Minor update with notes for catalog v2 integration

ding-lab · Aug 11, 2022 · bdb85c9 · bdb85c9
1 parent abdcfac
commit bdb85c9
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diff --git a/2_make_catalog2.sh b/2_make_catalog2.sh
@@ -1,10 +1,12 @@
-# Perform discovery for all cases in CASES file
+>&2 echo Unimplemented.  See TODO
+exit 1
 
-GDC_TOKEN="../token/gdc-user-token.2022-06-15T18_08_38.120Z.txt"
-PROJECT="DLBCL"  # Administrative project associated with these cases
+GDC_TOKEN="unused"
+PROJECT="CPTAC3"  # Administrative project associated with these cases
 
-#CASES="/home/mwyczalk_test/Projects/Catalog3/GDAN.catalog/Catalog3/DLBCL.cases.tsv"
-CASES="config/cases-test.dat"
+
+# this now excludes stopped cases
+CASES="/home/mwyczalk_test/Projects/CPTAC3/CPTAC3.catalog/CPTAC3.cases.dat"
 
 # Making catalog2 using data from previous discovery run
 SUFFIX_LIST="/home/mwyczalk_test/Projects/CPTAC3/CPTAC3.catalog/SampleRename.dat"

diff --git a/TODO.Catalog2-merge.md b/TODO.Catalog2-merge.md
@@ -0,0 +1,13 @@
+It would be good to merge "v2" style catalog creation with v3 style,
+so that discovery needs to take place just once.  Right now the code
+has support for this at a lower level, but upper level scripts make this
+difficult (e.g., hard coded catalog output filename).
+
+To make this work, need to run discovery and catalog scripts independently.
+Specifically, discovery creates per-case aliquot, read group, etc. data
+
+Catalog2 creation creates per-case catalog2 files, and then merges them to create final v2 catalog
+Catalog3 creation creates per-case catalog3 files, and creates final v3 catalog
+
+Continue this work on branch TCGA.  Make sure latest revisions are brought over from
+v2 branch