Bowtie2 Build error in CygWin

Question

[NGS-Newbie]

Hi All

I am trying to build bowtie2 on cygwin (Windows10). I tried to "make" it from the source file.

1) Even after installing Thread Building Blocks from Intel website, I get following error - 
$ 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 \
        -lreadline -ltermcap -lz -lpthread -ltbb -ltbbmalloc_proxy
In file included from bt2_idx.h:42:0,
                 from bt2_build.cpp:27:
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.
make: *** [Makefile:281: bowtie2-build-s] Error 1

2) So, I tried it with "NO_TBB=1" option. But I still get an error - 

$ make NO_TBB=1
g++ -O3 -m64 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY \
        -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 tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
        -lreadline -ltermcap -lz -lpthread
/usr/lib/gcc/x86_64-pc-cygwin/5.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -lreadline
/usr/lib/gcc/x86_64-pc-cygwin/5.4.0/../../../../x86_64-pc-cygwin/bin/ld: cannot find -ltermcap
collect2: error: ld returned 1 exit status
make: *** [Makefile:281: bowtie2-build-s] Error 1

Any suggestions?

Thanks so much to you all!

[GenoMax]

I have formatted your code correctly. In future use the icon shown below (after highlighting the text you want to format as code) when editing (screencap courtesy of @Wouter).

[NGS-Newbie]

Thanks genomax2!

I highly appreciate it!

[GenoMax]

Why not use the bash shell on windows 10 directly? It is known to work with native linux versions of most programs.

Answer 1

[h.mon]

Download a compiled version, they have Windows versions up to Bowtie2-2.3.0.