src/hg/makeDb/doc/mm9.txt 1.92

Index: src/hg/makeDb/doc/mm9.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/mm9.txt,v
retrieving revision 1.91
retrieving revision 1.92
diff -b -B -U 4 -r1.91 -r1.92
--- src/hg/makeDb/doc/mm9.txt	7 Apr 2009 14:37:10 -0000	1.91
+++ src/hg/makeDb/doc/mm9.txt	27 Apr 2009 23:32:56 -0000	1.92
@@ -8231,24 +8231,23 @@
 # loaded by Belinda Giardine, in same manner as hg18 ORegAnno track
 
 
 ############################################################################
-# JAX/MGI TRACKS (DONE 9/23/08 angie -- chrMT->M tweaked 9/24)
-    ssh kolossus
-    mkdir -p /cluster/data/mm9/bed/jax/2008_09
-    cd /cluster/data/mm9/bed/jax/2008_09
+# JAX/MGI TRACKS (DONE 4/24/09 angie)
+# Previously done 9/24/08 in /cluster/data/mm9/bed/jax/2008_09
+    mkdir -p /hive/data/genomes/mm9/bed/jax/2009_04
+    cd /hive/data/genomes/mm9/bed/jax/2009_04
     wget ftp://ftp.informatics.jax.org/pub/gbrowse/\*
     wget ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt
     # Jax Rep Transcript track
     # SEQ_RepTransGenomic_rpt.gff --> jaxRepTranscript{,Alias}
     # -- names like AK016604_4933401J01Rik, NM_001011874_AY534250
     # -- aliases ~ MGI:\d+
     # Use simple perl script to uniquify transcript names and make alias.tab.
     # Inspired by the mm6 version, but format has changed.
-  # NOTE FOR NEXT TIME: change chrMT -> chrM here.
     /cluster/data/mm8/bed/jax/2007_07/parseRepTranscript.pl \
       SEQ_RepTransGenomic_rpt.gff \
-    | sed -e 's/^/chr/' \
+    | sed -e 's/^/chr/; s/chrMT/chrM/;' \
       > jaxRepTranscript.gff
 
     # Jax Allele track
     # AL_*.gff --> jaxAllele{,Info}
@@ -8340,31 +8339,28 @@
     # The file "err" has messages about missing data (no gene name in 
     # PhenotypicAllele.rpt, or gene/mgiId not found in jaxAlleleInfo).
 
     # Load tables
-    ssh hgwdev
-    cd /cluster/data/mm9/bed/jax/2008_09
     # jaxRepTranscript
     ldHgGene mm9 jaxRepTranscript jaxRepTranscript.gff
     hgsql mm9 < fixJaxRepTranscript.sql
     sed -e 's/genericAlias/jaxRepTranscriptAlias/g' \
       ~/kent/src/hg/lib/genericAlias.sql > jaxRepTranscriptAlias.sql 
     hgLoadSqlTab mm9 jaxRepTranscriptAlias \
       jaxRepTranscriptAlias.sql jaxRepTranscriptAlias.tab
-    # 9/24/08: tweak chrMT->chrM -- shouldn't be necessary next time.
-    hgsql mm9 -e \
-      'update jaxRepTranscript set chrom = "chrM" where chrom = "chrMT";'
     checkTableCoords mm9 jaxRepTranscript
     # jaxAllele
     hgLoadBed -renameSqlTable -sqlTable=$HOME/kent/src/hg/lib/bed12Source.sql \
       mm9 jaxAllele jaxAllele.bed
-    hgsql mm9 < fixJaxAllele.sql
+    # fixJaxAllele.sql is empty so don't need to do this:
+    # hgsql mm9 < fixJaxAllele.sql
     hgLoadSqlTab mm9 jaxAlleleInfo \
       ~/kent/src/hg/lib/jaxAlleleInfo.sql jaxAlleleInfo.tab
     # jaxPhenotype
     hgLoadBed -renameSqlTable -sqlTable=$HOME/kent/src/hg/lib/bed12Source.sql \
       -tab mm9 jaxPhenotype jaxPhenotype.bed
-    hgsql mm9 < fixJaxPhenotype.sql
+    # fixJaxPhenotype.sql is empty so don't need to do this:
+    # hgsql mm9 < fixJaxPhenotype.sql
     sed -e 's/genericAlias/jaxPhenotypeAlias/' \
       ~/kent/src/hg/lib/genericAlias.sql > jaxPhenotypeAlias.sql
     hgLoadSqlTab mm9 jaxPhenotypeAlias \
       jaxPhenotypeAlias.sql jaxPhenotypeAlias.tab