sequenceserver 2.0.0.beta4 → 2.0.0.rc5

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Files changed (119) hide show
  1. checksums.yaml +5 -5
  2. data/.dockerignore +1 -0
  3. data/.travis.yml +7 -4
  4. data/AppImage/sequenceserver.sh +5 -0
  5. data/Dockerfile +14 -12
  6. data/bin/sequenceserver +37 -28
  7. data/lib/sequenceserver.rb +35 -7
  8. data/lib/sequenceserver/blast/job.rb +18 -25
  9. data/lib/sequenceserver/blast/report.rb +68 -34
  10. data/lib/sequenceserver/config.rb +1 -1
  11. data/lib/sequenceserver/database.rb +0 -129
  12. data/lib/sequenceserver/makeblastdb.rb +243 -0
  13. data/lib/sequenceserver/routes.rb +28 -2
  14. data/lib/sequenceserver/version.rb +1 -1
  15. data/public/SequenceServer_logo.png +0 -0
  16. data/public/css/grapher.css +8 -15
  17. data/public/css/sequenceserver.css +119 -55
  18. data/public/css/sequenceserver.min.css +3 -3
  19. data/public/js/circos.js +1 -1
  20. data/public/js/download_fasta.js +17 -0
  21. data/public/js/grapher.js +7 -9
  22. data/public/js/hit.js +217 -0
  23. data/public/js/hits_overview.js +12 -13
  24. data/public/js/hsp.js +104 -84
  25. data/public/js/{sequenceserver.js → jquery_world.js} +1 -18
  26. data/public/js/kablammo.js +337 -334
  27. data/public/js/length_distribution.js +1 -1
  28. data/public/js/query.js +147 -0
  29. data/public/js/report.js +216 -836
  30. data/public/js/search.js +194 -192
  31. data/public/js/sequence_modal.js +167 -0
  32. data/public/js/sidebar.js +210 -0
  33. data/public/js/utils.js +2 -19
  34. data/public/js/visualisation_helpers.js +2 -2
  35. data/public/sequenceserver-report.min.js +19 -19
  36. data/public/sequenceserver-search.min.js +11 -11
  37. data/public/vendor/github/twbs/bootstrap@3.3.5/js/bootstrap.js +2 -2
  38. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +15 -15
  39. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +15 -15
  40. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +15 -15
  41. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +15 -15
  42. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +15 -15
  43. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +15 -15
  44. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +15 -15
  45. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +15 -15
  46. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +15 -15
  47. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +6 -6
  48. data/spec/capybara_spec.rb +14 -3
  49. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ndb +0 -0
  50. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  51. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  52. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nos +0 -0
  53. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.not +0 -0
  54. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ntf +0 -0
  55. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nto +0 -0
  56. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pdb +0 -0
  57. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  58. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  59. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pos +0 -0
  60. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pot +0 -0
  61. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.ptf +0 -0
  62. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pto +0 -0
  63. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pdb +0 -0
  64. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
  65. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
  66. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pos +0 -0
  67. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pot +0 -0
  68. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.ptf +0 -0
  69. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pto +0 -0
  70. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ndb +0 -0
  71. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  72. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  73. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nos +0 -0
  74. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.not +0 -0
  75. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  76. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ntf +0 -0
  77. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nto +0 -0
  78. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +8 -0
  79. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
  80. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  81. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  82. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
  83. data/spec/database/{sample → v4}/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd +0 -0
  84. data/spec/database/{sample → v4}/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi +0 -0
  85. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
  86. data/spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +8 -0
  87. data/spec/database/v4/links.rb +23 -0
  88. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +6449 -0
  89. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +1189 -0
  90. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi +0 -0
  91. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  92. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  93. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
  94. data/spec/database/{sample → v4}/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +0 -0
  95. data/spec/database/{sample → v4}/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
  96. data/spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  97. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd +9140 -0
  98. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi +0 -0
  99. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
  100. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
  101. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog +0 -0
  102. data/spec/database/{sample → v4}/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd +0 -0
  103. data/spec/database/{sample → v4}/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi +0 -0
  104. data/spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +0 -0
  105. data/spec/database/v4/proteins/uniprot/URL +1 -0
  106. data/spec/database/v4/si_uniprot_idmap.yml +14180 -0
  107. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +5486 -0
  108. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd +473 -0
  109. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi +0 -0
  110. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  111. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  112. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
  113. data/spec/database/{sample → v4}/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +0 -0
  114. data/spec/database/{sample → v4}/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
  115. data/spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  116. data/spec/database_spec.rb +0 -76
  117. data/spec/makeblastdb_spec.rb +121 -0
  118. data/views/layout.erb +5 -1
  119. metadata +75 -15

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