[Bio-linux-dev] bash compatibility

[Tony Travis]

Hi, Tim.

There is a problem with bash compatibility in Bio-Linux 8 because "zsh"
does NOT source /etc/profile by default. Here's a patch to do it:

--- old/zprofile	2013-08-02 22:29:03.000000000 +0530
+++ zprofile	2015-02-04 01:14:06.747837184 +0530
@@ -5,3 +5,6 @@
 # shells invoked with the -l flag.)
 #
 # Global Order: zshenv, zprofile, zshrc, zlogin
+
+# for compatibility with "bash"
+emulate sh -c 'source /etc/profile'

In particular, "profile" fragments installed by packages (or manually)
are never sourced from /etc/profile.d by "zsh" and this breaks things
quite badly on our servers. I didn't notice this previously because we
don't use "zsh". However, the servers at Assam Agricultural University
are set up to use "zsh" for the course, so we can follow your tutorial.

We are installing our own GWAS pipeline called "ParSNP" that uses
/etc/profile.d to set the environment in the normal way for "bash".

Bye,

  Tony.

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