Tophat Error: Make in Mac OSX

Question

[vharshavardhanan]

Hi friends,

I am new to RNA-seq and I am trying to run tophat program in my Mac OS High Sierra. I have a problem when I try to make command in tophat.

For configuration: I used

./configure --prefix=/usr/local/bin/--with-boost=/usr/local/bin/boost --with-bam=/usr/local/bin/samtools` and it returned with an error `WARNING: unrecognized options: --with-bam

So I used ./configure instead of the above command and it worked fine without any warning or error. Then ran make

I got the following error during make command

Command:

Harshavardhanans-MacBook-Air:tophat-2.1.1 harshavardhanan$ make
/Library/Developer/CommandLineTools/usr/bin/make  all-recursive
Making all in src
Makefile:1672: warning: overriding commands for target `libbam.a'
Makefile:1203: warning: ignoring old commands for target `libbam.a'
cd ./samtools-0.1.18 && make samtools_0.1.18 && cp libbam.a samtools_0.1.18 ..
make[4]: Nothing to be done for `lib'.
make[4]: Nothing to be done for `lib'.
gcc -g -Wall -O2  -o samtools_0.1.18 bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools  libbam.a -lbcf -lm -lz #-lcurses
Undefined symbols for architecture x86_64:
  "___ks_insertsort_heap", referenced from:
      _ks_combsort_heap in libbam.a(bam_sort.o)
      _ks_introsort_heap in libbam.a(bam_sort.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [samtools_0.1.18] Error 1
make[2]: *** [libbam.a] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

I am not sure what to do after this. Any help is much appreciated.

Thank you.

[GenoMax]

You should know that the old 'Tuxedo' pipeline of Tophat(2) and Cufflinks is no longer the "advisable" tool for RNA-seq analysis. The software is deprecated/ in low maintenance and should be replaced by HISAT2, StringTie and ballgown. See this paper: Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. There are also other alternatives, including alignment with STAR and bbmap, or pseudo-alignment using salmon.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[vharshavardhanan]

Thank you Pachter.... I will look into these program.