Opened 8 years ago

Closed 21 months ago

#35068 closed update (fixed)

tophat: update to 2.1.1

Reported by: ryandesign (Ryan Schmidt) Owned by: MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)
Priority: Normal Milestone:
Component: ports Version:
Keywords: Cc: kurthindenburg (Kurt Hindenburg), MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)
Port: tophat bowtie bowtie2

Description

I see tophat 2.0.4 is available so the port should probably be updated. The livecheck also needs to be fixed because it does not work.

Change History (8)

comment:1 Changed 6 years ago by kurthindenburg (Kurt Hindenburg)

Cc: khindenburg@… added

Cc Me!

comment:2 Changed 6 years ago by kurthindenburg (Kurt Hindenburg)

r125156 - add livecheck and update homepage

comment:3 Changed 6 years ago by kurthindenburg (Kurt Hindenburg)

Port: bowtie added
Summary: tophat: update to 2.0.4 and fix livechecktophat and bowtie: update to 2+

bowtie also needs updated to 2.2.4; tophat 2+ says it should work with either bowtie version, but might as well do both.

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

comment:4 Changed 3 years ago by kurthindenburg (Kurt Hindenburg)

Owner: haroldpimentel@… deleted
Status: newassigned

comment:5 Changed 22 months ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)

Cc: MarcusCalhoun-Lopez added

comment:6 Changed 21 months ago by ryandesign (Ryan Schmidt)

Port: bowtie2 added
Summary: tophat and bowtie: update to 2+tophat: update to 2.1.1

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 updated bowtie to 1.2.2_p1. In switching to the github portgroup, the livecheck was also fixed. He also 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 fixed tophat's livecheck.

comment:7 Changed 21 months ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)

Owner: set to MarcusCalhoun-Lopez
Status: assignedaccepted

comment:8 Changed 21 months ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)

Resolution: fixed
Status: acceptedclosed

In 7dd634c4cf752145633edae38baca97af2f93b91/macports-ports (master):

tophat: update version 1.2.0->2.1.2

Fixes #35068

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