{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/761","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/761/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/761/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/761/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/761","id":57669744,"number":761,"title":"Error: bamtools install","user":{"login":"szuszmok","id":10985394,"avatar_url":"https://avatars.githubusercontent.com/u/10985394?v=3","gravatar_id":"","url":"https://api.github.com/users/szuszmok","html_url":"https://github.com/szuszmok","followers_url":"https://api.github.com/users/szuszmok/followers","following_url":"https://api.github.com/users/szuszmok/following{/other_user}","gists_url":"https://api.github.com/users/szuszmok/gists{/gist_id}","starred_url":"https://api.github.com/users/szuszmok/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/szuszmok/subscriptions","organizations_url":"https://api.github.com/users/szuszmok/orgs","repos_url":"https://api.github.com/users/szuszmok/repos","events_url":"https://api.github.com/users/szuszmok/events{/privacy}","received_events_url":"https://api.github.com/users/szuszmok/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-02-13T23:50:17Z","updated_at":"2015-02-14T08:53:20Z","closed_at":"2015-02-14T08:53:20Z","body":"Hi Brad,\r\n\r\nI couldn't finish the installation process, because of the bamtools download link is not available. At least I think this is the problem, but not sure.\r\n\r\nAny suggestions for solving are welcome and thank you much!\r\n\r\n[localhost] local: /usr/local/bin/brew info samtools\r\n[localhost] local: export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit   bamtools\r\n\r\nWarning: local() encountered an error (return code 1) while executing 'export CC=${CC:-`which gcc`} && export CXX=${CXX:-`which g++`} && export PERL5LIB=/usr/local/lib/perl5:${PERL5LIB} && /usr/local/bin/brew install --env=inherit   bamtools'\r\n\r\nTraceback (most recent call last):\r\n  File \"/usr/local/share/bcbio/anaconda/bin/bcbio_nextgen.py\", line 199, in <module>\r\n    install.upgrade_bcbio(kwargs[\"args\"])\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/install.py\", line 75, in upgrade_bcbio\r\n    upgrade_thirdparty_tools(args, REMOTES)\r\n  File \"/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/install.py\", line 335, in upgrade_thirdparty_tools\r\n    cbl_deploy.deploy(s)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py\", line 65, in deploy\r\n    _setup_vm(options, vm_launcher, actions)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py\", line 110, in _setup_vm\r\n    configure_instance(options, actions)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py\", line 255, in configure_instance\r\n    install_biolinux(options)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/cloudbio/deploy/__init__.py\", line 279, in install_biolinux\r\n    _perform_install(target=target, flavor=flavor, more_custom_add=options.get(\"custom_add\", None))\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/fabfile.py\", line 118, in _perform_install\r\n    install_brew(flavor=flavor, automated=True)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/fabfile.py\", line 308, in install_brew\r\n    brew.install_packages(env, to_install=pkg_install)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/cloudbio/package/brew.py\", line 49, in install_packages\r\n    _install_pkg(env, pkg_str, brew_cmd, ipkgs)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/cloudbio/package/brew.py\", line 87, in _install_pkg\r\n    _install_pkg_latest(env, pkg, args, brew_cmd, ipkgs)\r\n  File \"/home/szandra/tmpbcbio-install/cloudbiolinux/cloudbio/package/brew.py\", line 205, in _install_pkg_latest\r\n    raise ValueError(\"Failed to install brew formula: %s\" % pkg)\r\nValueError: Failed to install brew formula: bamtools\r\nTraceback (most recent call last):\r\n  File \"bcbio_nextgen_install.py\", line 255, in <module>\r\n    main(parser.parse_args(), sys.argv[1:])\r\n  File \"bcbio_nextgen_install.py\", line 41, in main\r\n    subprocess.check_call([bcbio[\"bcbio_nextgen.py\"], \"upgrade\"] + _clean_args(sys_argv, args, bcbio))\r\n  File \"/usr/lib64/python2.7/subprocess.py\", line 540, in check_call\r\n    raise CalledProcessError(retcode, cmd)\r\nsubprocess.CalledProcessError: Command '['/usr/local/share/bcbio/anaconda/bin/bcbio_nextgen.py', 'upgrade', '--tooldir=/usr/local', '--genomes', 'GRCh37', '--aligners', 'bwa', '--aligners', 'bowtie2', '--data']' returned non-zero exit status 1\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/74367597","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/761#issuecomment-74367597","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/761","id":74367597,"user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2015-02-14T08:53:20Z","updated_at":"2015-02-14T08:53:20Z","body":"Sorry about the installation issue. There was a new version of the cmake dependency released in homebrew and the pre-compiled bottle we'd prepared was not installing correctly. cmake can end up being tricky to build, so it is likely failing during the bamtools build here.\r\n\r\nI pushed a fix to CloudBioLinux to resolve this: https://github.com/chapmanb/cloudbiolinux/commit/49c6a6b1b0af9033c48c6eb0b8424e3aea7fe55f If you remove any cached CloudBioLinux installs:\r\n```\r\nrm -rf tmpbcbio-install\r\n```\r\nand re-run, it should now pre-fetch the cmake dependency and work cleanly. Sorry about the issue and thanks much for reporting it."}}