./gkno build failure on OS X 10.9.2

[bede]

I encounter an error running ./gkno build on an up to date 16GB Mac running OS 10.9.2, with deps Cmake and Ant installed via Homebrew. It's MOSAIK that I wish to use, so I will build that on its own, but thought you might be interested in this output. Let me know if I've missed something obvious.

bede-rmbp:gkno_launcher bede$ ./gkno  build

======================================================
  Boston College gkno package

  version:    0.164
  date:       March 2014
  git commit: e0401ed280228cd38ef29e599b7afc5ff92e541c
======================================================

Checking dependencies...done.
Initializing component data...ERROR: See logs/submodule_update.* files for more details.

================================================================================================
  TERMINATED: Errors found in running gkno.  See specific error messages above for resolution.
================================================================================================

bede-rmbp:gkno_launcher bede$ cd logs
bede-rmbp:logs bede$ ls
submodule_update.err submodule_update.out
bede-rmbp:logs bede$ cat *
Cloning into 'bamtools'...
Cloning into 'intervaltree'...
Cloning into 'vcflib'...
Cloning into 'fastahack'...
Cloning into 'filevercmp'...
Cloning into 'fsom'...
Cloning into 'intervaltree'...
Cloning into 'multichoose'...
Cloning into 'smithwaterman'...
Cloning into 'tabixpp'...
fatal: Needed a single revision
Unable to find current revision in submodule path 'tools/gatk'
Submodule path 'tools/freebayes/bamtools': checked out 'b307a397f7d818d0fa064b91229e312707e43951'
Submodule path 'tools/freebayes/intervaltree': checked out 'd151b487804861dc9f932e9f1fe4f8c499673cec'
Submodule path 'tools/freebayes/vcflib': checked out '060b734035ddb16884a756a97406a32d44f72fef'
Submodule 'fastahack' (git://github.com/ekg/fastahack.git) registered for path 'fastahack'
Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'filevercmp'
Submodule 'fsom' (git://github.com/ekg/fsom.git) registered for path 'fsom'
Submodule 'intervaltree' (git://github.com/ekg/intervaltree.git) registered for path 'intervaltree'
Submodule 'multichoose' (git://github.com/ekg/multichoose.git) registered for path 'multichoose'
Submodule 'smithwaterman' (git://github.com/ekg/smithwaterman.git) registered for path 'smithwaterman'
Submodule 'tabixpp' (git://github.com/ekg/tabixpp.git) registered for path 'tabixpp'
Submodule path 'tools/freebayes/vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd'
Submodule path 'tools/freebayes/vcflib/filevercmp': checked out '378bae779b897f1506043c1b647a5e5f8031ea4b'
Submodule path 'tools/freebayes/vcflib/fsom': checked out 'f688ef24bbe230ec46c7be3de8bf5e67fdbc1b4d'
Submodule path 'tools/freebayes/vcflib/intervaltree': checked out '1290744283cef8076bb8a2968d4899b7228435f4'
Submodule path 'tools/freebayes/vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5'
Submodule path 'tools/freebayes/vcflib/smithwaterman': checked out 'd9724f156c07cf16d00d251bebc20c6383eb6bde'
Submodule path 'tools/freebayes/vcflib/tabixpp': checked out 'c2d6c12eb827805fb13db4bab20f74b212b8b6d0'

[AlistairNWard]

You might have been unlucky on the version that you happened to clone. I
haven't put out the official release (version 1.0.0) yet, but I've fixed
some bugs. If you try recloning and building, hopefully version 0.166
works. I tested an install just now and it worked fine.

Keep me posted if it still doesn't work and I'll look into it in more
detail.

Thanks for letting me know,

Al

On Mon, Mar 24, 2014 at 10:18 AM, Bede Constantinides <
[email protected]> wrote:

I encounter an error running ./gkno build on an up to date 16GB Mac
running OS 10.9.2, with deps Cmake and Ant installed via Homebrew. It's
MOSAIK that I wish to use, so I will build that on its own, but thought you
might be interested in this output. Let me know if I've missed something
obvious.

bede-rmbp:gkno_launcher bede$ ./gkno build

Boston College gkno package

version: 0.164
date: March 2014

git commit: e0401ed

Checking dependencies...done.
Initializing component data...ERROR: See logs/submodule_update.* files for more details.

TERMINATED: Errors found in running gkno. See specific error messages above for resolution.

bede-rmbp:gkno_launcher bede$ cd logs
bede-rmbp:logs bede$ ls
submodule_update.err submodule_update.out
bede-rmbp:logs bede$ cat *
Cloning into 'bamtools'...
Cloning into 'intervaltree'...
Cloning into 'vcflib'...
Cloning into 'fastahack'...
Cloning into 'filevercmp'...
Cloning into 'fsom'...
Cloning into 'intervaltree'...
Cloning into 'multichoose'...
Cloning into 'smithwaterman'...
Cloning into 'tabixpp'...
fatal: Needed a single revision
Unable to find current revision in submodule path 'tools/gatk'
Submodule path 'tools/freebayes/bamtools': checked out 'b307a397f7d818d0fa064b91229e312707e43951'
Submodule path 'tools/freebayes/intervaltree': checked out 'd151b487804861dc9f932e9f1fe4f8c499673cec'
Submodule path 'tools/freebayes/vcflib': checked out '060b734035ddb16884a756a97406a32d44f72fef'
Submodule 'fastahack' (git://github.com/ekg/fastahack.git) registered for path 'fastahack'
Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered for path 'filevercmp'
Submodule 'fsom' (git://github.com/ekg/fsom.git) registered for path 'fsom'
Submodule 'intervaltree' (git://github.com/ekg/intervaltree.git) registered for path 'intervaltree'
Submodule 'multichoose' (git://github.com/ekg/multichoose.git) registered for path 'multichoose'
Submodule 'smithwaterman' (git://github.com/ekg/smithwaterman.git) registered for path 'smithwaterman'
Submodule 'tabixpp' (git://github.com/ekg/tabixpp.git) registered for path 'tabixpp'
Submodule path 'tools/freebayes/vcflib/fastahack': checked out 'c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd'
Submodule path 'tools/freebayes/vcflib/filevercmp': checked out '378bae779b897f1506043c1b647a5e5f8031ea4b'
Submodule path 'tools/freebayes/vcflib/fsom': checked out 'f688ef24bbe230ec46c7be3de8bf5e67fdbc1b4d'
Submodule path 'tools/freebayes/vcflib/intervaltree': checked out '1290744283cef8076bb8a2968d4899b7228435f4'
Submodule path 'tools/freebayes/vcflib/multichoose': checked out '73d35daa18bf35729b9ba758041a9247a72484a5'
Submodule path 'tools/freebayes/vcflib/smithwaterman': checked out 'd9724f156c07cf16d00d251bebc20c6383eb6bde'
Submodule path 'tools/freebayes/vcflib/tabixpp': checked out 'c2d6c12eb827805fb13db4bab20f74b212b8b6d0'

Reply to this email directly or view it on GitHubhttps://github.com//issues/9
.

[AlistairNWard]

Has this issue been solved? We have had a recent post that provides a list of steps that need to be followed to get all tools compiled on a Mac. See the last comment in:

#10

Please let me know if this resolves your problems. Thanks.