59c426e232a372f56cfe9a379d3b44e6a5d50895
hiram
  Thu May 23 09:17:02 2013 -0700
begin structure to fetch and build the user apps at an external location
diff --git src/userApps/fetchKentSource.sh src/userApps/fetchKentSource.sh
new file mode 100755
index 0000000..197ab41
--- /dev/null
+++ src/userApps/fetchKentSource.sh
@@ -0,0 +1,48 @@
+#!/bin/bash
+#
+# script to fetch extra source to use with the kent build,
+# and then selectively parts of the kent source tree, enough to
+# build just the user utilities
+
+# the combined samtabix source for the SAM/BAM/TABIX functions:
+echo "fetch samtabix" 1>&2
+git clone http://genome-source.cse.ucsc.edu/samtabix.git samtabix
+
+# These selective git archive commands only work up to a certain size
+# of fetched source, hence the multiple set of individual fetches to
+# get all the parts
+
+rm -f part1Src.zip part2Src.zip part3Src.zip part4Src.zip
+export partNumber=1
+export ofN="of 6"
+
+echo "fetch kent source part ${partNumber} ${ofN}" 1>&2
+git archive --format=zip -9 --remote=git://genome-source.cse.ucsc.edu/kent.git \
+--prefix=kent/ HEAD \
+src/machTest.sh \
+src/ameme \
+src/aladdin \
+src/blat \
+src/cdnaAli \
+src/dnaDust \
+src/fuse \
+src/getgene \
+src/gfClient \
+src/gfServer \
+src/idbQuery \
+src/index \
+src/makefile \
+src/meta \
+src/primeMate \
+src/product \
+src/protDust \
+src/reformat \
+src/scanIntrons \
+src/tracks \
+src/weblet \
+src/wormAli \
+src/xenoAli \
+src/inc \
+src/utils \
+src/jkOwnLib \
+src/lib > part${partNumber}.zip