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Old 02-16-2015, 05:03 AM   #1
nixstix
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Location: Belgium

Join Date: Feb 2015
Posts: 2
Default Tophat Installation Problems on Mac

Hi all. I am trying to install TopHat2 on a MAC. I have run ./configure and make, and have so far (I think), been successful. When I run make install I get the following error:

Code:
Making install in src
Makefile:1411: warning: overriding commands for target `libbam.a'
Makefile:1041: warning: ignoring old commands for target `libbam.a'
Makefile:1411: warning: overriding commands for target `libbam.a'
Makefile:1041: warning: ignoring old commands for target `libbam.a'
test -z "/usr/local/bin" || /usr/local/bin/tophat-2.0.13/install-sh -d "/usr/local/bin"
  /usr/local/bin/tophat-2.0.13/install -c 'samtools_0.1.18' '/usr/local/bin/samtools_0.1.18'
/usr/local/bin/tophat-2.0.13/install: line 1: Installation: command not found
/usr/local/bin/tophat-2.0.13/install: line 2: FastaTools.cpp: command not found
/usr/local/bin/tophat-2.0.13/install: line 4: syntax error near unexpected token `C'
/usr/local/bin/tophat-2.0.13/install: line 4: `Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005 Free'
make[2]: *** [install-binPROGRAMS] Error 1
make[1]: *** [install-am] Error 2
make: *** [install-recursive] Error 1
Can anyone help me?

Thanks!
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Old 02-16-2015, 05:06 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

Are you sure there was no error in configure and make commands? What OS X are you using and what version of Xcode?

You could just download the pre-compiled binary for Mac here and not worry about compilation: http://ccb.jhu.edu/software/tophat/d..._x86_64.tar.gz
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