a21f21b13b09a794b09e89168a51d4c8a1da85af
max
  Wed Sep 14 11:47:52 2016 -0700
finally committing all missing pieces of the crispr track pipeline, refs #17235

diff --git src/utils/doCrispr.sh src/utils/doCrispr.sh
index 35f7c47..c3570fd 100755
--- src/utils/doCrispr.sh
+++ src/utils/doCrispr.sh
@@ -1,36 +1,38 @@
 #/bin/bash
 set -euo pipefail
 # script to create a crispr track for an assembly
 # has only two arguments: the genome db and the gene track to use
 
 # steps:
 # - get 200bp-regions around exons
 # - get the 20bp-GG sequences in them
 # - take only the unique ones and split these into chunks
 set -e
 set -o pipefail
 # path to a git clone of the crispor github repo, must be under /hive
-CRISPOR=/hive/users/max/projects/crispor/crispor
+CRISPOR=/hive/data/outside/crisprTrack/crispor
 
 if [ ! -f $CRISPOR/crispor.py ]; then
     echo error: cannot find $CRISPOR/crispor.py
     exit 1
 fi
 
-# path to the crispr track tools, should be on /hive, from kent/src/utils/crisprTrack
-crisprTrack=/hive/groups/browser/crisprTrack
+# path to the crispr track pipeline scripts
+# look at ~/kent/src/hg/makeDb/crisprTrack/README.txt for
+# more info about these scripts in there
+crisprTrack= /hive/data/outside/crisprTrack/scripts
 
 db=$1
 geneTrackName=$2
 
 chromSizesPath=/hive/data/genomes/$db/chrom.sizes
 
 if [[ -z "$1" || -z "$2" ]]; then
     echo to build a crispr track, you need to specify two arguments:
     echo 1 - genome db
     echo 2 - name of a gene track
     exit 1
 fi
 
 genomeFname=$CRISPOR/genomes/$db/$db.fa.bwt