Question: How is Tophat installed?
0
gravatar for from the mountains
3.2 years ago by
United States
from the mountains40 wrote:

I'm trying to install Tophat. The manual says to use the following command: 

./configure --prefix=/path/to/tophat_base_dir \
 --with-boost=/path/to/boost_prefix_dir

but there is no configure file in the packages in either the linux or mac distributions. What am I missing? and why am i having so much trouble installing boost as well on either OS? 

boost install tophat • 3.9k views
ADD COMMENTlink modified 21 months ago by p.senadheera0 • written 3.2 years ago by from the mountains40

If you're on a Mac, I hope you have homebrew installed. That makes installing any piece of software as easy as brew install package_name

ADD REPLYlink written 3.2 years ago by Ram15k

i did try that, but had some failures nonetheless, even using --universal. I got it working on linux though (will post what I did below).

ADD REPLYlink written 3.2 years ago by from the mountains40

Tackle the failures and get homebrew working fine. It will pay off exponentially. Use this as a resource: https://www.topbug.net/blog/2013/04/14/install-and-use-gnu-command-line-tools-in-mac-os-x/

ADD REPLYlink written 3.2 years ago by Ram15k
0
gravatar for Sean Davis
3.2 years ago by
Sean Davis24k
National Institutes of Health, Bethesda, MD
Sean Davis24k wrote:

I'd suggest using a binary installation.  Binaries are available for both Mac and Linux:

http://ccb.jhu.edu/software/tophat/downloads/

 

ADD COMMENTlink written 3.2 years ago by Sean Davis24k

I'm not very good at terminal stuff yet, but I just realized I had downloaded the binaries even though configure was only in the source. in any case, i wasn't able to get boost installed on my mac, so i've got it installed on linux instead (will post below).

ADD REPLYlink written 3.2 years ago by from the mountains40
0
gravatar for from the mountains
3.2 years ago by
United States
from the mountains40 wrote:

I installed the source file of tophat instead and was able to find the ./configure file. 

As far as boost, even though the bootstrap.sh file gave the prefix as /usr/local, it didn't seem to be installing there. so as input i put in a new prefix: ./bootstrap.sh --prefix=<new-directory>

Thanks everyone for the input. hopefully i get better at all this!

ADD COMMENTlink written 3.2 years ago by from the mountains40
0
gravatar for p.senadheera
21 months ago by
p.senadheera0 wrote:

when i try to install tophat2 with boost in Mac osx 10.10.5 gave following error i used the source code of tophat. boost was installed in BOOST-installed. tophat-2.1.1 psenadheera$ ./configure --prefix=/Users/psenadheera/tophat-2.1.1 \ --with-boost= /Users/psenadheera/Boost_installed configure: error: invalid variable name: ` --with-boost'

can you please help me to sort out this issue?

ADD COMMENTlink written 21 months ago by p.senadheera0

I'd highly recommend using homebrew when you're on OS X.

ADD REPLYlink written 21 months ago by Ram15k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1046 users visited in the last hour