Inconsistent permissions

[Adrian Reich]

I installed bib (and the various other agalma dependencies) under an admin account on Ubuntu 14.04 in the default location /opt/bib/. Everything worked and the permissions in /opt/bib/active/bin/ where all rwx across the board. I then set up another user on the same machine in order to do analyses. I ran into a number of issues right away and I diagnosed it to many broken links within /opt/bib/active/bin. The permissions on the symbolic links were all fine, however, there were 26 links that were broken by folder permissions. 75% of the broken links were from samtools, partly because of this:

ls -lh /opt/bib/install/samtools/
drwxr-x--- 7 <admin> <admin> 4.0K May 15 13:56 0.1.19

However, once the permissions was corrected on that folder, other links were broken because a specific script did not have the permissions set correctly. So, please take a look at how the permissions are set during the installation of bib for all the necessary scripts as well as the nested folders.

[Adrian Reich]

In the end all of the broken links could be fixed with 4-5 chmods. An incomplete list of the offending folders (can't remember all, my shell crashed):

/opt/bib/install/samtools/0.1.19/
/opt/bib/install/samtools/0.1.19/misc/
/opt/bib/install/samtools/0.1.19/bcftools/
/opt/bib/install/bowtie/1.0.0/

[Mark Howison]

We've run into this problem as well on Oscar. An easy fix should be to add

chmod -R a+rX $PREFIX

to the end of the installer script to update the permissions after installing a package.