# See instruct: target for how to reproduce the results in this directory. # mnoble@broadinstitute.org 2013_03_19 # # Also note that: # $(Space) contains PANCAN12-AN sample set, which swapped # swapped LAML TP samples for TB. # awg_pancan12_v46__2013_03_14_copy_frozen is a backup copy # of above space, in case this needs to be reproduced "from scratch" # # # fiss flow_copy Analyses prod awg_pancan12__2013_03_19 # Copied workflow(s) : [Analyses] # fiss flow_copy CopyNumber_Gistic2 prod awg_pancan12__2013_03_19 # Copied workflow(s) : [CopyNumber_Gistic2] # fiss flow_copy Hotnet_Analysis prod awg_pancan12__2013_03_19 # Copied workflow(s) : [Hotnet_Analysis] # fiss flow_copy Mutation_Significance_2.0 prod awg_pancan12__2013_03_19 # Copied workflow(s) : [Mutation_Significance_2.0] # fiss flow_copy Mutation_Significance_CV prod awg_pancan12__2013_03_19 # Copied workflow(s) : [Mutation_Significance_CV] # fiss flow_copy Mutation_Significance_S2N prod awg_pancan12__2013_03_19 # Copied workflow(s) : [Mutation_Significance_S2N] # fiss flow_copy Pathway_Paradigm prod awg_pancan12__2013_03_19 # Copied workflow(s) : [Pathway_Paradigm] # fiss flow_copy stddata prod awg_pancan12__2013_03_19 # Copied workflow(s) : [stddata] # # fiss stddata_start awg_pancan12__2013_03_19 Diced=/xchip/gdac_data/normalized/loadfiles/normalized Space=awg_pancan12__2013_03_19 Added=loadfile_added-samples.tsv Removed=loadfile_removed-samples.tsv Stamp=normalized.PANCAN12.2013_03_19__18_00_00.samplestamp.txt instruct: @echo "Choose one of:" @echo " make loadfiles" @echo " make samplestamp" @echo " make update_workspace" @echo "or combine all 3 together with" @echo " make all" all: loadfiles samplestamp update_workspace loadfiles: $(Added) $(Removed) samplestamp: $(Diced)/$(Stamp) $(Diced)/$(Stamp): $(Stamp) @echo "Now attempting to copy $(Stamp) to $(Diced), via 'sudo -u gdac'" sudo -u gdac cp -f $(Stamp) $(Diced)/. $(Stamp): xMakeStamp.sh sh xMakeStamp.sh > $(Stamp) $(Added): xAdd.sh sh xAdd.sh > $(Added) $(Removed): xRemove.sh sh xRemove.sh > $(Removed) update_workspace: $(Stamp) $(Added) $(Removed) fiss sample_import $(Space) $(Added) fiss sample_import $(Space) $(Removed) # Reflect several completely new LAML samples in sset # (this pulls in normals, too, but that shouldn't matter) fiss sset_import $(Space) LAML-new-samples.sset fiss annot_set $(Space) sset=PANCAN12-AN samplestamp $(Diced)/$(Stamp) clean: \rm -f *~ tidy: clean \rm -f $(Added) $(Removed)