documents fixes to set_pipeline_environment whe OSTYPE -> darwin

Author: vinuesa

CHANGES.txt

@@ -1,12 +1,16 @@
 8Feb18: # 1. Changes to estimate_pangenome_phylogenies.sh v1.0.1_8Feb18
-          * Added: -v flag; check_scripts_in_path(); check_dependencies with verbosity; activated set_pipeline_environment; should find dependencies: Thanks to Felipe Lira
-	  2. Changes in run_get_phylomarkers_pipeline.sh 'v2.1.4_8Feb18'
-	  * fixed set_pipeline_environment (removed DEBUG messages, which broke the function return when the script was run with -D; 
+           * Added: -v flag; check_scripts_in_path(); check_dependencies with verbosity; activated set_pipeline_environment; should find dependencies: Thanks to Felipe Lira
+	   * v1.0.3_8Feb18; fix in set_pipeline_environment: changed to readlink -n when $OSTYPE -> darwin
+	  2. Changes in run_get_phylomarkers_pipeline.sh 'v2.1.4_8Feb18' v2.1.4_8Feb18
+	   * fixed set_pipeline_environment (removed DEBUG messages, which broke the function return when the script was run with -D; fixed for darwin: scriptdir=$(readlink -n "${BASH_SOURCE[0]}")
+
 7Feb18: * Moved print_codon_tables() back from get_phylomarkers_fun_lib to run_get_phylomarkers_pipeline.sh v2.1.3_7Feb18 so that -C can print them; Thanks to Stefano Romano!
         * relocated the assignment of logdir to top of main script; edited INSTALL.md, README.md and manual.md
+
 5Feb18: * Extended the tutorial on exploring the container's environment and file system
         * Updated the README.md file to include links to the tutorial and install instructions of the Docker environment and container usage
 4Feb18: * -v flag also prints list of required system binaries, like GET_HOMOLOGUES; minor fix in cleanup code.
+
 3Feb18: * Extended the INSTALL.md file to include instructions on how to setup a locak Docker environment and run image instances
         * Extended the tutorial material, to include instructions on How to access the sequence data on the host (your machine) from a container instance