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#260 bowtie installation failing in cygwin

closed
nobody
7
2013-01-08
2012-12-14
Bharat Ravi
No

What all dependencies does bowtie require for installation. I installed all the Dev libraries for cygwin but it is still showing this message:

$ make
cat ebwt_search.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cp p hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp ccnt_ lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp bitset.h aligner_see d_mm.h edit.h formats.h timer.h word_io.h sequence_io.h aligner_0mm.h hit_set.h color.h random_source.h zbox.h ref_read.h assert_helpers.h threading.h binary_sa _search.h refmap.h shmem.h range_source.h alphabet.h search_globals.h aligner.h ref_aligner.h tokenize.h auto_array.h aligner_23mm.h multikey_qsort.h reference. h sam.h ebwt_search_util.h bitpack.h str_util.h ebwt_search_backtrack.h color_de c.h annot.h aligner_metrics.h mm.h endian_swap.h range.h row_chaser.h blockwise_ sa.h log.h ebwt.h range_chaser.h qual.h diff_sample.h pat.h range_cache.h pool.h hit.h aligner_1mm.h filebuf.h spinlock.h search_seeded_phase1.c search_seeded_p hase4.c search_1mm_phase2.c search_23mm_phase3.c search_seeded_phase2.c search_1 mm_phase1.c search_23mm_phase1.c search_23mm_phase2.c search_seeded_phase3.c | m d5sum | awk '{print $1}' > .bowtie.md5
/usr/bin/g++ -O3 -DCOMPILER_OPTIONS="\"-O3 \"" \ -DEBWT_SEARCH_HASH=`cat .bowtie.md5` \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST ="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g+ + -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURC E -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DNDEBUG -Wall \ -I SeqAn-1.1 \ -o bowtie ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp qual.c pp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -L . -lpthreadGC2
/usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld: cannot find -lpthreadGC2
collect2: ld returned 1 exit status
Makefile:223: recipe for target `bowtie' failed
make: *** [bowtie] Error 1

Discussion

  • Bharat Ravi

    Bharat Ravi - 2012-12-14
    • labels: 1145370 --> Interface (example)
    • priority: 5 --> 7
     
  • Ben Langmead

    Ben Langmead - 2013-01-08

    Per the manual:

    http://bowtie-bio.sourceforge.net/manual.shtml#building-from-source

    You will need to install the win32 version of the pthreads library if you would like to compile with threads enabled. Otherwise, to compile without threads, use make BOWTIE_PTHREADS=0.

    Best,
    Ben

     
  • Ben Langmead

    Ben Langmead - 2013-01-08
    • status: open --> closed
     

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