
/usr/share/ugene/data/weight_matrix/pam20.txt
/usr/share/ugene/data/weight_matrix/pam200.cdi.txt
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/usr/share/ugene/data/weight_matrix/pam210.txt
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/usr/share/ugene/data/weight_matrix/pam300.txt
/usr/share/ugene/data/weight_matrix/pam310.txt
/usr/share/ugene/data/weight_matrix/pam320.txt
/usr/share/ugene/data/weight_matrix/pam330.txt
/usr/share/ugene/data/weight_matrix/pam340.txt
/usr/share/ugene/data/weight_matrix/pam350.txt
/usr/share/ugene/data/weight_matrix/pam360.txt
/usr/share/ugene/data/weight_matrix/pam370.txt
/usr/share/ugene/data/weight_matrix/pam380.txt
/usr/share/ugene/data/weight_matrix/pam390.txt
/usr/share/ugene/data/weight_matrix/pam40.cdi.txt
/usr/share/ugene/data/weight_matrix/pam40.txt
/usr/share/ugene/data/weight_matrix/pam400.txt
/usr/share/ugene/data/weight_matrix/pam410.txt
/usr/share/ugene/data/weight_matrix/pam420.txt
/usr/share/ugene/data/weight_matrix/pam430.txt
/usr/share/ugene/data/weight_matrix/pam440.txt
/usr/share/ugene/data/weight_matrix/pam450.txt
/usr/share/ugene/data/weight_matrix/pam460.txt
/usr/share/ugene/data/weight_matrix/pam470.txt
/usr/share/ugene/data/weight_matrix/pam480.txt
/usr/share/ugene/data/weight_matrix/pam490.txt
/usr/share/ugene/data/weight_matrix/pam50.txt
/usr/share/ugene/data/weight_matrix/pam500.txt
/usr/share/ugene/data/weight_matrix/pam60.txt
/usr/share/ugene/data/weight_matrix/pam70.txt
/usr/share/ugene/data/weight_matrix/pam80.cdi.txt
/usr/share/ugene/data/weight_matrix/pam80.txt
/usr/share/ugene/data/weight_matrix/pam90.txt
/usr/share/ugene/data/weight_matrix/rna.txt
/usr/share/ugene/data/weight_matrix/vtml160.txt
/usr/share/ugene/data/weight_matrix/vtml200.txt
/usr/share/ugene/data/workflow_samples
/usr/share/ugene/data/workflow_samples/Alignment
/usr/share/ugene/data/workflow_samples/Alignment/basic_align.uwl
/usr/share/ugene/data/workflow_samples/Alignment/extract_msa_consensus_as_seq.uwl
/usr/share/ugene/data/workflow_samples/Alignment/extract_msa_consensus_as_text.uwl
/usr/share/ugene/data/workflow_samples/Conversions
/usr/share/ugene/data/workflow_samples/Conversions/faqual2fastq.uwl
/usr/share/ugene/data/workflow_samples/Conversions/msa2clustal.uwl
/usr/share/ugene/data/workflow_samples/Conversions/query2alignment.uwl
/usr/share/ugene/data/workflow_samples/Conversions/seq2gen.uwl
/usr/share/ugene/data/workflow_samples/Custom elements
/usr/share/ugene/data/workflow_samples/Custom elements/casava-fastq-filter.uwl
/usr/share/ugene/data/workflow_samples/Custom elements/fastq-trimmer.uwl
/usr/share/ugene/data/workflow_samples/Custom elements/script-dump-sequence-info.uwl
/usr/share/ugene/data/workflow_samples/Custom elements/script-linkdata-fetch-seq.uwl
/usr/share/ugene/data/workflow_samples/Custom elements/script-quality-filter.uwl
/usr/share/ugene/data/workflow_samples/Data marking
/usr/share/ugene/data/workflow_samples/Data marking/annotation_marker.uwl
/usr/share/ugene/data/workflow_samples/Data marking/length_marker.uwl
/usr/share/ugene/data/workflow_samples/Data merging
/usr/share/ugene/data/workflow_samples/Data merging/find-substrings.uwl
/usr/share/ugene/data/workflow_samples/Data merging/merge-sequence.uwl
/usr/share/ugene/data/workflow_samples/Data merging/tfbs.uwl
/usr/share/ugene/data/workflow_samples/HMMER
/usr/share/ugene/data/workflow_samples/HMMER/build-test-HMM.uwl
/usr/share/ugene/data/workflow_samples/HMMER/searchHMM.uwl
/usr/share/ugene/data/workflow_samples/NGS
/usr/share/ugene/data/workflow_samples/NGS/chipseq_coverage.uwl
/usr/share/ugene/data/workflow_samples/NGS/cistrome
/usr/share/ugene/data/workflow_samples/NGS/cistrome.uwl
/usr/share/ugene/data/workflow_samples/NGS/cistrome/chip_seq.uwl
/usr/share/ugene/data/workflow_samples/NGS/cistrome/chip_seq_with_control.uwl
/usr/share/ugene/data/workflow_samples/NGS/consensus.uwl
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/usr/share/ugene/data/workflow_samples/NGS/extract_transcript_seq.uwl
/usr/share/ugene/data/workflow_samples/NGS/fastqc.uwl
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/usr/share/ugene/data/workflow_samples/NGS/from_tools_menu_only/ngs_assembly.uwl
/usr/share/ugene/data/workflow_samples/NGS/from_tools_menu_only/ngs_classification.uwl
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/usr/share/ugene/data/workflow_samples/NGS/ngs_assembly_illumina_pe_nanopore.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_assembly_illumina_se.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_paired.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification/ngs_classification_de_novo/ngs_classification_de_novo_single.uwl
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/usr/share/ugene/data/workflow_samples/NGS/ngs_classification/ngs_classification_parallel/ngs_classification_parallel_paired.uwl
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/usr/share/ugene/data/workflow_samples/NGS/ngs_classification/ngs_classification_serial
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_paired.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification/ngs_classification_serial/ngs_classification_serial_single.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification_de_novo.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification_parallel.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_classification_serial.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_transcriptomics_tophat_stringtie.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_transcriptomics_tuxedo.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_variant_annotation.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_variant_calling.uwl
/usr/share/ugene/data/workflow_samples/NGS/ngs_variant_calling_full.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_chip.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_dna.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_ngs
/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/chipseq
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/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/chipseq/chipseq_single.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/dnaseq
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/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/rnaseq
/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_paired.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_filtration_single.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_paired.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_ngs/rnaseq/rnaseq_single.uwl
/usr/share/ugene/data/workflow_samples/NGS/raw_rna.uwl
/usr/share/ugene/data/workflow_samples/NGS/tuxedo
/usr/share/ugene/data/workflow_samples/NGS/tuxedo/tuxedo_main.uwl
/usr/share/ugene/data/workflow_samples/NGS/tuxedo/tuxedo_main_paired.uwl
/usr/share/ugene/data/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr.uwl
/usr/share/ugene/data/workflow_samples/NGS/tuxedo/tuxedo_no_novel_transcr_paired.uwl
/usr/share/ugene/data/workflow_samples/NGS/tuxedo/tuxedo_single_dataset.uwl
/usr/share/ugene/data/workflow_samples/NGS/tuxedo/tuxedo_single_dataset_paired.uwl
/usr/share/ugene/data/workflow_samples/NGS/unmapped_reads.uwl
/usr/share/ugene/data/workflow_samples/Sanger sequencing
/usr/share/ugene/data/workflow_samples/Sanger sequencing/trim-and-align.uwl
/usr/share/ugene/data/workflow_samples/Scenarios
/usr/share/ugene/data/workflow_samples/Scenarios/filter_matched.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/find_inverted_repeats.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/find_sequences.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/gene_by_gene_report.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/group_primers_pairs.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/intersect_annotations.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/length_filter.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/merge_sequence_annotation.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/pcr.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/remote_blasting.uwl
/usr/share/ugene/data/workflow_samples/Scenarios/translate_seq_and_compl.uwl
/usr/share/ugene/data/workflow_samples/Transcriptomics
/usr/share/ugene/data/workflow_samples/Transcriptomics/SearchTFBS.uwl
/usr/share/ugene/data/workflow_samples/users
/usr/share/ugene/data/workflow_samples/users/CASAVA FASTQ filter.usa
/usr/share/ugene/data/workflow_samples/users/Dump sequence info.usa
/usr/share/ugene/data/workflow_samples/users/FASTQ Trimmer.usa
/usr/share/ugene/data/workflow_samples/users/Get the first half of sequence.usa
/usr/share/ugene/data/workflow_samples/users/Get the second half of sequence.usa
/usr/share/ugene/data/workflow_samples/users/LengthMarker.usa
/usr/share/ugene/data/workflow_samples/users/LinkData Fetch.usa
/usr/share/ugene/data/workflow_samples/users/QualityFilter.usa
/usr/share/ugene/data/workflow_samples/users/Read one sequence.usa

The spaces in files are asking for trouble, please consider replacing them with underscore in next release. Thank you.

DmitriiSukhomlinov commented 3 years ago

Hello,

First of all, check if the "plugins" folder really exists in the "ugene" directory. If it exists, that means, that the problem somewhere else. What is it - your own build or UGENE you've got from somewhere?

About possibility to choose plugins - now it's not supported, because it's a bit different way they work. Users no need to do something about it, plugins are included. Maybe, it the future, if we create some additional plugins, which are not included in the UGENE pack, we will improve it.

mmokrejs commented 3 years ago

Hi, thank your for your answer. The layout of the fiels and directories is shown above. Is it looking a placement of the plugin directory elsewhere? How about introducing say UGENE_PLUGINS variable which would point to /usr/lib/ugene/plugins? We are trying to get it installed properly on Gentoo Linux, see https://github.com/gentoo/sci/issues/1067#issuecomment-802045304 and latter.

yalgaer commented 3 years ago

Hi,

Before loading any plugin UGENE reads plugin metadata from the ".plugin" file. For example, to load 'libgor4.so' UGENE needs 'gor4.plugin' file in the same folder.

In your listing I can't see such files and this may be the reason of the error.

yalgaer commented 3 years ago

Closing the issue. Please reopen if the last recommendation didn't help.

mmokrejs commented 3 years ago

Hi, thank you for your answer. It is awkward e.g. libgor4.so should be in the same directory as the ugene executable (in /usr/bin/). Please come up with a proper way how to install you application. The structure which we hoped for is shown above. Try to adjust you code to anticipate that layout. The UGENE_PLUGINS variable would be one way to go.

Why the qmake install does not install any gor4.plugin files which are necessary I do not know. Placing them into /usr/bin does not sound right and maybe Gentoo filters them somewhere, maybe they are lacking exec bit set or so? I am just speculating here. They should not be there at all, /usr/lib/ugene/plugins or /usr/share/ugene/ seem better fit. The libs are found via LD_LIBRARY_PATH and unless the gor4.plugin are to be found by the loader there is no reason to smash them into /usr/lib/ugene/plugins/.

You can study the *.ebuild file at https://github.com/gentoo/sci/tree/master/sci-biology/ugene to see what we eventually do wrong.

If you can, please replace as I proposed the spaces in the files installed with some non-whitespace char, like underscore. I can't actually reopen this.