1. 18 Sep, 2020 1 commit
  2. 17 Sep, 2020 3 commits
  3. 16 Sep, 2020 1 commit
  4. 15 Sep, 2020 4 commits
  5. 10 Sep, 2020 1 commit
  6. 04 Sep, 2020 1 commit
  7. 03 Sep, 2020 1 commit
  8. 02 Sep, 2020 4 commits
  9. 09 Oct, 2019 2 commits
  10. 07 Oct, 2019 2 commits
  11. 02 Oct, 2019 2 commits
  12. 01 Oct, 2019 2 commits
  13. 30 Sep, 2019 2 commits
  14. 26 Sep, 2019 3 commits
  15. 25 Sep, 2019 1 commit
    • Blaise Li's avatar
      Hopefully cleaner compilng process. · 482453e0
      Blaise Li authored
      Moved most code to the QafDemux package, added a "snoopfile" in the hope
      that code will be more exhaustively analyzed during compilation.
      
      This does not avoid runtime error:
      
          fatal: error thrown and no exception handler available.
          MethodError(f=typeof(Base.convert)(), args=(Int32, nothing),
          world=0x00000000000065d9)
          rec_backtrace at /home/bli/src/julia/src/stackwalk.c:94
          record_backtrace at /home/bli/src/julia/src/task.c:219 [inlined]
          jl_throw at /home/bli/src/julia/src/task.c:429
          jl_method_error_bare at /home/bli/src/julia/src/gf.c:1606
          jl_method_error at /home/bli/src/julia/src/gf.c:1624
          jl_apply_generic at /home/bli/src/julia/src/gf.c:2161
          julia_main at
          /home/bli/src/qaf_demux/Julia/QafDemux/bin/qaf_demux_to_compile.jl:12
          julia_main at
          /home/bli/src/qaf_demux/Julia/QafDemux/deps/builddir/qaf_demux.so
          (unknown line)
          main at ./deps/builddir/qaf_demux (unknown line)
          __libc_start_main at
          /build/glibc-LK5gWL/glibc-2.23/csu/../csu/libc-start.c:291
          _start at ./deps/builddir/qaf_demux (unknown line)
      
      See also https://stackoverflow.com/q/58105935/1878788
      482453e0
  16. 24 Sep, 2019 10 commits
    • Blaise Li's avatar
      Fixing FASTX version. · 82b4f39a
      Blaise Li authored
      Now the test using the plain non-compiled version works.
      82b4f39a
    • Blaise Li's avatar
      Some info about version of FASTX needed. · f3ff921e
      Blaise Li authored
      f3ff921e
    • Blaise Li's avatar
      Changing variable name to debug. · 1ad670be
      Blaise Li authored
      This is what happens when testing during the %post phase of the build of
      a singularity container:
      
      ```
      ERROR: LoadError: UndefVarError: stream not defined
      Stacktrace:
       [1] check_channel_state at ./channels.jl:117 [inlined]
       [2] take_unbuffered(::Channel{Any}) at ./channels.jl:366
       [3] take! at ./channels.jl:344 [inlined]
       [4] iterate(::Channel{Any}, ::Nothing) at ./channels.jl:410
       [5] iterate at ./channels.jl:409 [inlined]
       [6] (::getfield(Main,
      Symbol("##5#8")){String,Array{String,1},UInt8,Float64})(::Dict{String,FASTX.FASTQ.Writer})
      at /usr/local/src/qaf_demux/Julia/QafDemux/bin/qaf_demux.jl:105
       [7] make_record_writers(::getfield(Main,
      Symbol("##5#8")){String,Array{String,1},UInt8,Float64},
      ::Dict{String,String}) at
      /usr/local/src/qaf_demux/Julia/QafDemux/src/QafDemux.jl:258
       [8] julia_main() at
      /usr/local/src/qaf_demux/Julia/QafDemux/bin/qaf_demux.jl:102
       [9] top-level scope at
      /usr/local/src/qaf_demux/Julia/QafDemux/bin/qaf_demux.jl:118
       [10] include at ./boot.jl:328 [inlined]
       [11] include_relative(::Module, ::String) at ./loading.jl:1094
       [12] include(::Module, ::String) at ./Base.jl:31
       [13] exec_options(::Base.JLOptions) at ./client.jl:295
       [14] _start() at ./client.jl:464
      in expression starting at
      /usr/local/src/qaf_demux/Julia/QafDemux/bin/qaf_demux.jl:118
      ```
      1ad670be
    • Blaise Li's avatar
      Make the main script active again. · 78d80efc
      Blaise Li authored
      It did not have an active `julia_main`.
      A separate script is now used for compilation.
      78d80efc
    • Blaise Li's avatar
      The compiled executable crashes. Debugging. · 2c156c39
      Blaise Li authored
      2c156c39
    • Blaise Li's avatar
      More details in the README. · 6d7b765a
      Blaise Li authored
      6d7b765a
    • Blaise Li's avatar
      Build and usage information for Julia version. · 6fef93b0
      Blaise Li authored
      6fef93b0
    • Blaise Li's avatar
      Testing one compilation option. · 09c31ab0
      Blaise Li authored
      09c31ab0
    • Blaise Li's avatar
      Trying to make executable more portable. · 3774863b
      Blaise Li authored
      3774863b
    • Blaise Li's avatar
      Singularity containers for debian stretch. · 10557266
      Blaise Li authored
      Still do not work on tars:
      
          $ ./qaf_demux_local --help
          ERROR: Unable to find compatible target in system image.
      10557266