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DecodeGenetics / graphtyper-pipelines

Recommended Graphtyper pipelines
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bamShrink dependency? #7

Open jmonlong opened 4 years ago

jmonlong commented 4 years ago

I'm trying to build a docker container with GraphTyper, the pipeline repo and the necessary dependencies (see current Dockerfile). I'm having problems installing bamShrink. You mentioned in #6 that you might be integrating it to GraphTyper? I've tried different gcc versions but I'm not sure if I should continue down this road. Do you have a recommendation?

For bamShrink I'm trying this in the Dockerfile:

RUN git clone https://github.com/DecodeGenetics/bamShrink.git && \
        cd bamShrink && \
        git checkout 7c6c4497575409b1afd8f84625ac3b5e256f53af && \
        unzip seqan.zip && \
        make bamShrink && \
        mv bamShrink /bin/

I'm getting an error during the compilation:

g++ -Iinclude -pthread -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -lz -DSEQAN_HAS_ZLIB=1 -DNDEBUG=1 -std=c++0x    bamShrink.cpp   -o bamShrink
In file included from include/seqan/basic/basic_allocator.h:53:0,
                 from include/seqan/basic.h:74,
                 from include/seqan/sequence.h:51,
                 from include/seqan/file.h:58,
                 from bamShrink.cpp:2:
In function ‘void seqan::allocate(T&, TValue*&, TSize, const seqan::Tag<TUsage>&) [with T = seqan::String<seqan::CigarElement<> >; TValue = seqan::CigarElement<>; TSize = long unsigned int; TUsage = seqan::AllocateStorage_]’,
    inlined from ‘typename seqan::Value<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type* seqan::_allocateStorage(seqan::String<TValue, seqan::Alloc<TSpec> >&, TSize) [with TValue = seqan::CigarElement<>; TSpec = void; TSize = long unsigned int]’ at include/seqan/sequence/string_alloc.h:360:13,
    inlined from ‘bool removeSoftClipped(seqan::BamAlignmentRecord&, std::map<seqan::String<char, seqan::Alloc<> >, seqan::Pair<MateEditInfo> >&, unsigned int)’ at include/seqan/sequence/string_base.h:1509:45:
include/seqan/basic/allocator_interface.h:227:35: warning: argument 1 value ‘18446744073709551600’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 */  data = (TValue *) operator new(count * sizeof(TValue));
                       ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/exception_ptr.h:40:0,
                 from /usr/include/c++/7/exception:142,
                 from /usr/include/c++/7/ios:39,
                 from /usr/include/c++/7/ostream:38,
                 from /usr/include/c++/7/iostream:39,
                 from bamShrink.cpp:1:
/usr/include/c++/7/new: In function ‘bool removeSoftClipped(seqan::BamAlignmentRecord&, std::map<seqan::String<char, seqan::Alloc<> >, seqan::Pair<MateEditInfo> >&, unsigned int)’:
/usr/include/c++/7/new:120:7: note: in a call to allocation function ‘void* operator new(std::size_t)’ declared here
 void* operator new(std::size_t) _GLIBCXX_THROW (std::bad_alloc)
       ^~~~~~~~
/tmp/ccfbgYEl.o: In function `zlib_stream::basic_zip_streambuf<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::overflow(int)':
bamShrink.cpp:(.text._ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE8overflowEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE8overflowEi]+0x55): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE8overflowEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE8overflowEi]+0x79): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `zlib_stream::basic_unzip_streambuf<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_unzip_streambuf()':
bamShrink.cpp:(.text._ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEED2Ev[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEED5Ev]+0x14): undefined reference to `inflateEnd'
/tmp/ccfbgYEl.o: In function `non-virtual thunk to zlib_stream::basic_zip_istream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_istream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev]+0xab): undefined reference to `inflateEnd'
/tmp/ccfbgYEl.o: In function `virtual thunk to zlib_stream::basic_zip_istream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_istream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev]+0x149): undefined reference to `inflateEnd'
/tmp/ccfbgYEl.o: In function `zlib_stream::basic_unzip_streambuf<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::underflow()':
bamShrink.cpp:(.text._ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEE9underflowEv]+0x89): undefined reference to `inflate'
bamShrink.cpp:(.text._ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEE9underflowEv[_ZN11zlib_stream21basic_unzip_streambufIcSt11char_traitsIcESaIcEhSaIhEE9underflowEv]+0x101): undefined reference to `crc32'
/tmp/ccfbgYEl.o: In function `virtual thunk to zlib_stream::basic_zip_istream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_istream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0xa9): undefined reference to `inflateEnd'
/tmp/ccfbgYEl.o: In function `non-virtual thunk to zlib_stream::basic_zip_istream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_istream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_istreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0x160): undefined reference to `inflateEnd'
/tmp/ccfbgYEl.o: In function `zlib_stream::basic_zip_streambuf<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::sync()':
bamShrink.cpp:(.text._ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE4syncEv[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE4syncEv]+0x6e): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE4syncEv[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE4syncEv]+0x91): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `seqan::VirtualStreamContext_<char, seqan::Tag<seqan::Input_>, std::char_traits<char>, seqan::Tag<seqan::GZFile_> >::~VirtualStreamContext_()':
bamShrink.cpp:(.text._ZN5seqan21VirtualStreamContext_IcNS_3TagINS_6Input_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED2Ev[_ZN5seqan21VirtualStreamContext_IcNS_3TagINS_6Input_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED5Ev]+0x4e): undefined reference to `inflateEnd'
/tmp/ccfbgYEl.o: In function `seqan::Value<seqan::VirtualStreamFactoryContext_<seqan::VirtualStream<char, seqan::Tag<seqan::Input_>, std::char_traits<char> > >, 0>::Type seqan::tagApply<seqan::VirtualStreamFactoryContext_<seqan::VirtualStream<char, seqan::Tag<seqan::Input_>, std::char_traits<char> > >, seqan::TagList<seqan::Tag<seqan::BgzfFile_>, seqan::TagList<seqan::Tag<seqan::GZFile_>, seqan::TagList<seqan::Tag<seqan::Nothing_>, void> > > >(seqan::VirtualStreamFactoryContext_<seqan::VirtualStream<char, seqan::Tag<seqan::Input_>, std::char_traits<char> > >&, seqan::TagSelector<seqan::TagList<seqan::Tag<seqan::BgzfFile_>, seqan::TagList<seqan::Tag<seqan::GZFile_>, seqan::TagList<seqan::Tag<seqan::Nothing_>, void> > > >&)':
bamShrink.cpp:(.text._ZN5seqan8tagApplyINS_28VirtualStreamFactoryContext_INS_13VirtualStreamIcNS_3TagINS_6Input_EEESt11char_traitsIcEEEEENS_7TagListINS3_INS_9BgzfFile_EEENSA_INS3_INS_7GZFile_EEENSA_INS3_INS_8Nothing_EEEvEEEEEEEENS_5ValueIT_Li0EE4TypeERSL_RNS_11TagSelectorIT0_EE[_ZN5seqan8tagApplyINS_28VirtualStreamFactoryContext_INS_13VirtualStreamIcNS_3TagINS_6Input_EEESt11char_traitsIcEEEEENS_7TagListINS3_INS_9BgzfFile_EEENSA_INS3_INS_7GZFile_EEENSA_INS3_INS_8Nothing_EEEvEEEEEEEENS_5ValueIT_Li0EE4TypeERSL_RNS_11TagSelectorIT0_EE]+0xb62): undefined reference to `inflateInit2_'
/tmp/ccfbgYEl.o: In function `zlib_stream::basic_zip_streambuf<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::flush(int)':
bamShrink.cpp:(.text._ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE5flushEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE5flushEi]+0x49): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE5flushEi[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEE5flushEi]+0x5b): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `zlib_stream::basic_zip_streambuf<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_streambuf()':
bamShrink.cpp:(.text._ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEED2Ev[_ZN11zlib_stream19basic_zip_streambufIcSt11char_traitsIcESaIcEhSaIhEED5Ev]+0x26): undefined reference to `deflateEnd'
/tmp/ccfbgYEl.o: In function `non-virtual thunk to zlib_stream::basic_zip_ostream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_ostream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev]+0x166): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev]+0x177): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `virtual thunk to zlib_stream::basic_zip_ostream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_ostream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev]+0x2ed): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED1Ev]+0x301): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `non-virtual thunk to zlib_stream::basic_zip_ostream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_ostream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0x7d): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0x8e): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `virtual thunk to zlib_stream::basic_zip_ostream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_ostream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0x20d): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0x221): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `zlib_stream::basic_zip_ostream<char, std::char_traits<char>, std::allocator<char>, unsigned char, std::allocator<unsigned char> >::~basic_zip_ostream()':
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0x3b6): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev[_ZN11zlib_stream17basic_zip_ostreamIcSt11char_traitsIcESaIcEhSaIhEED0Ev]+0x3ca): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `seqan::VirtualStreamContext_<char, seqan::Tag<seqan::Output_>, std::char_traits<char>, seqan::Tag<seqan::GZFile_> >::~VirtualStreamContext_()':
bamShrink.cpp:(.text._ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED2Ev[_ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED5Ev]+0x84): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED2Ev[_ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED5Ev]+0x98): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `seqan::VirtualStreamContext_<char, seqan::Tag<seqan::Output_>, std::char_traits<char>, seqan::Tag<seqan::GZFile_> >::~VirtualStreamContext_()':
bamShrink.cpp:(.text._ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED0Ev[_ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED5Ev]+0x84): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED0Ev[_ZN5seqan21VirtualStreamContext_IcNS_3TagINS_7Output_EEESt11char_traitsIcENS1_INS_7GZFile_EEEED5Ev]+0x98): undefined reference to `deflate'
/tmp/ccfbgYEl.o: In function `unsigned long seqan::_decompressBlock<char, unsigned long, char, unsigned int>(char*, unsigned long, char*, unsigned int, seqan::CompressionContext<seqan::Tag<seqan::BgzfFile_> >&)':
bamShrink.cpp:(.text._ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE[_ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE]+0xe4): undefined reference to `inflateInit2_'
bamShrink.cpp:(.text._ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE[_ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE]+0x114): undefined reference to `inflate'
bamShrink.cpp:(.text._ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE[_ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE]+0x125): undefined reference to `inflateEnd'
bamShrink.cpp:(.text._ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE[_ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE]+0x13f): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE[_ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE]+0x14d): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE[_ZN5seqan16_decompressBlockIcmcjEET0_PT_S1_PT1_T2_RNS_18CompressionContextINS_3TagINS_9BgzfFile_EEEEE]+0x1ff): undefined reference to `inflateEnd'
/tmp/ccfbgYEl.o: In function `seqan::FormattedFile<seqan::Tag<seqan::Bam_>, seqan::Tag<seqan::Output_>, void>::FormattedFile(seqan::BamIOContext<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::NameStoreCache<seqan::StringSet<seqan::String<char, seqan::Alloc<void> >, seqan::Owner<seqan::Tag<seqan::Default_> > >, seqan::String<char, seqan::Alloc<void> > >, seqan::Dependent<seqan::Tag<seqan::TagInsist_> > >&, char const*, int)':
bamShrink.cpp:(.text._ZN5seqan13FormattedFileINS_3TagINS_4Bam_EEENS1_INS_7Output_EEEvEC2ERNS_12BamIOContextINS_9StringSetINS_6StringIcNS_5AllocIvEEEENS_5OwnerINS1_INS_8Default_EEEEEEENS_14NameStoreCacheISH_SC_EENS_9DependentINS1_INS_10TagInsist_EEEEEEEPKci[_ZN5seqan13FormattedFileINS_3TagINS_4Bam_EEENS1_INS_7Output_EEEvEC5ERNS_12BamIOContextINS_9StringSetINS_6StringIcNS_5AllocIvEEEENS_5OwnerINS1_INS_8Default_EEEEEEENS_14NameStoreCacheISH_SC_EENS_9DependentINS1_INS_10TagInsist_EEEEEEEPKci]+0x14a3): undefined reference to `deflateInit2_'
/tmp/ccfbgYEl.o: In function `seqan::Thread<seqan::basic_bgzf_streambuf<char, std::char_traits<char>, std::allocator<char>, char, std::allocator<char> >::CompressionThread>::_start(void*)':
bamShrink.cpp:(.text._ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv[_ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv]+0x152): undefined reference to `deflateInit2_'
bamShrink.cpp:(.text._ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv[_ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv]+0x18b): undefined reference to `deflate'
bamShrink.cpp:(.text._ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv[_ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv]+0x19d): undefined reference to `deflateEnd'
bamShrink.cpp:(.text._ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv[_ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv]+0x1ca): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv[_ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv]+0x1d8): undefined reference to `crc32'
bamShrink.cpp:(.text._ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv[_ZN5seqan6ThreadINS_20basic_bgzf_streambufIcSt11char_traitsIcESaIcEcS4_E17CompressionThreadEE6_startEPv]+0x9fa): undefined reference to `deflateEnd'
collect2: error: ld returned 1 exit status
<builtin>: recipe for target 'bamShrink' failed
make: *** [bamShrink] Error 1
hannespetur commented 4 years ago

Yes, bamShrink has been integrated in GraphTyper so it's no longer needed to compile it. The full SV genotyping pipeline (BAM/CRAM+SV sites -> SV genotypes in VCF) is now included in the genotype_sv subcommand. The genotype and genotype_sv commands replace the graphtyper-pipelines scripts so you only need the graphtyper binary in your dockerfile. I think you can remove everything after line 36 in your file.

In case you need bamShrink for something else; I think the linking error you get is because it is trying to link to bzip2 but isn't finding it. I am not sure why bzip2 is sometimes needed but adding the flag -lbz2 should fix the issue.

Best, Hannes