chapmanb
commented
11 years ago Thanks again for the detailed report. The script was making the assumption that the directory you're installed in was on the PATH. To avoid around this assumption, cloudbiolinux now adds the directory to the users path if not present:
https://github.com/chapmanb/cloudbiolinux/commit/835c356a9d32ba8274b58e82f7038e13b591f585
You'll need to remove the tmpbcbio-install directory and the install script will grab this latest revision. Hope this moves things along for you.
I am trying to insyall the software and I am getting the following error. I have pasted the complete output in case you may want to see it.
thanks in advance into
$ python2.7 bcbio_nextgen_install.py --distribution centos --nosudo /home/pedrosoi/APP/bcbio_nextgen/install_directory /home/pedrosoi/APP/bcbio_nextgen/data_directory Installing tools... [localhost] Executing task 'install_biolinux' INFO: Config start time: 2013-02-05 22:41:40.486109 INFO: This is a Base Flavor - no overrides DBG [init.py]: Minimal Edition 1.5.3 INFO: This is a minimal INFO: Distribution centos INFO: Get local environment INFO: CentOS setup DBG [distribution.py]: Checking target distribution centos DBG [distribution.py]: Unknown target distro DBG [distribution.py]: NixPkgs: Ignored [localhost] run: echo $HOME [localhost] out: /home/pedrosoi [localhost] out:
[localhost] run: uname -m [localhost] out: x86_64 [localhost] out:
INFO: Now, testing connection to host... INFO: Connection to host appears to work! DBG [utils.py]: Expand paths DBG [fabfile.py]: Target is 'None' DBG [config.py]: Using config file /home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline/main.yaml INFO: Meta-package information from /home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/cloudbio/../contrib/flavor/ngs_pipeline/main.yaml
[localhost] run: wget --no-check-certificate https://raw.github.com/technomancy/leiningen/stable/bin/lein [localhost] out: --2013-02-05 22:41:42-- https://raw.github.com/technomancy/leiningen/stable/bin/lein [localhost] out: Resolving raw.github.com... 199.27.77.130 [localhost] out: Connecting to raw.github.com|199.27.77.130|:443... connected. [localhost] out: WARNING: certificate common name “*.a.ssl.fastly.net” doesn’t match requested host name “raw.github.com”. [localhost] out: HTTP request sent, awaiting response... 200 OK [localhost] out: Length: 10250 (10K) [text/plain] [localhost] out: Saving to: “lein.1” [localhost] out: [localhost] out: [localhost] out: 0% [ ] 0 --.-K/s
[localhost] out: 100%[==========================================================================>] 10,250 --.-K/s in 0s
[localhost] out: [localhost] out: 2013-02-05 22:41:42 (49.4 MB/s) - “lein.1” saved [10250/10250] [localhost] out: [localhost] out:
[localhost] run: chmod a+rwx lein [localhost] run: mv lein /home/pedrosoi/APP/bcbio_nextgen/install_directory/bin [localhost] run: lein [localhost] out: /bin/bash: lein: command not found [localhost] out:
Fatal error: run() received nonzero return code 127 while executing!
Requested: lein Executed: /bin/bash -l -c "cd /home/pedrosoi/tmp/cloudbiolinux && lein"
Aborting. Disconnecting from localhost... done. Traceback (most recent call last): File "bcbio_nextgen_install.py", line 159, in
main(parser.parse_args())
File "bcbio_nextgen_install.py", line 37, in main
install_tools(cbl["tool_fabfile"], fabricrc)
File "bcbio_nextgen_install.py", line 71, in install_tools
"install_biolinux:flavor=ngs_pipeline"])
File "/home/pedrosoi/python/lib/python2.7/subprocess.py", line 511, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['fab', '-f', '/home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/cloudbiolinux/fabfile.py', '-H', 'localhost', '-c', '/home/pedrosoi/APP/bcbio_nextgen/tmpbcbio-install/fabricrc.txt', 'install_biolinux:flavor=ngs_pipeline']' returned non-zero exit status 1