Version of Jellyfish required

[colinbrislawn]

Good afternoon,

I'm trying to build a conda recipe for Quorum, and would like to know the version of Jellyfish required. There is a recipy for Jellyfish 2.2.3 on bioconda. Is that sufficient?

While I'm asking, does Quorum require autoconf/automake and yaggo to run, or just to install? Any guidance you have on how to build this software would be greatly appreciated.

[gmarcais]

Hi,

you do not need any extra software to build Jellyfish or Quorum, beside gcc and make, provided that you start from the release distribution. Download the file called jellyfish-<version>.tar.gz, unpack, configure and make. You do NOT need autoconf/automake, and you do NOT need yaggo to either build, install or run Jellyfish (or Quorum for that matter). That's because automake bundled every generated file in the distribution tarball, including the configure shell script. The recipe for Jellyfish in bioconda is doing too much by requiring autoconf, yaggo and pkg-config.

Now, to build quorum, jellyfish should be installed and the jellyfish-2.0.pc file should be found by pkg-config. That should hold true by default if you installed Jellyfish in /usr/local (the default). Otherwise, you may have to adjust the PKG_CONFIG_PATH variable or pass extra arguments to ./configure: JELLYFISH2_0_CFLAGS and JELLYFISH2_0_LIBS.

Now version 2.2.3 of Jellyfish should be perfectly fine to run Quorum.

[colinbrislawn]

Thank you for your feedback. I'm not sure where conda installs jellyfish by default or if it's found by pkg-config, but this is a great place to start.

Thank you for your time.

[colinbrislawn]

When running make, I get this error:

/Library/Developer/CommandLineTools/usr/bin/make  all-am
  CXX      src/error_correct_reads.o
In file included from src/error_correct_reads.cc:26:
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/stream_manager.hpp:65:16: error: no type named 'unique_ptr' in namespace 'std'
  typedef std::unique_ptr<std::istream> stream_type;
          ~~~~~^
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/stream_manager.hpp:65:26: error: expected member name or ';' after declaration specifiers
  typedef std::unique_ptr<std::istream> stream_type;
  ~~~~~~~~~~~~~~~~~~~~~~~^
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/stream_manager.hpp:92:3: error: unknown type name 'stream_type'
  stream_type next() {
  ^
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/stream_manager.hpp:108:23: error: unknown type name 'stream_type'
  void open_next_file(stream_type& res) {
                      ^
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/stream_manager.hpp:122:23: error: unknown type name 'stream_type'
  void open_next_pipe(stream_type& res) {
                      ^
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/stream_manager.hpp:94:5: error: unknown type name 'stream_type'
    stream_type res;
    ^
In file included from src/error_correct_reads.cc:27:
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/whole_sequence_parser.hpp:25:16: error: no type named 'unique_ptr' in namespace 'std'
  typedef std::unique_ptr<std::istream> stream_type;
          ~~~~~^
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/whole_sequence_parser.hpp:25:26: error: expected member name or ';' after declaration specifiers
  typedef std::unique_ptr<std::istream> stream_type;
  ~~~~~~~~~~~~~~~~~~~~~~~^
/Users/bris469/miniconda3/conda-bld/quorum_1480468782763/_b_env_placehold_placeh/include/jellyfish-2.2.6/jellyfish/whole_sequence_parser.hpp:31:5: error: unknown type name 'stream_type'
    stream_type stream;
    ^
In file included from src/error_correct_reads.cc:29:

...<I'll omit the rest of the error>

I'm not sure if this error is coming from jellyfish, quorum, or my build environment.

Thank you for helping me out with this!

[colinbrislawn]

Hello there,

I've been working on installing this package, and this works fine when I install jellyfish to /usr/local. However, I can't get it to find jellyfish when I install it with conda install jellyfish, even with I set the PKG_CONFIG_PATH to my conda environment.

Any other settings I should change so that Quorum can work in a non-default location?