Re: Installing biopieces as a non root

[Martin Asser Hansen]

Hello Saad (CC Biopieces Google Group)

Good job on installing Biopieces and the requirements. The Biopieces installer doesn't require root access - it simply requires a modern version of Ruby (> 1.9) and a few gems like narray. Of cause if you are using the system's version of Ruby you need admin rights to install these gems, if they are missing. I always end up downloading, compiling and installing a local version of Ruby myself.

The permission 770 on your home directory means that group members can write to your home directory - that is probably not what you want - and why you get that Ruby error. I suggest 750 permissions.

Cheers,

Martin

On Thu, Mar 20, 2014 at 1:01 AM, Khan, Saad M. (MU-Student) <smk...@mail.missouri.edu> wrote:

Hi,

I was able to install biopieces by installing the ruby dependencies using rvm (ruby virtual manager). My home directory I have made accessible to other group members so the permissions are set to 770 so that they can access some of my code and programs. Now that I have installed and configured biopieces everytime I try to run read_fastq or read_fasta or any other biopiece executable that requires input data I get the following error. 

/home/skhan is insecure (40770). It may not be group or world writable. Exiting.

Please advice what can I do to correct it.

regards

Saad Khan

---

From: Khan, Saad M. (MU-Student)
Sent: Wednesday, March 19, 2014 5:03 PM
To: ma...@maasha.dk
Subject: Installing biopieces as a non root

 

Hi,

I am trying to install biopieces as a non-root and I keep getting the following error when trying to install the prerequisites of the shell script 

/biopieces_installer-0.51.sh 

Following is the error that I get :- 

    Try: gem install narray 

    Try: gem install narray

abort

When I try to install using  gem install narray I get the following error.

Building native extensions.  This could take a while...

ERROR:  Error installing narray:

        ERROR: Failed to build gem native extension.

    /home/skhan/bin/ruby extconf.rb

/home/skhan/bin/ruby: invalid option -/  (-h will show valid options) (RuntimeError)

extconf failed, exit code 1

Gem files will remain installed in /home/skhan/gems/gems/narray-0.6.0.8 for inspection.

Results logged to /home/skhan/gems/extensions/x86_64-linux/2.1.0-static/narray-0.6.0.8/gem_make.ou

Please let me know any easy way to install biopieces without root permissions.

regards

Saad

 

[Martin Asser Hansen]

The $BP_TMP folder needs to be writable for those who use your Biopieces installation - mine is 777.

The $BP_BIN folder needs to be read/executable - mine is 755.

My /home and /home/maasha is 755

Cheers,

Martin

On Thu, Mar 20, 2014 at 3:12 PM, Khan, Saad M. (MU-Student) <smk...@mail.missouri.edu> wrote:

Which folders need 770 permissions the installation folder only or others as wee

Martin Asser Hansen <ma...@maasha.dk> wrote: