Bug fixes for 3 tools (rebased #222)

#234 Merged at 1c22e43
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Deleted repository
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default (c61cc2f91c59)
Repository
galaxy-central
Branch
default
Author
  1. Nicola Soranzo
Reviewers
Description

Small bug fixes for "Draw phylogeny", NGS "Simulate" and Bowtie2.

Martin already approved pull request #222.

Aysam, you introduced the Bowtie2 bug in https://bitbucket.org/galaxy/galaxy-central/commits/883d7c4b387c0e701539b49e593144b7c027a64c#chg-tools/sr_mapping/bowtie2_wrapper.xml and seems to be the actual Bowtie2 wrapper maintainer.

John, you are involved in the mailing list thread http://dev.list.galaxyproject.org/RFC-remove-trailing-semicolons-from-command-line-gt-Broken-bowtie2-wrapper-on-some-SGE-systems-tt4662099.html

Ross, you fixed the Bowtie2 bug and then reverted the fix in your recent commits.

  • Issues #222: Tool pane improvements new

Comments (3)

  1. John Chilton

    One issue with the ngs_simulation tool seems to be the warning about no option selected doesn't go away when options are selected (https://trello.com/c/7Xm500yM). I have created a Trello card for this, but it is not a problem with the tool changes though so I think these should be merged.

  2. Martin Cech

    I don't know about the trailing semicolon, Aysam wrote the wrapper so he or maybe Nate should look at it

    everything else looks ok