[MacPorts] #35068: tophat: update to 2.1.1 (was: tophat and bowtie: update to 2+)

[MacPorts]

#35068: tophat: update to 2.1.1
------------------------------------+----------------------
  Reporter:  ryandesign             |      Owner:  (none)
      Type:  update                 |     Status:  assigned
  Priority:  Normal                 |  Milestone:
 Component:  ports                  |    Version:
Resolution:                         |   Keywords:
      Port:  tophat bowtie bowtie2  |
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Changes (by ryandesign):

 * port:  tophat bowtie => tophat bowtie bowtie2


Comment:

 The bowtie port should not be updated to version 2. bowtie 2 is a little
 different from bowtie 1, such that the authors thought a user might want
 to install both, and set the names of the installed files and directories
 so that they would not conflict. MacPorts already has a bowtie2 port for
 version 2 of the software.

 Marcus [changeset:901c641d0185b175757c7a7e5b507bb9cbf39638/macports-ports
 updated bowtie to 1.2.2_p1]. In switching to the github portgroup, the
 livecheck was also fixed. He also
 [changeset:e6904a6282252b88211c829bb7153c251b4c33f4/macports-ports updated
 bowtie2 to 2.3.4.3]. It already used the github portgroup and its
 livecheck works fine.

 tophat should be updated to 1.4.1 or 2.1.1. Kurt already
 [changeset:ec878b143b11d084e75e8e93e746b7944e150ae8/macports-ports fixed
 tophat's livecheck].

-- 
Ticket URL: <https://trac.macports.org/ticket/35068#comment:6>
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