AlistairNWard
commented
10 years ago 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 < notifications@github.com> 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: 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'
Reply to this email directly or view it on GitHubhttps://github.com/gkno/gkno_launcher/issues/9 .
I encounter an error running
./gkno buildon 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.