added running scripts doc

scripts/running_scripts

@@ -0,0 +1,51 @@
+#========
+# foldx
+#========
+./runFoldx.py -d pyrazinamide -g pncA 
+
+#========
+# mcsm
+#========
+./run_mcsm.py -d pyrazinamide -g pncA -s submit -l PZA
+./run_mcsm.py -d pyrazinamide -g pncA -s get
+./run_mcsm.py -d pyrazinamide -g pncA -s format
+
+#====================
+# other struct params
+#====================
+./dssp_df.py -d pyrazinamide -g pncA
+./kd_df.py -d pyrazinamide -g pncA # fixme: NO of cols says 2,but is actually 3
+./rd_df.py -d pyrazinamide -g pncA # fixme: input tsv file is sourced manually from website!
+
+#==============================
+# af_or calcs: different types
+#==============================
+./af_or_calcs.R --d pyrazinamide --gene pncA # fixme: No conditional dir structure
+
+#==============================
+# af_or calcs: kinship
+#==============================
+#FIXME: configure preformattinga and linking scripts to be generic
+/home/tanu/git/Misc/jody_pza/
+
+USE THE BELOW from within the or_kinship_link.py script or something?! as part of resolving this!
+/home/tanu/git/LSHTM_analysis/scripts_old/nssnp_info_format.py
+
+# for now use the file already created using some manual wrestling to link
+# the OR for kinship with mutations
+
+./or_kinship_link.py  -d pyrazinamide -g pncA -sc 2288681 -ec 2289241
+
+#==============================
+# formatting: ns<gene>_snp_info.txt
+#==============================
+# This adds mcsm style muts
+./snpinfo_format.py -d pyrazinamide -g pncA
+
+#==============================
+# combining dfs: combining_dfs.py
+#==============================
+# FIXME: combining_FIXME.py
+./combining_dfs.py -d pyrazinamide -g pncA
+
+