b1cabf573dc930b78de2f4e5a369c68f7655d9ba hiram Mon Apr 11 15:36:26 2022 -0700 initial set of files for chm13v2.0 hub construction refs #29203 diff --git src/hg/makeDb/doc/chm13v2.0/makefile src/hg/makeDb/doc/chm13v2.0/makefile new file mode 100644 index 0000000..865f669 --- /dev/null +++ src/hg/makeDb/doc/chm13v2.0/makefile @@ -0,0 +1,51 @@ + +# default set of hub track html description files + +htmlFiles = html/GCA_009914755.4_T2T-CHM13v2.0.assembly.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.chainNet.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.cpgIslands.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.description.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.html + +# these html files come from the T2T porting project, not maintained here +outsideSource = GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenes.html \ +GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1.html \ +GCA_009914755.4_T2T-CHM13v2.0.censat.html \ +GCA_009914755.4_T2T-CHM13v2.0.clinVar20220313.html \ +GCA_009914755.4_T2T-CHM13v2.0.dbSNP155.html \ +GCA_009914755.4_T2T-CHM13v2.0.gwasSNPs2022-03-08.html \ +GCA_009914755.4_T2T-CHM13v2.0.hgCactus.html \ +GCA_009914755.4_T2T-CHM13v2.0.hgLiftOver.html \ +GCA_009914755.4_T2T-CHM13v2.0.hgUnique.html \ +GCA_009914755.4_T2T-CHM13v2.0.proseq.html \ +GCA_009914755.4_T2T-CHM13v2.0.rdnaModel.html \ +GCA_009914755.4_T2T-CHM13v2.0.rnaseq.html \ +GCA_009914755.4_T2T-CHM13v2.0.sedefSegDups.html + +# tracks not used, and userTrackDb comes from T2T porting project + +notPushed = html/GCA_009914755.4_T2T-CHM13v2.0.augustus.html \ +html/GCA_009914755.4_T2T-CHM13v2.0.tanDups.html \ +trackDb/GCA_009914755.4_T2T-CHM13v2.0.userTrackDb.txt + +# files used to construct a useOneFile hub.txt +hubTxt = hub/GCA_009914755.4_T2T-CHM13v2.0.hub.txt \ +hub/GCA_009914755.4_T2T-CHM13v2.0.genomes.txt \ +trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt + +singleFileHub: ${hubTxt} + @rm -f hub.txt + @grep -v genomesFile hub/GCA_009914755.4_T2T-CHM13v2.0.hub.txt > hub.txt + @printf "useOneFile on\n\n" >> hub.txt + @grep -v trackDb hub/GCA_009914755.4_T2T-CHM13v2.0.genomes.txt >> hub.txt + @echo >> hub.txt + @cat trackDb/GCA_009914755.4_T2T-CHM13v2.0.trackDb.txt >> hub.txt + +alpha: singleFileHub + +clean:: + rm -f hub.txt