Opened 12 years ago
Closed 6 years ago
#35068 closed update (fixed)
tophat: update to 2.1.1
| Reported by: | ryandesign (Ryan Carsten 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 10 years ago by kurthindenburg (Kurt Hindenburg)
| Cc: | khindenburg@… added |
|---|
comment:2 Changed 10 years ago by kurthindenburg (Kurt Hindenburg)
r125156 - add livecheck and update homepage
comment:3 Changed 10 years ago by kurthindenburg (Kurt Hindenburg)
| Port: | bowtie added |
|---|---|
| Summary: | tophat: update to 2.0.4 and fix livecheck → tophat 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.
comment:4 Changed 7 years ago by kurthindenburg (Kurt Hindenburg)
| Owner: | haroldpimentel@… deleted |
|---|---|
| Status: | new → assigned |
comment:5 Changed 6 years ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)
| Cc: | MarcusCalhoun-Lopez added |
|---|
comment:6 Changed 6 years ago by ryandesign (Ryan Carsten 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 6 years ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)
| Owner: | set to MarcusCalhoun-Lopez |
|---|---|
| Status: | assigned → accepted |
comment:8 Changed 6 years ago by MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Cc Me!