Question: Build Bowtie2 2.3.3.1 with make on linux 64 bit
1
gravatar for marongiu.luigi
9 months ago by
Germany, Mannheim, UMM
marongiu.luigi210 wrote:

Hello,

I am trying to build bowtie 2 version 2.3.3.1 from source using the command make but I get the following:

/bowtie2$ make
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -DPOPCNT_CAPABILITY -DWITH_TBB -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
    -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
     -I third_party \
    -o bowtie2-build-s bt2_build.cpp \
    ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
      -lz -lpthread -ltbb -ltbbmalloc_proxy 
In file included from bt2_idx.h:42:0,
                 from bt2_build.cpp:28:
blockwise_sa.h:24:21: fatal error: tbb/tbb.h: No such file or directory
compilation terminated.
In file included from ds.h:30:0,
                 from ref_read.h:33,
                 from ref_read.cpp:20:
threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory
compilation terminated.
In file included from ds.h:30:0,
                 from edit.h:29,
                 from edit.cpp:21:
threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory
compilation terminated.
In file included from bt2_idx.h:42:0,
                 from bt2_idx.cpp:25:
blockwise_sa.h:24:21: fatal error: tbb/tbb.h: No such file or directory
compilation terminated.
In file included from bt2_idx.h:42:0,
                 from bt2_io.cpp:25:
blockwise_sa.h:24:21: fatal error: tbb/tbb.h: No such file or directory
compilation terminated.
In file included from bt2_idx.h:42:0,
                 from bt2_util.cpp:26:
blockwise_sa.h:24:21: fatal error: tbb/tbb.h: No such file or directory
compilation terminated.
In file included from ds.h:30:0,
                 from ref_read.h:33,
                 from reference.h:32,
                 from reference.cpp:22:
threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory
compilation terminated.
In file included from ds.h:30:0,
                 from ds.cpp:20:
threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory
compilation terminated.
In file included from ds.h:30:0,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from multikey_qsort.cpp:20:
threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory
compilation terminated.
In file included from ds.h:30:0,
                 from random_util.h:25,
                 from random_source.cpp:21:
threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory
compilation terminated.
In file included from diff_sample.cpp:20:0:
diff_sample.h:24:21: fatal error: tbb/tbb.h: No such file or directory
compilation terminated.
In file included from ds.h:30:0,
                 from bowtie_build_main.cpp:25:
threading.h:29:24: fatal error: tbb/mutex.h: No such file or directory
compilation terminated.
Makefile:283: recipe for target 'bowtie2-build-s' failed
make: *** [bowtie2-build-s] Error 1

Would you know what went wrong?

Thank you

software error • 732 views
ADD COMMENTlink written 9 months ago by marongiu.luigi210

Could I suggest just using bioconda to install bowtie2? It'll be much easier than working out what libraries are missing and installing them yourself manually.

ADD REPLYlink written 9 months ago by James Ashmore2.5k

Install libtbb-dev and retry.

ADD REPLYlink written 9 months ago by ATpoint5.5k

Yes, it worked (I did not need libtbb-dev when I built the previous version). Thank you.

ADD REPLYlink written 9 months ago by marongiu.luigi210

Newer versions have started requiring that. You could build without TBB by doing WITH_TBB=0 make, if I recollect.

ADD REPLYlink written 9 months ago by genomax51k

Hello, you first install the Threading Building Blocks library, but if unable to do so please specify make NO_TBB=1. TBB comes installed by default on many popular Linux distros. Please note, packages built without TBB will have -legacy appended to the name.

Install TBB library: sudo apt-get update sudo apt-get install libtbb2 # or : sudo apt-get install libtbb-dev

ADD REPLYlink written 9 weeks ago by Lakshman Teja0
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