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Showing with 419 additions and 393 deletions.
  1. +13 −6 Changes
  2. +4 −4 lib/Bio/Factory/EMBOSS.pm
  3. +4 −4 lib/Bio/Installer/Clustalw.pm
  4. +4 −4 lib/Bio/Installer/EMBOSS.pm
  5. +4 −4 lib/Bio/Installer/Generic.pm
  6. +4 −4 lib/Bio/Installer/Hyphy.pm
  7. +4 −4 lib/Bio/Installer/Muscle.pm
  8. +4 −4 lib/Bio/Installer/PAML.pm
  9. +4 −4 lib/Bio/Installer/Probcons.pm
  10. +4 −4 lib/Bio/Installer/SLR.pm
  11. +4 −4 lib/Bio/Installer/TCoffee.pm
  12. +4 −4 lib/Bio/Tools/Run/Alignment/Amap.pm
  13. +4 −4 lib/Bio/Tools/Run/Alignment/Blat.pm
  14. +4 −4 lib/Bio/Tools/Run/Alignment/Clustalw.pm
  15. +4 −4 lib/Bio/Tools/Run/Alignment/DBA.pm
  16. +1 −1 lib/Bio/Tools/Run/Alignment/Exonerate.pm
  17. +4 −4 lib/Bio/Tools/Run/Alignment/Kalign.pm
  18. +4 −4 lib/Bio/Tools/Run/Alignment/Lagan.pm
  19. +4 −4 lib/Bio/Tools/Run/Alignment/MAFFT.pm
  20. +4 −4 lib/Bio/Tools/Run/Alignment/Muscle.pm
  21. +4 −4 lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
  22. +4 −4 lib/Bio/Tools/Run/Alignment/Probalign.pm
  23. +4 −4 lib/Bio/Tools/Run/Alignment/Probcons.pm
  24. +4 −4 lib/Bio/Tools/Run/Alignment/Proda.pm
  25. +4 −4 lib/Bio/Tools/Run/Alignment/Sim4.pm
  26. +4 −4 lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
  27. +5 −5 lib/Bio/Tools/Run/Alignment/TCoffee.pm
  28. +4 −4 lib/Bio/Tools/Run/Analysis.pm
  29. +4 −4 lib/Bio/Tools/Run/Analysis/soap.pm
  30. +4 −4 lib/Bio/Tools/Run/AnalysisFactory.pm
  31. +4 −4 lib/Bio/Tools/Run/AnalysisFactory/soap.pm
  32. +4 −4 lib/Bio/Tools/Run/Cap3.pm
  33. +4 −4 lib/Bio/Tools/Run/Coil.pm
  34. +4 −4 lib/Bio/Tools/Run/EMBOSSApplication.pm
  35. +4 −4 lib/Bio/Tools/Run/EMBOSSacd.pm
  36. +4 −4 lib/Bio/Tools/Run/ERPIN.pm
  37. +4 −4 lib/Bio/Tools/Run/Ensembl.pm
  38. +4 −4 lib/Bio/Tools/Run/Eponine.pm
  39. +4 −4 lib/Bio/Tools/Run/FootPrinter.pm
  40. +4 −4 lib/Bio/Tools/Run/Genemark.pm
  41. +4 −4 lib/Bio/Tools/Run/Genewise.pm
  42. +4 −4 lib/Bio/Tools/Run/Genscan.pm
  43. +4 −4 lib/Bio/Tools/Run/Glimmer.pm
  44. +4 −4 lib/Bio/Tools/Run/Hmmer.pm
  45. +8 −5 lib/Bio/Tools/Run/Infernal.pm
  46. +4 −4 lib/Bio/Tools/Run/MCS.pm
  47. +4 −4 lib/Bio/Tools/Run/Match.pm
  48. +4 −4 lib/Bio/Tools/Run/Mdust.pm
  49. +4 −4 lib/Bio/Tools/Run/Meme.pm
  50. +4 −4 lib/Bio/Tools/Run/Phrap.pm
  51. +4 −4 lib/Bio/Tools/Run/Phylo/Gerp.pm
  52. +4 −4 lib/Bio/Tools/Run/Phylo/Gumby.pm
  53. +4 −4 lib/Bio/Tools/Run/Phylo/Hyphy/Base.pm
  54. +4 −4 lib/Bio/Tools/Run/Phylo/Hyphy/FEL.pm
  55. +4 −4 lib/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm
  56. +4 −4 lib/Bio/Tools/Run/Phylo/Hyphy/REL.pm
  57. +4 −4 lib/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm
  58. +4 −4 lib/Bio/Tools/Run/Phylo/LVB.pm
  59. +4 −4 lib/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
  60. +4 −4 lib/Bio/Tools/Run/Phylo/Njtree/Best.pm
  61. +4 −4 lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
  62. +4 −4 lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm
  63. +4 −4 lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
  64. +4 −4 lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
  65. +4 −4 lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
  66. +4 −4 lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
  67. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/Base.pm
  68. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
  69. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
  70. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm
  71. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/Neighbor.pm
  72. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/PhylipConf.pm
  73. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/ProtDist.pm
  74. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/ProtPars.pm
  75. +4 −4 lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.pm
  76. +4 −4 lib/Bio/Tools/Run/Phylo/PhyloBase.pm
  77. +4 −4 lib/Bio/Tools/Run/Phylo/Phyml.pm
  78. +4 −4 lib/Bio/Tools/Run/Phylo/QuickTree.pm
  79. +4 −4 lib/Bio/Tools/Run/Phylo/SLR.pm
  80. +4 −4 lib/Bio/Tools/Run/Phylo/Semphy.pm
  81. +4 −4 lib/Bio/Tools/Run/Primate.pm
  82. +4 −4 lib/Bio/Tools/Run/Primer3.pm
  83. +4 −4 lib/Bio/Tools/Run/Prints.pm
  84. +4 −4 lib/Bio/Tools/Run/Profile.pm
  85. +4 −4 lib/Bio/Tools/Run/Promoterwise.pm
  86. +4 −4 lib/Bio/Tools/Run/Pseudowise.pm
  87. +4 −4 lib/Bio/Tools/Run/RNAMotif.pm
  88. +4 −4 lib/Bio/Tools/Run/RepeatMasker.pm
  89. +4 −4 lib/Bio/Tools/Run/Seg.pm
  90. +4 −4 lib/Bio/Tools/Run/Signalp.pm
  91. +4 −4 lib/Bio/Tools/Run/Simprot.pm
  92. +4 −4 lib/Bio/Tools/Run/TigrAssembler.pm
  93. +4 −4 lib/Bio/Tools/Run/TribeMCL.pm
  94. +4 −4 lib/Bio/Tools/Run/Vista.pm
  95. +4 −4 lib/Bio/Tools/Run/tRNAscanSE.pm
  96. +12 −8 t/Infernal.t
  97. +8 −0 t/data/purine.added.fa
  98. +8 −4 t/gmap-run.t
View
19 Changes
@@ -4,17 +4,24 @@ Revision history for bioperl-run modules
Full details of changes between all versions are available online at:
http://www.bioperl.org/wiki/Change_log
+1.6.2 Release
+
+* [bug 2713] - Bio::Tools::Run::Infernal now works with Infernal 1.0 (older
+ versions deprecated) [cjfields]
+* Bio::Tools::Run::Alignment::Gmap added [hartzell]
+* [bug 2798] - patch to fix clustalw premature file unlinking error [Wei Zhou]
+
1.6.0 Release
- o All Pise and Pise-related modules and scripts have been moved to the
- new bioperl-pise repository. The Pise service is no longer available and
- has been replaced by Mobyle. They have been retained as one can still
- install a Pise server, and as these modules can possibly be used to create
- a new BioPerl API for Mobyle.
+* All Pise and Pise-related modules and scripts have been moved to the new
+ bioperl-pise repository. The Pise service is no longer available and has been
+ replaced by Mobyle. They have been retained as one can still install a Pise
+ server, and as these modules can possibly be used to create a new BioPerl API
+ for Mobyle.
1.5.2 Release in sync with bioperl core
- o Several wrappers updated for newer versions of the programs.
+* Several wrappers updated for newer versions of the programs.
1.5.1 Release in sync with bioperl core
View
8 lib/Bio/Factory/EMBOSS.pm
@@ -70,11 +70,11 @@ Bioperl mailing lists Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/Clustalw.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/EMBOSS.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/Generic.pm
@@ -34,11 +34,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/Hyphy.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/Muscle.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/PAML.pm
@@ -34,11 +34,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/Probcons.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/SLR.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Installer/TCoffee.pm
@@ -35,11 +35,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Amap.pm
@@ -110,11 +110,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Blat.pm
@@ -37,11 +37,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Clustalw.pm
@@ -321,11 +321,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/DBA.pm
@@ -67,11 +67,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
2 lib/Bio/Tools/Run/Alignment/Exonerate.pm
@@ -66,7 +66,7 @@ of the Bioperl mailing lists. Your participation is much appreciated.
Please direct usage questions or support issues to the mailing list:
-L<bioperl-l@bioperl.org>
+I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
View
8 lib/Bio/Tools/Run/Alignment/Kalign.pm
@@ -80,11 +80,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Lagan.pm
@@ -97,11 +97,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/MAFFT.pm
@@ -38,11 +38,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/MailList.html - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Muscle.pm
@@ -78,11 +78,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
@@ -79,11 +79,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Probalign.pm
@@ -84,11 +84,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Probcons.pm
@@ -106,11 +106,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Proda.pm
@@ -84,11 +84,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/Sim4.pm
@@ -64,11 +64,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
@@ -87,11 +87,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
10 lib/Bio/Tools/Run/Alignment/TCoffee.pm
@@ -498,11 +498,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
@@ -768,7 +768,7 @@ sub align {
or references to 2 Bio::SimpleAlign objects.
Note : Needs to be updated to run with newer TCoffee code, which
allows more than two profile alignments.
-
+
Throws an exception if arguments are not either strings (eg filenames)
or references to SimpleAlign objects.
View
8 lib/Bio/Tools/Run/Analysis.pm
@@ -155,11 +155,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Analysis/soap.pm
@@ -43,11 +43,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/AnalysisFactory.pm
@@ -91,11 +91,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/AnalysisFactory/soap.pm
@@ -40,11 +40,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Cap3.pm
@@ -38,11 +38,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
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-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
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8 lib/Bio/Tools/Run/Coil.pm
@@ -55,11 +55,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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8 lib/Bio/Tools/Run/EMBOSSApplication.pm
@@ -69,11 +69,11 @@ Bioperl mailing lists Your participation is much appreciated.
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-
+
Please direct usage questions or support issues to the mailing list:
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+
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+
rather than to the module maintainer directly. Many experienced and
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address it. Please include a thorough description of the problem
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8 lib/Bio/Tools/Run/EMBOSSacd.pm
@@ -80,11 +80,11 @@ Bioperl mailing lists Your participation is much appreciated.
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-
+
Please direct usage questions or support issues to the mailing list:
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+
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+
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8 lib/Bio/Tools/Run/ERPIN.pm
@@ -75,11 +75,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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+
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8 lib/Bio/Tools/Run/Ensembl.pm
@@ -51,11 +51,11 @@ Bioperl mailing list. Your participation is much appreciated.
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@@ -62,11 +62,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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8 lib/Bio/Tools/Run/FootPrinter.pm
@@ -134,11 +134,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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@@ -58,11 +58,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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8 lib/Bio/Tools/Run/Genewise.pm
@@ -64,11 +64,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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@@ -75,11 +75,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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@@ -74,11 +74,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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13 lib/Bio/Tools/Run/Infernal.pm
@@ -106,11 +106,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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rather than to the module maintainer directly. Many experienced and
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address it. Please include a thorough description of the problem
@@ -685,7 +685,7 @@ sub set_parameters {
@_;
# set the parameters passed in, but only ones supported for the program
my ($prog, $validate) = ($self->program, $self->validate_parameters);
-
+
# parameter cleanup
%args = map { my $a = $_;
$a =~ s{^-}{};
@@ -856,6 +856,9 @@ sub to_exe_string {
$self->program_name,
$self->model_file,
$self->outfile_name);
+
+ $self->throw("Executable not found") unless defined($exe);
+
delete $params{o} if exists $params{o};
if (!defined($model) && $prog ne 'cmbuild') {
View
8 lib/Bio/Tools/Run/MCS.pm
@@ -94,11 +94,11 @@ the Bioperl mailing list. Your participation is much appreciated.
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+
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8 lib/Bio/Tools/Run/Match.pm
@@ -79,11 +79,11 @@ the Bioperl mailing list. Your participation is much appreciated.
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8 lib/Bio/Tools/Run/Mdust.pm
@@ -58,11 +58,11 @@ the Bioperl mailing list. Your participation is much appreciated.
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@@ -57,11 +57,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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8 lib/Bio/Tools/Run/Phylo/Gerp.pm
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@@ -38,11 +38,11 @@ the Bioperl mailing list. Your participation is much appreciated.
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Please direct usage questions or support issues to the mailing list:
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Please direct usage questions or support issues to the mailing list:
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Please direct usage questions or support issues to the mailing list:
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+
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8 lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
@@ -165,11 +165,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
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Please direct usage questions or support issues to the mailing list:
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+
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8 lib/Bio/Tools/Run/Phylo/Phylip/DrawGram.pm
@@ -40,11 +40,11 @@ the Bioperl mailing list. Your participation is much appreciated.
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Please direct usage questions or support issues to the mailing list:
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@@ -52,11 +52,11 @@ Bioperl mailing list. Your participation is much appreciated.
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-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Phylo/PhyloBase.pm
@@ -40,11 +40,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Phylo/Phyml.pm
@@ -116,11 +116,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Phylo/QuickTree.pm
@@ -71,11 +71,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Phylo/SLR.pm
@@ -79,11 +79,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Phylo/Semphy.pm
@@ -87,11 +87,11 @@ the Bioperl mailing list. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Primate.pm
@@ -48,11 +48,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Primer3.pm
@@ -100,11 +100,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://www.bioperl.org/MailList.html - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Prints.pm
@@ -35,11 +35,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Profile.pm
@@ -37,11 +37,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Promoterwise.pm
@@ -63,11 +63,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Pseudowise.pm
@@ -41,11 +41,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/RNAMotif.pm
@@ -99,11 +99,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/RepeatMasker.pm
@@ -76,11 +76,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Seg.pm
@@ -37,11 +37,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Signalp.pm
@@ -36,11 +36,11 @@ of the Bioperl mailing lists. Your participation is much appreciated.
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
-
+
Please direct usage questions or support issues to the mailing list:
-
-L<bioperl-l@bioperl.org>
-
+
+I<bioperl-l@bioperl.org>
+
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
View
8 lib/Bio/Tools/Run/Simprot.pm