Compile items

[wasade]

Address a few items that blocked compilation. With these changes, I was able to successfully compile using the following command:

$ PREFIX=../ariadne-1.0 C_INCLUDE_PATH=~/miniconda3/envs/ariadne-gcc8.5.0/include/ CPLUS_INCLUDE_PATH=~/miniconda3/envs/ariadne-gcc8.5.0/include/ ./spades_compile.sh -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++)

However, while the compilation completed without error, runtime execution was unsuccessful. Details are below. I'm not sure how to resolve these without investiging how spades init works, which I suspect must be tinkering with python path

$ ./spades.py 
Traceback (most recent call last):
  File "/home/mcdonadt/2023.08.29-ariadne/ariadne/ariadne-1.0/bin/./spades.py", line 22, in <module>
    spades_init.init()
  File "/home/mcdonadt/2023.08.29-ariadne/ariadne/ariadne-1.0/bin/spades_init.py", line 42, in init
    spades_version = open(join(spades_home, 'VERSION'), 'r').readline().strip()
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/mcdonadt/2023.08.29-ariadne/ariadne/ariadne-1.0/bin/VERSION'

If VERSION is provided, the runtime execution still encounters an issue:

$ cp ../../VERSION .
$ ./spades.py 
Traceback (most recent call last):
  File "/home/mcdonadt/2023.08.29-ariadne/ariadne/ariadne-1.0/bin/./spades.py", line 29, in <module>
    import support
ModuleNotFoundError: No module named 'support'

The environment used is specified below:

$ conda env export
name: ariadne-gcc8.5.0
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - binutils_impl_linux-64=2.40=hf600244_0
  - bzip2=1.0.8=h7f98852_4
  - gcc=8.5.0=h143be6b_10
  - gcc_impl_linux-64=8.5.0=hef569ad_19
  - gxx=8.5.0=h143be6b_10
  - gxx_impl_linux-64=8.5.0=hef569ad_19
  - kernel-headers_linux-64=2.6.32=he073ed8_16
  - ld_impl_linux-64=2.40=h41732ed_0
  - libgcc-devel_linux-64=8.5.0=ha5d7ed8_19
  - libgcc-ng=13.1.0=he5830b7_0
  - libgomp=13.1.0=he5830b7_0
  - libsanitizer=8.5.0=hb70a093_19
  - libstdcxx-devel_linux-64=8.5.0=ha5d7ed8_19
  - libstdcxx-ng=13.1.0=hfd8a6a1_0
  - libzlib=1.2.13=hd590300_5
  - ncurses=6.4=hcb278e6_0
  - readline=8.2=h8228510_1
  - sysroot_linux-64=2.12=he073ed8_16
  - zlib=1.2.13=hd590300_5
prefix: /home/mcdonadt/miniconda3/envs/ariadne-gcc8.5.0