Issue installing RAMBL

[igorspp]

I have been trying to install RAMBL but an error is raised during compiling. This is what I have done so far:

# Create conda environment
conda create -n rambl python=2.7.10

source activate rambl

# Install bowtie, samtools, bedtools, seqtk and python libraries
conda install -c bioconda bowtie2=2.2.4 samtools=0.1.19 bedtools=2.24.0 seqtk=1.2 ete2=2.3.10 scipy=0.15.1 numpy=1.9.2 scikit-bio=0.4.0 biopython=1.65

# Install sickle
cd /wrk/stelmach/DONOTREMOVE/bioconda3_env/rambl/
wget http://www.zlib.net/zlib-1.2.11.tar.gz
tar zxf zlib-1.2.11.tar.gz

cd zlib-1.2.11
./configure --prefix=/wrk/stelmach/DONOTREMOVE/bioconda3_env/rambl/
make install prefix=/wrk/stelmach/DONOTREMOVE/bioconda3_env/rambl/

cd ..
git clone https://github.com/najoshi/sickle.git

cd sickle
make
mv sickle ../bin/

# Install RAMBL
export CXX=$(which gcc)
git clone https://github.com/homopolymer/RAMBL.git
cd RAMBL
python setup.py install --prefix=/wrk/stelmach/DONOTREMOVE/bioconda3_env/rambl/

These are the last lines of output during compiling, before the error is raised:

extract_mapped_reads.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSs4ReadESt10_Select1stIS3_ESt4lessISsESaIS3_EE14_M_create_nodeIIRKSt21piecewise_construct_tSt5tupleIIRS1_EESE_IIEEEEEPSt13_Rb_tree_nodeIS3_EDpOT_[_ZNSt8_Rb_treeISsSt4pairIKSs4ReadESt10_Select1stIS3_ESt4lessISsESaIS3_EE14_M_create_nodeIIRKSt21piecewise_construct_tSt5tupleIIRS1_EESE_IIEEEEEPSt13_Rb_tree_nodeIS3_EDpOT_]+0xb9): undefined reference to `__cxa_begin_catch'
extract_mapped_reads.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSs4ReadESt10_Select1stIS3_ESt4lessISsESaIS3_EE14_M_create_nodeIIRKSt21piecewise_construct_tSt5tupleIIRS1_EESE_IIEEEEEPSt13_Rb_tree_nodeIS3_EDpOT_[_ZNSt8_Rb_treeISsSt4pairIKSs4ReadESt10_Select1stIS3_ESt4lessISsESaIS3_EE14_M_create_nodeIIRKSt21piecewise_construct_tSt5tupleIIRS1_EESE_IIEEEEEPSt13_Rb_tree_nodeIS3_EDpOT_]+0xd1): undefined reference to `__cxa_rethrow'
/tmp/stelmach/cchCsp64.o: In function `std::_Rb_tree<std::string, std::pair<std::string const, Read>, std::_Select1st<std::pair<std::string const, Read> >, std::less<std::string>, std::allocator<std::pair<std::string const, Read> > >::_M_insert_node(std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node<std::pair<std::string const, Read> >*)':
extract_mapped_reads.cpp:(.text._ZNSt8_Rb_treeISsSt4pairIKSs4ReadESt10_Select1stIS3_ESt4lessISsESaIS3_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSB_PSt13_Rb_tree_nodeIS3_E[_ZNSt8_Rb_treeISsSt4pairIKSs4ReadESt10_Select1stIS3_ESt4lessISsESaIS3_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSB_PSt13_Rb_tree_nodeIS3_E]+0x8c): undefined reference to `std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)'
/tmp/stelmach/cchCsp64.o: In function `std::_Rb_tree_iterator<std::pair<std::string const, Read> >::operator--()':
extract_mapped_reads.cpp:(.text._ZNSt17_Rb_tree_iteratorISt4pairIKSs4ReadEEmmEv[_ZNSt17_Rb_tree_iteratorISt4pairIKSs4ReadEEmmEv]+0x17): undefined reference to `std::_Rb_tree_decrement(std::_Rb_tree_node_base*)'
/tmp/stelmach/cchCsp64.o: In function `std::_Rb_tree_iterator<std::pair<std::string const, Read> >::operator++()':
extract_mapped_reads.cpp:(.text._ZNSt17_Rb_tree_iteratorISt4pairIKSs4ReadEEppEv[_ZNSt17_Rb_tree_iteratorISt4pairIKSs4ReadEEppEv]+0x17): undefined reference to `std::_Rb_tree_increment(std::_Rb_tree_node_base*)'
/tmp/stelmach/cchCsp64.o: In function `__gnu_cxx::new_allocator<std::_Rb_tree_node<std::pair<std::string const, Read> > >::allocate(unsigned long, void const*)':
extract_mapped_reads.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeISt4pairIKSs4ReadEEE8allocateEmPKv[_ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeISt4pairIKSs4ReadEEE8allocateEmPKv]+0x2c): undefined reference to `std::__throw_bad_alloc()'
extract_mapped_reads.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeISt4pairIKSs4ReadEEE8allocateEmPKv[_ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeISt4pairIKSs4ReadEEE8allocateEmPKv]+0x3c): undefined reference to `operator new(unsigned long)'
/tmp/stelmach/cchCsp64.o: In function `__gnu_cxx::new_allocator<std::_Rb_tree_node<std::pair<std::string const, Read> > >::deallocate(std::_Rb_tree_node<std::pair<std::string const, Read> >*, unsigned long)':
extract_mapped_reads.cpp:(.text._ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeISt4pairIKSs4ReadEEE10deallocateEPS6_m[_ZN9__gnu_cxx13new_allocatorISt13_Rb_tree_nodeISt4pairIKSs4ReadEEE10deallocateEPS6_m]+0x1c): undefined reference to `operator delete(void*)'
/tmp/stelmach/cchCsp64.o: In function `std::pair<std::string const, Read>::~pair()':
extract_mapped_reads.cpp:(.text._ZNSt4pairIKSs4ReadED2Ev[_ZNSt4pairIKSs4ReadED5Ev]+0x24): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()'
/tmp/stelmach/cchCsp64.o: In function `std::pair<std::string const, Read>::pair<std::string const&, 0ul>(std::tuple<std::string const&>&, std::tuple<>&, std::_Index_tuple<0ul>, std::_Index_tuple<>)':
extract_mapped_reads.cpp:(.text._ZNSt4pairIKSs4ReadEC2IIRS0_EILm0EEIEIEEERSt5tupleIIDpT_EERS5_IIDpT1_EESt12_Index_tupleIIXspT0_EEESE_IIXspT2_EEE[_ZNSt4pairIKSs4ReadEC5IIRS0_EILm0EEIEIEEERSt5tupleIIDpT_EERS5_IIDpT1_EESt12_Index_tupleIIXspT0_EEESE_IIXspT2_EEE]+0x37): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
extract_mapped_reads.cpp:(.text._ZNSt4pairIKSs4ReadEC2IIRS0_EILm0EEIEIEEERSt5tupleIIDpT_EERS5_IIDpT1_EESt12_Index_tupleIIXspT0_EEESE_IIXspT2_EEE[_ZNSt4pairIKSs4ReadEC5IIRS0_EILm0EEIEIEEERSt5tupleIIDpT_EERS5_IIDpT1_EESt12_Index_tupleIIXspT0_EEESE_IIXspT2_EEE]+0x58): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()'
/tmp/stelmach/cchCsp64.o:(.eh_frame+0xcb): undefined reference to `__gxx_personality_v0'
collect2: error: ld returned 1 exit status
creating build/lib
error: can't copy '/wrk/stelmach/DONOTREMOVE/bioconda3_env/rambl/RAMBL/StrainCall/StrainCall': doesn't exist or not a regular file

Any thoughts on this? Cheers!