Question: Build Bowtie2 2.3.3.1 with make on linux 64 bit
1
gravatar for marongiu.luigi
2.0 years ago by
Germany, Mannheim, UMM
marongiu.luigi380 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 • 1.8k views
ADD COMMENTlink written 2.0 years ago by marongiu.luigi380

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 2.0 years ago by James Ashmore2.7k

Install libtbb-dev and retry.

ADD REPLYlink written 2.0 years ago by ATpoint24k

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

ADD REPLYlink written 2.0 years ago by marongiu.luigi380

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

ADD REPLYlink written 2.0 years ago by genomax73k

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 17 months ago by Lakshman Teja30
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: 2127 users visited in the last hour