fatal errors (Bowtie 2 installation)

Question

[healing80]

Hello. I am a newbie in bioinfomatics. I have downloaded bowtie 2 and type 'make' to install. The computer gave me messages below.

Is bowtie2 installed properly? and what is fatal errors?

-------
1 error generated.
In file included from bowtie_build_main.cpp:25:
In file included from ./ds.h:30:

./threading.h:29:11: fatal error: 'tbb/mutex.h' file not found
include <tbb/mutex.h>
          ^~~~~~~~~~~~~
1 error generated.
make: [bowtie2-build-s] Error 1

---

Also, I tried installing tophat 2, but 'make' does not work. it gave me this message.

$ ln -s ~/tophat-2.1.1.Linux_x86_64/tophat2
ln: ./tophat2: File exists

kimh2@XXXXX ~/desktop
$ cd tophat-2.1.1.Linux_x86_64

kimh2@XXXXX ~/bin
$ ./configure --prefix=/path/to/tophat_base_dir  --with-boost=/path/to/boost_prefix_dir
-bash: ./configure: No such file or directory

Anybody gives me some advice? I am learning ABC for bioinformatics, so please give me advice to follow easily.

Thank you.

Answer 1

[GenoMax]

You have not installed tbb library. You have following options.

• turn tbb off as last resort (make NO_TBB=1)
• install TBB library from here.
• Get binary compiled version of bowtie2 for linux from here (macOS also available).

Finally the advice you should take to heart:

Avoid using TopHat2 for any new projects. Use STAR, BBMap or any of other current splice aware aligners.

[ATpoint]

Or use a package manager like anaconda.

[healing80]

Thanks a lot. it is really helpful.