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add weblogo #114

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@tanglingfung

add weblogo as well as (template.pm, logo.pm and template.eps) to the path

hope this one will work

(I copied from the way how vcftools is installed, please advice)

@tanglingfung tanglingfung add weblogo
add weblogo as well as (template.pm, logo.pm and template.eps) to the path
bebccb6
@afgane afgane added a commit that referenced this pull request
@afgane afgane Merge #114 49acdc9
@afgane
Collaborator

Merged in 49acdc9 as a follow up to my version of the fix (which just happened to take place at the same minute)

However, I'm still not able to run successfully this to completion and it's starting to feel it's beyond me.
Running fab -f fabfile.py -H ubuntu@<IP> -i <key> install_custom:weblogo, it comes up with the following error (I added a bunch of extra log statements while debugging this):

[ubuntu@118.138.241.73] run: tar -xzpf weblogo.2.8.2.tar.gz
DBG [shared.py]: dir_name: weblogo.2.8.2; need_dir True
DBG [shared.py]: Found a nasty dir name as weblogo/
DBG [shared.py]: Done unpacking; heading for work_dir /home/ubuntu/tmp/cloudbiolinux and tool dir weblogo/
DBG [shared.py]: No post_unpack_fn provided
DBG [shared.py]: Running make command
DBG [shared.py]: Running find_cmd find -perm -100 -type f
DBG [shared.py]: getting install subdir; sys install dir: /usr & subdir bin
DBG [shared.py]: Got path: /usr/bin (exists? False)
DBG [shared.py]: Path /usr/bin does not exist!
[ubuntu@118.138.241.73] sudo: mkdir -p '/usr/bin'
[ubuntu@118.138.241.73] out: bash: cd: /home/ubuntu/tmp/cloudbiolinux/: No such file or directory
[ubuntu@118.138.241.73] out: bash: 34mweblogo/: No such file or directory
[ubuntu@118.138.241.73] out:

Fatal error: sudo() received nonzero return code 127 while executing!

Requested: mkdir -p '/usr/bin'
Executed: sudo -S -p 'sudo password:' /bin/bash -i -c "cd /home/ubuntu/tmp/cloudbiolinux/weblogo/ && mkdir -p '/usr/bin'"

Aborting.
Disconnecting from ubuntu@118.138.241.73... done.

How come it's not seeing /usr/bin???

If I run the same command for a different but comparable tool (star or vcf tools, for example), it works fine:

$ fab -f fabfile.py -H ubuntu@ -i install_custom:star
...
DBG [shared.py]: Running find_cmd find -name 'STAR'
DBG [shared.py]: getting install subdir; sys install dir: /usr & subdir bin
DBG [shared.py]: Got path: /usr/bin (exists? True)
DBG [shared.py]: _get_install_subdir returning /usr/bin
DBG [shared.py]: Got install_dir as /usr/bin
[ubuntu@118.138.241.73] run: find -name 'STAR'
[ubuntu@118.138.241.73] out: ./STAR
[ubuntu@118.138.241.73] out:

DBG [shared.py]: env.safe_run_output(find_cmd).split("
"): ['./STAR']
[ubuntu@118.138.241.73] run: find -name 'STAR'
[ubuntu@118.138.241.73] out: ./STAR
[ubuntu@118.138.241.73] out:

[ubuntu@118.138.241.73] sudo: cp -rf ./STAR /usr/bin
DBG [shared.py]: _do_work done
[ubuntu@118.138.241.73] run: rm -rf /home/ubuntu/tmp/cloudbiolinux
INFO: Custom install for 'star' end time: 2013-09-03 10:11:04.638655; duration: 0:01:23.031771

Done.
Disconnecting from ubuntu@118.138.241.73... done.

Is it just me or is there still a problem with it? And where?

@roryk
Collaborator

Closing a stale p/r just for general cleanup. Feel free to reopen!

@roryk roryk closed this
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Commits on Sep 3, 2013
  1. @tanglingfung

    add weblogo

    tanglingfung committed
    add weblogo as well as (template.pm, logo.pm and template.eps) to the path
Showing with 4 additions and 0 deletions.
  1. +4 −0 cloudbio/custom/bio_nextgen.py
View
4 cloudbio/custom/bio_nextgen.py
@@ -1108,3 +1108,7 @@ def install_weblogo(env):
version = "2.8.2"
url = "http://weblogo.berkeley.edu/release/weblogo.%s.tar.gz" % version
_get_install(url, env, _make_copy("find -perm -100 -type f", do_make=False))
+ def _cp_pm(env):
+ for perl_module in ["template.pm", "logo.pm", "template.eps"]:
+ env.safe_sudo("cp %s %s/lib/perl5" % (perl_module, env.system_install))
+ _get_install(url, env, _cp_pm(env))
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